From d185e9ce2cf125f5ec0b79207f3613f0540feca4 Mon Sep 17 00:00:00 2001 From: "Bogdan I. Iorga" Date: Fri, 5 Aug 2022 07:30:55 +0200 Subject: [PATCH] fix broken symlinks and add missing oplsaa folders - replaced broken .mol2 and .pdb symlinks with the actual files (#3) - added missing oplsaa folders --- top/cgenff/SM25/SM25.mol2 | 93 ++++- top/cgenff/SM25/SM25.pdb | 75 +++- top/cgenff/SM26/SM26.mol2 | 78 +++- top/cgenff/SM26/SM26.pdb | 61 +++- top/cgenff/SM27/SM27.mol2 | 91 ++++- top/cgenff/SM27/SM27.pdb | 73 +++- top/cgenff/SM28/SM28.mol2 | 93 ++++- top/cgenff/SM28/SM28.pdb | 75 +++- top/cgenff/SM29/SM29.mol2 | 91 ++++- top/cgenff/SM29/SM29.pdb | 73 +++- top/cgenff/SM30/SM30.mol2 | 106 +++++- top/cgenff/SM30/SM30.pdb | 87 ++++- top/cgenff/SM31/SM31.mol2 | 101 +++++- top/cgenff/SM31/SM31.pdb | 83 ++++- top/cgenff/SM32/SM32.mol2 | 91 ++++- top/cgenff/SM32/SM32.pdb | 73 +++- top/cgenff/SM33/SM33.mol2 | 106 +++++- top/cgenff/SM33/SM33.pdb | 87 ++++- top/cgenff/SM34/SM34.mol2 | 101 +++++- top/cgenff/SM34/SM34.pdb | 83 ++++- top/cgenff/SM35/SM35.mol2 | 93 ++++- top/cgenff/SM35/SM35.pdb | 75 +++- top/cgenff/SM36/SM36.mol2 | 108 +++++- top/cgenff/SM36/SM36.pdb | 89 ++++- top/cgenff/SM37/SM37.mol2 | 103 +++++- top/cgenff/SM37/SM37.pdb | 85 ++++- top/cgenff/SM38/SM38.mol2 | 95 ++++- top/cgenff/SM38/SM38.pdb | 77 +++- top/cgenff/SM39/SM39.mol2 | 110 +++++- top/cgenff/SM39/SM39.pdb | 91 ++++- top/cgenff/SM40/SM40.mol2 | 105 +++++- top/cgenff/SM40/SM40.pdb | 87 ++++- top/cgenff/SM41/SM41.mol2 | 75 +++- top/cgenff/SM41/SM41.pdb | 57 ++- top/cgenff/SM42/SM42.mol2 | 90 ++++- top/cgenff/SM42/SM42.pdb | 71 +++- top/cgenff/SM43/SM43.mol2 | 85 ++++- top/cgenff/SM43/SM43.pdb | 67 +++- top/cgenff/SM44/SM44.mol2 | 75 +++- top/cgenff/SM44/SM44.pdb | 57 ++- top/cgenff/SM45/SM45.mol2 | 90 ++++- top/cgenff/SM45/SM45.pdb | 71 +++- top/cgenff/SM46/SM46.mol2 | 85 ++++- top/cgenff/SM46/SM46.pdb | 67 +++- top/cgenff/refCMC26/refCMC26.mol2 | 81 ++++- top/cgenff/refCMC26/refCMC26.pdb | 62 ++++ top/cgenff/refJMC11/refJMC11.mol2 | 80 ++++- top/cgenff/refJMC11/refJMC11.pdb | 62 ++++ top/cgenff/refJMC12/refJMC12.mol2 | 78 +++- top/cgenff/refJMC12/refJMC12.pdb | 60 ++++ top/cgenff/refJMC13/refJMC13.mol2 | 88 ++++- top/cgenff/refJMC13/refJMC13.pdb | 70 ++++ top/cgenff/refJMC14/refJMC14.mol2 | 76 +++- top/cgenff/refJMC14/refJMC14.pdb | 58 +++ top/gaff/SM25/SM25.pdb | 75 +++- top/gaff/SM26/SM26.pdb | 61 +++- top/gaff/SM27/SM27.pdb | 73 +++- top/gaff/SM28/SM28.pdb | 75 +++- top/gaff/SM29/SM29.pdb | 73 +++- top/gaff/SM30/SM30.pdb | 87 ++++- top/gaff/SM31/SM31.pdb | 83 ++++- top/gaff/SM32/SM32.pdb | 73 +++- top/gaff/SM33/SM33.pdb | 87 ++++- top/gaff/SM34/SM34.pdb | 83 ++++- top/gaff/SM35/SM35.pdb | 75 +++- top/gaff/SM36/SM36.pdb | 89 ++++- top/gaff/SM37/SM37.pdb | 85 ++++- top/gaff/SM38/SM38.pdb | 77 +++- top/gaff/SM39/SM39.pdb | 91 ++++- top/gaff/SM40/SM40.pdb | 87 ++++- top/gaff/SM41/SM41.pdb | 57 ++- top/gaff/SM42/SM42.pdb | 71 +++- top/gaff/SM43/SM43.pdb | 67 +++- top/gaff/SM44/SM44.pdb | 57 ++- top/gaff/SM45/SM45.pdb | 71 +++- top/gaff/SM46/SM46.pdb | 67 +++- top/gaff/refCMC26/refCMC26.pdb | 63 +++- top/gaff/refJMC11/refJMC11.pdb | 63 +++- top/gaff/refJMC12/refJMC12.pdb | 61 +++- top/gaff/refJMC13/refJMC13.pdb | 71 +++- top/gaff/refJMC14/refJMC14.pdb | 59 ++- top/oplsaa/SM25/SM25.itp | 1 + top/oplsaa/SM25/SM25.mol2 | 92 +++++ top/oplsaa/SM25/SM25.mol2.1.itp | 361 +++++++++++++++++++ top/oplsaa/SM25/SM25.mol2.1.pdb | 36 ++ top/oplsaa/SM25/SM25.pdb | 1 + top/oplsaa/SM26/SM26.itp | 1 + top/oplsaa/SM26/SM26.mol2 | 77 ++++ top/oplsaa/SM26/SM26.mol2.1.itp | 284 +++++++++++++++ top/oplsaa/SM26/SM26.mol2.1.pdb | 29 ++ top/oplsaa/SM26/SM26.pdb | 1 + top/oplsaa/SM27/SM27.mol2 | 91 ++++- top/oplsaa/SM28/SM28.mol2 | 93 ++++- top/oplsaa/SM29/SM29.mol2 | 91 ++++- top/oplsaa/SM30/SM30.mol2 | 106 +++++- top/oplsaa/SM31/SM31.itp | 1 + top/oplsaa/SM31/SM31.mol2 | 100 ++++++ top/oplsaa/SM31/SM31.mol2.1.itp | 402 +++++++++++++++++++++ top/oplsaa/SM31/SM31.mol2.1.pdb | 40 +++ top/oplsaa/SM31/SM31.pdb | 1 + top/oplsaa/SM32/SM32.itp | 1 + top/oplsaa/SM32/SM32.mol2 | 90 +++++ top/oplsaa/SM32/SM32.mol2.1.itp | 362 +++++++++++++++++++ top/oplsaa/SM32/SM32.mol2.1.pdb | 35 ++ top/oplsaa/SM32/SM32.pdb | 1 + top/oplsaa/SM33/SM33.itp | 1 + top/oplsaa/SM33/SM33.mol2 | 105 ++++++ top/oplsaa/SM33/SM33.mol2.1.itp | 439 +++++++++++++++++++++++ top/oplsaa/SM33/SM33.mol2.1.pdb | 42 +++ top/oplsaa/SM33/SM33.pdb | 1 + top/oplsaa/SM34/SM34.itp | 1 + top/oplsaa/SM34/SM34.mol2 | 100 ++++++ top/oplsaa/SM34/SM34.mol2.1.itp | 402 +++++++++++++++++++++ top/oplsaa/SM34/SM34.mol2.1.pdb | 40 +++ top/oplsaa/SM34/SM34.pdb | 1 + top/oplsaa/SM35/SM35.itp | 1 + top/oplsaa/SM35/SM35.mol2 | 92 +++++ top/oplsaa/SM35/SM35.mol2.1.itp | 378 ++++++++++++++++++++ top/oplsaa/SM35/SM35.mol2.1.pdb | 36 ++ top/oplsaa/SM35/SM35.pdb | 1 + top/oplsaa/SM36/SM36.itp | 1 + top/oplsaa/SM36/SM36.mol2 | 107 ++++++ top/oplsaa/SM36/SM36.mol2.1.itp | 455 ++++++++++++++++++++++++ top/oplsaa/SM36/SM36.mol2.1.pdb | 43 +++ top/oplsaa/SM36/SM36.pdb | 1 + top/oplsaa/SM37/SM37.itp | 1 + top/oplsaa/SM37/SM37.mol2 | 102 ++++++ top/oplsaa/SM37/SM37.mol2.1.itp | 418 ++++++++++++++++++++++ top/oplsaa/SM37/SM37.mol2.1.pdb | 41 +++ top/oplsaa/SM37/SM37.pdb | 1 + top/oplsaa/SM38/SM38.mol2 | 95 ++++- top/oplsaa/SM39/SM39.mol2 | 110 +++++- top/oplsaa/SM40/SM40.itp | 1 + top/oplsaa/SM40/SM40.mol2 | 104 ++++++ top/oplsaa/SM40/SM40.mol2.1.itp | 435 ++++++++++++++++++++++ top/oplsaa/SM40/SM40.mol2.1.pdb | 42 +++ top/oplsaa/SM40/SM40.pdb | 1 + top/oplsaa/SM41/SM41.itp | 1 + top/oplsaa/SM41/SM41.mol2 | 74 ++++ top/oplsaa/SM41/SM41.mol2.1.itp | 267 ++++++++++++++ top/oplsaa/SM41/SM41.mol2.1.pdb | 27 ++ top/oplsaa/SM41/SM41.pdb | 1 + top/oplsaa/SM42/SM42.itp | 1 + top/oplsaa/SM42/SM42.mol2 | 89 +++++ top/oplsaa/SM42/SM42.mol2.1.itp | 344 ++++++++++++++++++ top/oplsaa/SM42/SM42.mol2.1.pdb | 34 ++ top/oplsaa/SM42/SM42.pdb | 1 + top/oplsaa/SM43/SM43.itp | 1 + top/oplsaa/SM43/SM43.mol2 | 84 +++++ top/oplsaa/SM43/SM43.mol2.1.itp | 307 ++++++++++++++++ top/oplsaa/SM43/SM43.mol2.1.pdb | 32 ++ top/oplsaa/SM43/SM43.pdb | 1 + top/oplsaa/SM44/SM44.itp | 1 + top/oplsaa/SM44/SM44.mol2 | 74 ++++ top/oplsaa/SM44/SM44.mol2.1.itp | 267 ++++++++++++++ top/oplsaa/SM44/SM44.mol2.1.pdb | 27 ++ top/oplsaa/SM44/SM44.pdb | 1 + top/oplsaa/SM45/SM45.mol2 | 90 ++++- top/oplsaa/SM46/SM46.itp | 1 + top/oplsaa/SM46/SM46.mol2 | 84 +++++ top/oplsaa/SM46/SM46.mol2.1.itp | 307 ++++++++++++++++ top/oplsaa/SM46/SM46.mol2.1.pdb | 32 ++ top/oplsaa/SM46/SM46.pdb | 1 + top/oplsaa/refCMC26/refCMC26.itp | 1 + top/oplsaa/refCMC26/refCMC26.mol2 | 80 +++++ top/oplsaa/refCMC26/refCMC26.mol2.1.itp | 301 ++++++++++++++++ top/oplsaa/refCMC26/refCMC26.mol2.1.pdb | 30 ++ top/oplsaa/refCMC26/refCMC26.pdb | 1 + top/oplsaa/refJMC11/refJMC11.mol2 | 80 ++++- top/oplsaa/refJMC12/refJMC12.itp | 1 + top/oplsaa/refJMC12/refJMC12.mol2 | 77 ++++ top/oplsaa/refJMC12/refJMC12.mol2.1.itp | 284 +++++++++++++++ top/oplsaa/refJMC12/refJMC12.mol2.1.pdb | 29 ++ top/oplsaa/refJMC12/refJMC12.pdb | 1 + top/oplsaa/refJMC13/refJMC13.itp | 1 + top/oplsaa/refJMC13/refJMC13.mol2 | 87 +++++ top/oplsaa/refJMC13/refJMC13.mol2.1.itp | 324 +++++++++++++++++ top/oplsaa/refJMC13/refJMC13.mol2.1.pdb | 34 ++ top/oplsaa/refJMC13/refJMC13.pdb | 1 + top/oplsaa/refJMC14/refJMC14.itp | 1 + top/oplsaa/refJMC14/refJMC14.mol2 | 75 ++++ top/oplsaa/refJMC14/refJMC14.mol2.1.itp | 270 ++++++++++++++ top/oplsaa/refJMC14/refJMC14.mol2.1.pdb | 28 ++ top/oplsaa/refJMC14/refJMC14.pdb | 1 + 184 files changed, 16092 insertions(+), 84 deletions(-) mode change 120000 => 100644 top/cgenff/SM25/SM25.mol2 mode change 120000 => 100644 top/cgenff/SM25/SM25.pdb mode change 120000 => 100644 top/cgenff/SM26/SM26.mol2 mode change 120000 => 100644 top/cgenff/SM26/SM26.pdb mode change 120000 => 100644 top/cgenff/SM27/SM27.mol2 mode change 120000 => 100644 top/cgenff/SM27/SM27.pdb mode change 120000 => 100644 top/cgenff/SM28/SM28.mol2 mode change 120000 => 100644 top/cgenff/SM28/SM28.pdb mode change 120000 => 100644 top/cgenff/SM29/SM29.mol2 mode change 120000 => 100644 top/cgenff/SM29/SM29.pdb mode change 120000 => 100644 top/cgenff/SM30/SM30.mol2 mode change 120000 => 100644 top/cgenff/SM30/SM30.pdb mode change 120000 => 100644 top/cgenff/SM31/SM31.mol2 mode change 120000 => 100644 top/cgenff/SM31/SM31.pdb mode change 120000 => 100644 top/cgenff/SM32/SM32.mol2 mode change 120000 => 100644 top/cgenff/SM32/SM32.pdb mode change 120000 => 100644 top/cgenff/SM33/SM33.mol2 mode change 120000 => 100644 top/cgenff/SM33/SM33.pdb mode change 120000 => 100644 top/cgenff/SM34/SM34.mol2 mode change 120000 => 100644 top/cgenff/SM34/SM34.pdb mode change 120000 => 100644 top/cgenff/SM35/SM35.mol2 mode change 120000 => 100644 top/cgenff/SM35/SM35.pdb mode change 120000 => 100644 top/cgenff/SM36/SM36.mol2 mode change 120000 => 100644 top/cgenff/SM36/SM36.pdb mode change 120000 => 100644 top/cgenff/SM37/SM37.mol2 mode change 120000 => 100644 top/cgenff/SM37/SM37.pdb mode change 120000 => 100644 top/cgenff/SM38/SM38.mol2 mode change 120000 => 100644 top/cgenff/SM38/SM38.pdb mode change 120000 => 100644 top/cgenff/SM39/SM39.mol2 mode change 120000 => 100644 top/cgenff/SM39/SM39.pdb mode change 120000 => 100644 top/cgenff/SM40/SM40.mol2 mode change 120000 => 100644 top/cgenff/SM40/SM40.pdb mode change 120000 => 100644 top/cgenff/SM41/SM41.mol2 mode change 120000 => 100644 top/cgenff/SM41/SM41.pdb mode change 120000 => 100644 top/cgenff/SM42/SM42.mol2 mode change 120000 => 100644 top/cgenff/SM42/SM42.pdb mode change 120000 => 100644 top/cgenff/SM43/SM43.mol2 mode change 120000 => 100644 top/cgenff/SM43/SM43.pdb mode change 120000 => 100644 top/cgenff/SM44/SM44.mol2 mode change 120000 => 100644 top/cgenff/SM44/SM44.pdb mode change 120000 => 100644 top/cgenff/SM45/SM45.mol2 mode change 120000 => 100644 top/cgenff/SM45/SM45.pdb mode change 120000 => 100644 top/cgenff/SM46/SM46.mol2 mode change 120000 => 100644 top/cgenff/SM46/SM46.pdb mode change 120000 => 100644 top/cgenff/refCMC26/refCMC26.mol2 create mode 100644 top/cgenff/refCMC26/refCMC26.pdb mode change 120000 => 100644 top/cgenff/refJMC11/refJMC11.mol2 create mode 100644 top/cgenff/refJMC11/refJMC11.pdb mode change 120000 => 100644 top/cgenff/refJMC12/refJMC12.mol2 create mode 100644 top/cgenff/refJMC12/refJMC12.pdb mode change 120000 => 100644 top/cgenff/refJMC13/refJMC13.mol2 create mode 100644 top/cgenff/refJMC13/refJMC13.pdb mode change 120000 => 100644 top/cgenff/refJMC14/refJMC14.mol2 create mode 100644 top/cgenff/refJMC14/refJMC14.pdb mode change 120000 => 100644 top/gaff/SM25/SM25.pdb mode change 120000 => 100644 top/gaff/SM26/SM26.pdb mode change 120000 => 100644 top/gaff/SM27/SM27.pdb mode change 120000 => 100644 top/gaff/SM28/SM28.pdb mode change 120000 => 100644 top/gaff/SM29/SM29.pdb mode change 120000 => 100644 top/gaff/SM30/SM30.pdb mode change 120000 => 100644 top/gaff/SM31/SM31.pdb mode change 120000 => 100644 top/gaff/SM32/SM32.pdb mode change 120000 => 100644 top/gaff/SM33/SM33.pdb mode change 120000 => 100644 top/gaff/SM34/SM34.pdb mode change 120000 => 100644 top/gaff/SM35/SM35.pdb mode change 120000 => 100644 top/gaff/SM36/SM36.pdb mode change 120000 => 100644 top/gaff/SM37/SM37.pdb mode change 120000 => 100644 top/gaff/SM38/SM38.pdb mode change 120000 => 100644 top/gaff/SM39/SM39.pdb mode change 120000 => 100644 top/gaff/SM40/SM40.pdb mode change 120000 => 100644 top/gaff/SM41/SM41.pdb mode change 120000 => 100644 top/gaff/SM42/SM42.pdb mode change 120000 => 100644 top/gaff/SM43/SM43.pdb mode change 120000 => 100644 top/gaff/SM44/SM44.pdb mode change 120000 => 100644 top/gaff/SM45/SM45.pdb mode change 120000 => 100644 top/gaff/SM46/SM46.pdb mode change 120000 => 100644 top/gaff/refCMC26/refCMC26.pdb mode change 120000 => 100644 top/gaff/refJMC11/refJMC11.pdb mode change 120000 => 100644 top/gaff/refJMC12/refJMC12.pdb mode change 120000 => 100644 top/gaff/refJMC13/refJMC13.pdb mode change 120000 => 100644 top/gaff/refJMC14/refJMC14.pdb create mode 120000 top/oplsaa/SM25/SM25.itp create mode 100644 top/oplsaa/SM25/SM25.mol2 create mode 100644 top/oplsaa/SM25/SM25.mol2.1.itp create mode 100644 top/oplsaa/SM25/SM25.mol2.1.pdb create mode 120000 top/oplsaa/SM25/SM25.pdb create mode 120000 top/oplsaa/SM26/SM26.itp create mode 100644 top/oplsaa/SM26/SM26.mol2 create mode 100644 top/oplsaa/SM26/SM26.mol2.1.itp create mode 100644 top/oplsaa/SM26/SM26.mol2.1.pdb create mode 120000 top/oplsaa/SM26/SM26.pdb mode change 120000 => 100644 top/oplsaa/SM27/SM27.mol2 mode change 120000 => 100644 top/oplsaa/SM28/SM28.mol2 mode change 120000 => 100644 top/oplsaa/SM29/SM29.mol2 mode change 120000 => 100644 top/oplsaa/SM30/SM30.mol2 create mode 120000 top/oplsaa/SM31/SM31.itp create mode 100644 top/oplsaa/SM31/SM31.mol2 create mode 100644 top/oplsaa/SM31/SM31.mol2.1.itp create mode 100644 top/oplsaa/SM31/SM31.mol2.1.pdb create mode 120000 top/oplsaa/SM31/SM31.pdb create mode 120000 top/oplsaa/SM32/SM32.itp create mode 100644 top/oplsaa/SM32/SM32.mol2 create mode 100644 top/oplsaa/SM32/SM32.mol2.1.itp create mode 100644 top/oplsaa/SM32/SM32.mol2.1.pdb create mode 120000 top/oplsaa/SM32/SM32.pdb create mode 120000 top/oplsaa/SM33/SM33.itp create mode 100644 top/oplsaa/SM33/SM33.mol2 create mode 100644 top/oplsaa/SM33/SM33.mol2.1.itp create mode 100644 top/oplsaa/SM33/SM33.mol2.1.pdb create mode 120000 top/oplsaa/SM33/SM33.pdb create mode 120000 top/oplsaa/SM34/SM34.itp create mode 100644 top/oplsaa/SM34/SM34.mol2 create mode 100644 top/oplsaa/SM34/SM34.mol2.1.itp create mode 100644 top/oplsaa/SM34/SM34.mol2.1.pdb create mode 120000 top/oplsaa/SM34/SM34.pdb create mode 120000 top/oplsaa/SM35/SM35.itp create mode 100644 top/oplsaa/SM35/SM35.mol2 create mode 100644 top/oplsaa/SM35/SM35.mol2.1.itp create mode 100644 top/oplsaa/SM35/SM35.mol2.1.pdb create mode 120000 top/oplsaa/SM35/SM35.pdb create mode 120000 top/oplsaa/SM36/SM36.itp create mode 100644 top/oplsaa/SM36/SM36.mol2 create mode 100644 top/oplsaa/SM36/SM36.mol2.1.itp create mode 100644 top/oplsaa/SM36/SM36.mol2.1.pdb create mode 120000 top/oplsaa/SM36/SM36.pdb create mode 120000 top/oplsaa/SM37/SM37.itp create mode 100644 top/oplsaa/SM37/SM37.mol2 create mode 100644 top/oplsaa/SM37/SM37.mol2.1.itp create mode 100644 top/oplsaa/SM37/SM37.mol2.1.pdb create mode 120000 top/oplsaa/SM37/SM37.pdb mode change 120000 => 100644 top/oplsaa/SM38/SM38.mol2 mode change 120000 => 100644 top/oplsaa/SM39/SM39.mol2 create mode 120000 top/oplsaa/SM40/SM40.itp create mode 100644 top/oplsaa/SM40/SM40.mol2 create mode 100644 top/oplsaa/SM40/SM40.mol2.1.itp create mode 100644 top/oplsaa/SM40/SM40.mol2.1.pdb create mode 120000 top/oplsaa/SM40/SM40.pdb create mode 120000 top/oplsaa/SM41/SM41.itp create mode 100644 top/oplsaa/SM41/SM41.mol2 create mode 100644 top/oplsaa/SM41/SM41.mol2.1.itp create mode 100644 top/oplsaa/SM41/SM41.mol2.1.pdb create mode 120000 top/oplsaa/SM41/SM41.pdb create mode 120000 top/oplsaa/SM42/SM42.itp create mode 100644 top/oplsaa/SM42/SM42.mol2 create mode 100644 top/oplsaa/SM42/SM42.mol2.1.itp create mode 100644 top/oplsaa/SM42/SM42.mol2.1.pdb create mode 120000 top/oplsaa/SM42/SM42.pdb create mode 120000 top/oplsaa/SM43/SM43.itp create mode 100644 top/oplsaa/SM43/SM43.mol2 create mode 100644 top/oplsaa/SM43/SM43.mol2.1.itp create mode 100644 top/oplsaa/SM43/SM43.mol2.1.pdb create mode 120000 top/oplsaa/SM43/SM43.pdb create mode 120000 top/oplsaa/SM44/SM44.itp create mode 100644 top/oplsaa/SM44/SM44.mol2 create mode 100644 top/oplsaa/SM44/SM44.mol2.1.itp create mode 100644 top/oplsaa/SM44/SM44.mol2.1.pdb create mode 120000 top/oplsaa/SM44/SM44.pdb mode change 120000 => 100644 top/oplsaa/SM45/SM45.mol2 create mode 120000 top/oplsaa/SM46/SM46.itp create mode 100644 top/oplsaa/SM46/SM46.mol2 create mode 100644 top/oplsaa/SM46/SM46.mol2.1.itp create mode 100644 top/oplsaa/SM46/SM46.mol2.1.pdb create mode 120000 top/oplsaa/SM46/SM46.pdb create mode 120000 top/oplsaa/refCMC26/refCMC26.itp create mode 100644 top/oplsaa/refCMC26/refCMC26.mol2 create mode 100644 top/oplsaa/refCMC26/refCMC26.mol2.1.itp create mode 100644 top/oplsaa/refCMC26/refCMC26.mol2.1.pdb create mode 120000 top/oplsaa/refCMC26/refCMC26.pdb mode change 120000 => 100644 top/oplsaa/refJMC11/refJMC11.mol2 create mode 120000 top/oplsaa/refJMC12/refJMC12.itp create mode 100644 top/oplsaa/refJMC12/refJMC12.mol2 create mode 100644 top/oplsaa/refJMC12/refJMC12.mol2.1.itp create mode 100644 top/oplsaa/refJMC12/refJMC12.mol2.1.pdb create mode 120000 top/oplsaa/refJMC12/refJMC12.pdb create mode 120000 top/oplsaa/refJMC13/refJMC13.itp create mode 100644 top/oplsaa/refJMC13/refJMC13.mol2 create mode 100644 top/oplsaa/refJMC13/refJMC13.mol2.1.itp create mode 100644 top/oplsaa/refJMC13/refJMC13.mol2.1.pdb create mode 120000 top/oplsaa/refJMC13/refJMC13.pdb create mode 120000 top/oplsaa/refJMC14/refJMC14.itp create mode 100644 top/oplsaa/refJMC14/refJMC14.mol2 create mode 100644 top/oplsaa/refJMC14/refJMC14.mol2.1.itp create mode 100644 top/oplsaa/refJMC14/refJMC14.mol2.1.pdb create mode 120000 top/oplsaa/refJMC14/refJMC14.pdb diff --git a/top/cgenff/SM25/SM25.mol2 b/top/cgenff/SM25/SM25.mol2 deleted file mode 120000 index ed7042d..0000000 --- a/top/cgenff/SM25/SM25.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM25/SM25.mol2 \ No newline at end of file diff --git a/top/cgenff/SM25/SM25.mol2 b/top/cgenff/SM25/SM25.mol2 new file mode 100644 index 0000000..a0302ac --- /dev/null +++ b/top/cgenff/SM25/SM25.mol2 @@ -0,0 +1,92 @@ +# Name: SM25 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 35 36 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -2.0952 5.2001 -1.8761 O.2 + 2 C2 -1.1555 5.8189 -2.3288 C.2 + 3 N3 -0.0945 6.1007 -1.5469 N.am + 4 S4 -0.0740 5.6020 0.0321 S.o2 + 5 C5 -0.0501 3.8402 0.0223 C.ar + 6 C6 1.1563 3.1654 0.0081 C.ar + 7 C7 1.1750 1.7832 0.0004 C.ar + 8 C8 -0.0126 1.0758 0.0080 C.ar + 9 C9 -1.2190 1.7506 0.0173 C.ar + 10 C10 -1.2377 3.1328 0.0294 C.ar + 11 O11 -1.3242 5.9833 0.5896 O.2 + 12 O12 1.1750 6.0173 0.5678 O.2 + 13 C13 -1.1742 6.2728 -3.7657 C.3 + 14 C14 -2.4814 5.8273 -4.4243 C.3 + 15 C15 -2.5001 6.2811 -5.8612 C.ar + 16 C16 -3.0310 7.5145 -6.1896 C.ar + 17 C17 -3.0437 7.9329 -7.5071 C.ar + 18 C18 -2.5352 7.1134 -8.4974 C.ar + 19 C19 -2.0092 5.8778 -8.1696 C.ar + 20 C20 -1.9916 5.4617 -6.8515 C.ar + 21 H21 0.6570 6.5957 -1.9090 H + 22 H22 2.0842 3.7181 0.0025 H + 23 H23 2.1175 1.2560 -0.0111 H + 24 H24 0.0021 -0.0041 0.0020 H + 25 H25 -2.1469 1.1980 0.0187 H + 26 H26 -2.1802 3.6600 0.0409 H + 27 H27 -1.0998 7.3595 -3.8045 H + 28 H28 -0.3309 5.8316 -4.2971 H + 29 H29 -2.5559 4.7405 -4.3855 H + 30 H30 -3.3247 6.2685 -3.8929 H + 31 H31 -3.4323 8.1529 -5.4164 H + 32 H32 -3.4551 8.8981 -7.7632 H + 33 H33 -2.5493 7.4383 -9.5273 H + 34 H34 -1.6122 5.2374 -8.9434 H + 35 H35 -1.5810 4.4962 -6.5955 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 13 1 + 4 3 4 am + 5 3 21 1 + 6 4 5 1 + 7 4 11 2 + 8 4 12 2 + 9 5 10 ar + 10 5 6 ar + 11 6 7 ar + 12 6 22 1 + 13 7 8 ar + 14 7 23 1 + 15 8 9 ar + 16 8 24 1 + 17 9 10 ar + 18 9 25 1 + 19 10 26 1 + 20 13 14 1 + 21 13 27 1 + 22 13 28 1 + 23 14 15 1 + 24 14 29 1 + 25 14 30 1 + 26 15 20 ar + 27 15 16 ar + 28 16 17 ar + 29 16 31 1 + 30 17 18 ar + 31 17 32 1 + 32 18 19 ar + 33 18 33 1 + 34 19 20 ar + 35 19 34 1 + 36 20 35 1 + +# End of record + diff --git a/top/cgenff/SM25/SM25.pdb b/top/cgenff/SM25/SM25.pdb deleted file mode 120000 index d725256..0000000 --- a/top/cgenff/SM25/SM25.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM25/SM25.pdb \ No newline at end of file diff --git a/top/cgenff/SM25/SM25.pdb b/top/cgenff/SM25/SM25.pdb new file mode 100644 index 0000000..e6cb765 --- /dev/null +++ b/top/cgenff/SM25/SM25.pdb @@ -0,0 +1,74 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM25 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.095 5.200 -1.876 1.00 20.00 +HETATM 2 C2 UNK 1 -1.156 5.819 -2.329 1.00 20.00 +HETATM 3 N3 UNK 1 -0.095 6.101 -1.547 1.00 20.00 +HETATM 4 S4 UNK 1 -0.074 5.602 0.032 1.00 20.00 +HETATM 5 C5 UNK 1 -0.050 3.840 0.022 1.00 20.00 +HETATM 6 C6 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 7 C7 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 8 C8 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 9 C9 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 10 C10 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 11 O11 UNK 1 -1.324 5.983 0.590 1.00 20.00 +HETATM 12 O12 UNK 1 1.175 6.017 0.568 1.00 20.00 +HETATM 13 C13 UNK 1 -1.174 6.273 -3.766 1.00 20.00 +HETATM 14 C14 UNK 1 -2.481 5.827 -4.424 1.00 20.00 +HETATM 15 C15 UNK 1 -2.500 6.281 -5.861 1.00 20.00 +HETATM 16 C16 UNK 1 -3.031 7.515 -6.190 1.00 20.00 +HETATM 17 C17 UNK 1 -3.044 7.933 -7.507 1.00 20.00 +HETATM 18 C18 UNK 1 -2.535 7.113 -8.497 1.00 20.00 +HETATM 19 C19 UNK 1 -2.009 5.878 -8.170 1.00 20.00 +HETATM 20 C20 UNK 1 -1.992 5.462 -6.852 1.00 20.00 +HETATM 21 H21 UNK 1 0.657 6.596 -1.909 1.00 20.00 +HETATM 22 H22 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 23 H23 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 24 H24 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 25 H25 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 26 H26 UNK 1 -2.180 3.660 0.041 1.00 20.00 +HETATM 27 H27 UNK 1 -1.100 7.360 -3.805 1.00 20.00 +HETATM 28 H28 UNK 1 -0.331 5.832 -4.297 1.00 20.00 +HETATM 29 H29 UNK 1 -2.556 4.741 -4.386 1.00 20.00 +HETATM 30 H30 UNK 1 -3.325 6.268 -3.893 1.00 20.00 +HETATM 31 H31 UNK 1 -3.432 8.153 -5.416 1.00 20.00 +HETATM 32 H32 UNK 1 -3.455 8.898 -7.763 1.00 20.00 +HETATM 33 H33 UNK 1 -2.549 7.438 -9.527 1.00 20.00 +HETATM 34 H34 UNK 1 -1.612 5.237 -8.943 1.00 20.00 +HETATM 35 H35 UNK 1 -1.581 4.496 -6.595 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 13 +CONECT 3 2 4 21 +CONECT 4 3 5 11 12 +CONECT 5 4 10 6 +CONECT 6 5 7 22 +CONECT 7 6 8 23 +CONECT 8 7 9 24 +CONECT 9 8 10 25 +CONECT 10 9 5 26 +CONECT 11 4 +CONECT 12 4 +CONECT 13 2 14 27 28 +CONECT 14 13 15 29 30 +CONECT 15 14 20 16 +CONECT 16 15 17 31 +CONECT 17 16 18 32 +CONECT 18 17 19 33 +CONECT 19 18 20 34 +CONECT 20 19 15 35 +CONECT 21 3 +CONECT 22 6 +CONECT 23 7 +CONECT 24 8 +CONECT 25 9 +CONECT 26 10 +CONECT 27 13 +CONECT 28 13 +CONECT 29 14 +CONECT 30 14 +CONECT 31 16 +CONECT 32 17 +CONECT 33 18 +CONECT 34 19 +CONECT 35 20 +END diff --git a/top/cgenff/SM26/SM26.mol2 b/top/cgenff/SM26/SM26.mol2 deleted file mode 120000 index edf6448..0000000 --- a/top/cgenff/SM26/SM26.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM26/SM26.mol2 \ No newline at end of file diff --git a/top/cgenff/SM26/SM26.mol2 b/top/cgenff/SM26/SM26.mol2 new file mode 100644 index 0000000..463b3e1 --- /dev/null +++ b/top/cgenff/SM26/SM26.mol2 @@ -0,0 +1,77 @@ +# Name: SM26 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 28 28 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -1.3540 8.1583 -0.8917 O.2 + 2 S2 -0.1147 7.6796 -1.3959 S.o2 + 3 C3 -0.0901 5.8658 -1.4071 C.3 + 4 C4 -0.0705 5.3471 0.0321 C.3 + 5 C5 -0.0501 3.8402 0.0228 C.ar + 6 C6 1.1563 3.1654 0.0081 C.ar + 7 C7 1.1750 1.7832 0.0004 C.ar + 8 C8 -0.0126 1.0758 0.0080 C.ar + 9 C9 -1.2190 1.7506 0.0173 C.ar + 10 C10 -1.2377 3.1328 0.0294 C.ar + 11 N11 -0.1344 8.1025 -2.9968 N.am + 12 C12 -1.1948 7.7833 -3.7651 C.2 + 13 C13 -1.2127 8.1682 -5.2221 C.3 + 14 O14 -2.1345 7.1864 -3.2840 O.2 + 15 O15 1.1197 8.1920 -0.9132 O.2 + 16 H16 0.8001 5.5177 -1.9309 H + 17 H17 -0.9796 5.4935 -1.9154 H + 18 H18 -0.9608 5.6951 0.5560 H + 19 H19 0.8190 5.7193 0.5404 H + 20 H20 2.0842 3.7181 0.0029 H + 21 H21 2.1175 1.2560 -0.0111 H + 22 H22 0.0021 -0.0041 0.0020 H + 23 H23 -2.1469 1.1980 0.0187 H + 24 H24 -2.1802 3.6600 0.0413 H + 25 H25 0.6172 8.5799 -3.3817 H + 26 H26 -0.3689 7.7026 -5.7313 H + 27 H27 -2.1436 7.8284 -5.6762 H + 28 H28 -1.1387 9.2519 -5.3125 H +@BOND + 1 1 2 2 + 2 2 3 1 + 3 2 11 am + 4 2 15 2 + 5 3 4 1 + 6 3 16 1 + 7 3 17 1 + 8 4 5 1 + 9 4 18 1 + 10 4 19 1 + 11 5 10 ar + 12 5 6 ar + 13 6 7 ar + 14 6 20 1 + 15 7 8 ar + 16 7 21 1 + 17 8 9 ar + 18 8 22 1 + 19 9 10 ar + 20 9 23 1 + 21 10 24 1 + 22 11 12 am + 23 11 25 1 + 24 12 13 1 + 25 12 14 2 + 26 13 26 1 + 27 13 27 1 + 28 13 28 1 + +# End of record + diff --git a/top/cgenff/SM26/SM26.pdb b/top/cgenff/SM26/SM26.pdb deleted file mode 120000 index 09329c9..0000000 --- a/top/cgenff/SM26/SM26.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM26/SM26.pdb \ No newline at end of file diff --git a/top/cgenff/SM26/SM26.pdb b/top/cgenff/SM26/SM26.pdb new file mode 100644 index 0000000..5776ab0 --- /dev/null +++ b/top/cgenff/SM26/SM26.pdb @@ -0,0 +1,60 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM26 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -1.354 8.158 -0.892 1.00 20.00 +HETATM 2 S2 UNK 1 -0.115 7.680 -1.396 1.00 20.00 +HETATM 3 C3 UNK 1 -0.090 5.866 -1.407 1.00 20.00 +HETATM 4 C4 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 5 C5 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 6 C6 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 7 C7 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 8 C8 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 9 C9 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 10 C10 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 11 N11 UNK 1 -0.134 8.102 -2.997 1.00 20.00 +HETATM 12 C12 UNK 1 -1.195 7.783 -3.765 1.00 20.00 +HETATM 13 C13 UNK 1 -1.213 8.168 -5.222 1.00 20.00 +HETATM 14 O14 UNK 1 -2.134 7.186 -3.284 1.00 20.00 +HETATM 15 O15 UNK 1 1.120 8.192 -0.913 1.00 20.00 +HETATM 16 H16 UNK 1 0.800 5.518 -1.931 1.00 20.00 +HETATM 17 H17 UNK 1 -0.980 5.493 -1.915 1.00 20.00 +HETATM 18 H18 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 19 H19 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 20 H20 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 21 H21 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 22 H22 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 23 H23 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 24 H24 UNK 1 -2.180 3.660 0.041 1.00 20.00 +HETATM 25 H25 UNK 1 0.617 8.580 -3.382 1.00 20.00 +HETATM 26 H26 UNK 1 -0.369 7.703 -5.731 1.00 20.00 +HETATM 27 H27 UNK 1 -2.144 7.828 -5.676 1.00 20.00 +HETATM 28 H28 UNK 1 -1.139 9.252 -5.313 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 11 15 +CONECT 3 2 4 16 17 +CONECT 4 3 5 18 19 +CONECT 5 4 10 6 +CONECT 6 5 7 20 +CONECT 7 6 8 21 +CONECT 8 7 9 22 +CONECT 9 8 10 23 +CONECT 10 9 5 24 +CONECT 11 2 12 25 +CONECT 12 11 13 14 +CONECT 13 12 26 27 28 +CONECT 14 12 +CONECT 15 2 +CONECT 16 3 +CONECT 17 3 +CONECT 18 4 +CONECT 19 4 +CONECT 20 6 +CONECT 21 7 +CONECT 22 8 +CONECT 23 9 +CONECT 24 10 +CONECT 25 11 +CONECT 26 13 +CONECT 27 13 +CONECT 28 13 +END diff --git a/top/cgenff/SM27/SM27.mol2 b/top/cgenff/SM27/SM27.mol2 deleted file mode 120000 index 158d642..0000000 --- a/top/cgenff/SM27/SM27.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM27/SM27.mol2 \ No newline at end of file diff --git a/top/cgenff/SM27/SM27.mol2 b/top/cgenff/SM27/SM27.mol2 new file mode 100644 index 0000000..9be2629 --- /dev/null +++ b/top/cgenff/SM27/SM27.mol2 @@ -0,0 +1,90 @@ +# Name: SM27 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 34 35 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 0.3235 2.7098 -4.4476 O.2 + 2 S2 -0.7929 2.5197 -3.5892 S.o2 + 3 C3 -1.6284 4.0985 -3.2726 C.3 + 4 C4 -2.2952 4.5896 -4.5591 C.3 + 5 C5 -2.9893 5.9011 -4.2960 C.ar + 6 C6 -4.3097 5.9145 -3.8869 C.ar + 7 C7 -4.9449 7.1174 -3.6410 C.ar + 8 C8 -4.2628 8.3072 -3.8138 C.ar + 9 C9 -2.9441 8.2940 -4.2284 C.ar + 10 C10 -2.3073 7.0910 -4.4693 C.ar + 11 N11 -0.1225 2.1075 -2.1322 N.am + 12 C12 -0.9825 1.8800 -0.9683 C.3 + 13 C13 -2.2401 1.0742 -1.3001 C.3 + 14 C14 -0.2268 1.3701 0.2733 C.3 + 15 O15 -1.0305 2.3108 1.0135 O.3 + 16 C16 -1.2575 3.1495 -0.1404 C.3 + 17 O17 -1.7437 1.4940 -3.8402 O.2 + 18 H18 -2.3856 3.9604 -2.5007 H + 19 H19 -0.8982 4.8352 -2.9377 H + 20 H20 -1.5381 4.7276 -5.3310 H + 21 H21 -3.0254 3.8529 -4.8940 H + 22 H22 -4.8438 4.9850 -3.7558 H + 23 H23 -5.9752 7.1277 -3.3174 H + 24 H24 -4.7602 9.2471 -3.6252 H + 25 H25 -2.4113 9.2236 -4.3637 H + 26 H26 -1.2771 7.0807 -4.7932 H + 27 H27 0.8397 2.0168 -2.0495 H + 28 H28 -2.8702 1.0026 -0.4136 H + 29 H29 -2.7908 1.5725 -2.0980 H + 30 H30 -1.9553 0.0736 -1.6252 H + 31 H31 -0.4315 0.3276 0.5169 H + 32 H32 0.8373 1.6063 0.2697 H + 33 H33 -0.5086 3.9309 -0.2693 H + 34 H34 -2.2792 3.5194 -0.2267 H +@BOND + 1 1 2 2 + 2 2 3 1 + 3 2 11 am + 4 2 17 2 + 5 3 4 1 + 6 3 18 1 + 7 3 19 1 + 8 4 5 1 + 9 4 20 1 + 10 4 21 1 + 11 5 10 ar + 12 5 6 ar + 13 6 7 ar + 14 6 22 1 + 15 7 8 ar + 16 7 23 1 + 17 8 9 ar + 18 8 24 1 + 19 9 10 ar + 20 9 25 1 + 21 10 26 1 + 22 11 12 1 + 23 11 27 1 + 24 12 16 1 + 25 12 13 1 + 26 12 14 1 + 27 13 28 1 + 28 13 29 1 + 29 13 30 1 + 30 14 15 1 + 31 14 31 1 + 32 14 32 1 + 33 15 16 1 + 34 16 33 1 + 35 16 34 1 + +# End of record + diff --git a/top/cgenff/SM27/SM27.pdb b/top/cgenff/SM27/SM27.pdb deleted file mode 120000 index fed8a0a..0000000 --- a/top/cgenff/SM27/SM27.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM27/SM27.pdb \ No newline at end of file diff --git a/top/cgenff/SM27/SM27.pdb b/top/cgenff/SM27/SM27.pdb new file mode 100644 index 0000000..4d28d81 --- /dev/null +++ b/top/cgenff/SM27/SM27.pdb @@ -0,0 +1,72 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM27 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 0.323 2.710 -4.448 1.00 20.00 +HETATM 2 S2 UNK 1 -0.793 2.520 -3.589 1.00 20.00 +HETATM 3 C3 UNK 1 -1.628 4.098 -3.273 1.00 20.00 +HETATM 4 C4 UNK 1 -2.295 4.590 -4.559 1.00 20.00 +HETATM 5 C5 UNK 1 -2.989 5.901 -4.296 1.00 20.00 +HETATM 6 C6 UNK 1 -4.310 5.915 -3.887 1.00 20.00 +HETATM 7 C7 UNK 1 -4.945 7.117 -3.641 1.00 20.00 +HETATM 8 C8 UNK 1 -4.263 8.307 -3.814 1.00 20.00 +HETATM 9 C9 UNK 1 -2.944 8.294 -4.228 1.00 20.00 +HETATM 10 C10 UNK 1 -2.307 7.091 -4.469 1.00 20.00 +HETATM 11 N11 UNK 1 -0.122 2.108 -2.132 1.00 20.00 +HETATM 12 C12 UNK 1 -0.982 1.880 -0.968 1.00 20.00 +HETATM 13 C13 UNK 1 -2.240 1.074 -1.300 1.00 20.00 +HETATM 14 C14 UNK 1 -0.227 1.370 0.273 1.00 20.00 +HETATM 15 O15 UNK 1 -1.030 2.311 1.013 1.00 20.00 +HETATM 16 C16 UNK 1 -1.258 3.149 -0.140 1.00 20.00 +HETATM 17 O17 UNK 1 -1.744 1.494 -3.840 1.00 20.00 +HETATM 18 H18 UNK 1 -2.386 3.960 -2.501 1.00 20.00 +HETATM 19 H19 UNK 1 -0.898 4.835 -2.938 1.00 20.00 +HETATM 20 H20 UNK 1 -1.538 4.728 -5.331 1.00 20.00 +HETATM 21 H21 UNK 1 -3.025 3.853 -4.894 1.00 20.00 +HETATM 22 H22 UNK 1 -4.844 4.985 -3.756 1.00 20.00 +HETATM 23 H23 UNK 1 -5.975 7.128 -3.317 1.00 20.00 +HETATM 24 H24 UNK 1 -4.760 9.247 -3.625 1.00 20.00 +HETATM 25 H25 UNK 1 -2.411 9.224 -4.364 1.00 20.00 +HETATM 26 H26 UNK 1 -1.277 7.081 -4.793 1.00 20.00 +HETATM 27 H27 UNK 1 0.840 2.017 -2.049 1.00 20.00 +HETATM 28 H28 UNK 1 -2.870 1.003 -0.414 1.00 20.00 +HETATM 29 H29 UNK 1 -2.791 1.572 -2.098 1.00 20.00 +HETATM 30 H30 UNK 1 -1.955 0.074 -1.625 1.00 20.00 +HETATM 31 H31 UNK 1 -0.431 0.328 0.517 1.00 20.00 +HETATM 32 H32 UNK 1 0.837 1.606 0.270 1.00 20.00 +HETATM 33 H33 UNK 1 -0.509 3.931 -0.269 1.00 20.00 +HETATM 34 H34 UNK 1 -2.279 3.519 -0.227 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 11 17 +CONECT 3 2 4 18 19 +CONECT 4 3 5 20 21 +CONECT 5 4 10 6 +CONECT 6 5 7 22 +CONECT 7 6 8 23 +CONECT 8 7 9 24 +CONECT 9 8 10 25 +CONECT 10 9 5 26 +CONECT 11 2 12 27 +CONECT 12 11 16 13 14 +CONECT 13 12 28 29 30 +CONECT 14 12 15 31 32 +CONECT 15 14 16 +CONECT 16 15 12 33 34 +CONECT 17 2 +CONECT 18 3 +CONECT 19 3 +CONECT 20 4 +CONECT 21 4 +CONECT 22 6 +CONECT 23 7 +CONECT 24 8 +CONECT 25 9 +CONECT 26 10 +CONECT 27 11 +CONECT 28 13 +CONECT 29 13 +CONECT 30 13 +CONECT 31 14 +CONECT 32 14 +CONECT 33 16 +CONECT 34 16 +END diff --git a/top/cgenff/SM28/SM28.mol2 b/top/cgenff/SM28/SM28.mol2 deleted file mode 120000 index 30917fb..0000000 --- a/top/cgenff/SM28/SM28.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM28/SM28.mol2 \ No newline at end of file diff --git a/top/cgenff/SM28/SM28.mol2 b/top/cgenff/SM28/SM28.mol2 new file mode 100644 index 0000000..04681e2 --- /dev/null +++ b/top/cgenff/SM28/SM28.mol2 @@ -0,0 +1,92 @@ +# Name: SM28 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 35 36 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -0.5009 6.5095 0.4338 O.2 + 2 S2 -1.2787 5.6296 1.2338 S.o2 + 3 C3 -2.3249 4.5238 0.2467 C.3 + 4 C4 -1.1155 3.6256 -0.0234 C.3 + 5 N5 -1.4690 2.2109 -0.1650 N.am + 6 C6 -2.2435 1.8094 -1.1923 C.2 + 7 C7 -2.5146 0.3420 -1.4029 C.3 + 8 O8 -2.7264 2.6293 -1.9442 O.2 + 9 C9 -0.2379 4.1275 -1.1718 C.3 + 10 C10 0.9995 3.2362 -1.2951 C.3 + 11 C11 1.8035 3.6567 -2.4983 C.ar + 12 C12 1.5570 3.0801 -3.7302 C.ar + 13 C13 2.2912 3.4692 -4.8349 C.ar + 14 C14 3.2791 4.4275 -4.7057 C.ar + 15 C15 3.5292 5.0004 -3.4727 C.ar + 16 C16 2.7914 4.6150 -2.3691 C.ar + 17 C17 -0.5553 3.9704 1.3584 C.3 + 18 O18 -1.9048 6.0481 2.4388 O.2 + 19 H19 -2.7175 4.9961 -0.6538 H + 20 H20 -3.1013 4.0322 0.8328 H + 21 H21 -1.1456 1.5632 0.4806 H + 22 H22 -1.7515 -0.0781 -2.0580 H + 23 H23 -2.4927 -0.1730 -0.4425 H + 24 H24 -3.4958 0.2158 -1.8605 H + 25 H25 -0.8038 4.0943 -2.1028 H + 26 H26 0.0715 5.1532 -0.9710 H + 27 H27 1.6099 3.3357 -0.3975 H + 28 H28 0.6893 2.1977 -1.4102 H + 29 H29 0.7881 2.3282 -3.8304 H + 30 H30 2.0960 3.0214 -5.7981 H + 31 H31 3.8557 4.7283 -5.5679 H + 32 H32 4.3012 5.7488 -3.3716 H + 33 H33 2.9871 5.0623 -1.4057 H + 34 H34 -0.9907 3.3722 2.1588 H + 35 H35 0.5342 3.9792 1.3891 H +@BOND + 1 1 2 2 + 2 2 3 1 + 3 2 17 1 + 4 2 18 2 + 5 3 4 1 + 6 3 19 1 + 7 3 20 1 + 8 4 17 1 + 9 4 5 1 + 10 4 9 1 + 11 5 6 am + 12 5 21 1 + 13 6 7 1 + 14 6 8 2 + 15 7 22 1 + 16 7 23 1 + 17 7 24 1 + 18 9 10 1 + 19 9 25 1 + 20 9 26 1 + 21 10 11 1 + 22 10 27 1 + 23 10 28 1 + 24 11 16 ar + 25 11 12 ar + 26 12 13 ar + 27 12 29 1 + 28 13 14 ar + 29 13 30 1 + 30 14 15 ar + 31 14 31 1 + 32 15 16 ar + 33 15 32 1 + 34 16 33 1 + 35 17 34 1 + 36 17 35 1 + +# End of record + diff --git a/top/cgenff/SM28/SM28.pdb b/top/cgenff/SM28/SM28.pdb deleted file mode 120000 index 8cf1b01..0000000 --- a/top/cgenff/SM28/SM28.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM28/SM28.pdb \ No newline at end of file diff --git a/top/cgenff/SM28/SM28.pdb b/top/cgenff/SM28/SM28.pdb new file mode 100644 index 0000000..775cb83 --- /dev/null +++ b/top/cgenff/SM28/SM28.pdb @@ -0,0 +1,74 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM28 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -0.501 6.510 0.434 1.00 20.00 +HETATM 2 S2 UNK 1 -1.279 5.630 1.234 1.00 20.00 +HETATM 3 C3 UNK 1 -2.325 4.524 0.247 1.00 20.00 +HETATM 4 C4 UNK 1 -1.116 3.626 -0.023 1.00 20.00 +HETATM 5 N5 UNK 1 -1.469 2.211 -0.165 1.00 20.00 +HETATM 6 C6 UNK 1 -2.244 1.809 -1.192 1.00 20.00 +HETATM 7 C7 UNK 1 -2.515 0.342 -1.403 1.00 20.00 +HETATM 8 O8 UNK 1 -2.726 2.629 -1.944 1.00 20.00 +HETATM 9 C9 UNK 1 -0.238 4.127 -1.172 1.00 20.00 +HETATM 10 C10 UNK 1 1.000 3.236 -1.295 1.00 20.00 +HETATM 11 C11 UNK 1 1.804 3.657 -2.498 1.00 20.00 +HETATM 12 C12 UNK 1 1.557 3.080 -3.730 1.00 20.00 +HETATM 13 C13 UNK 1 2.291 3.469 -4.835 1.00 20.00 +HETATM 14 C14 UNK 1 3.279 4.427 -4.706 1.00 20.00 +HETATM 15 C15 UNK 1 3.529 5.000 -3.473 1.00 20.00 +HETATM 16 C16 UNK 1 2.791 4.615 -2.369 1.00 20.00 +HETATM 17 C17 UNK 1 -0.555 3.970 1.358 1.00 20.00 +HETATM 18 O18 UNK 1 -1.905 6.048 2.439 1.00 20.00 +HETATM 19 H19 UNK 1 -2.717 4.996 -0.654 1.00 20.00 +HETATM 20 H20 UNK 1 -3.101 4.032 0.833 1.00 20.00 +HETATM 21 H21 UNK 1 -1.146 1.563 0.481 1.00 20.00 +HETATM 22 H22 UNK 1 -1.751 -0.078 -2.058 1.00 20.00 +HETATM 23 H23 UNK 1 -2.493 -0.173 -0.442 1.00 20.00 +HETATM 24 H24 UNK 1 -3.496 0.216 -1.860 1.00 20.00 +HETATM 25 H25 UNK 1 -0.804 4.094 -2.103 1.00 20.00 +HETATM 26 H26 UNK 1 0.072 5.153 -0.971 1.00 20.00 +HETATM 27 H27 UNK 1 1.610 3.336 -0.397 1.00 20.00 +HETATM 28 H28 UNK 1 0.689 2.198 -1.410 1.00 20.00 +HETATM 29 H29 UNK 1 0.788 2.328 -3.830 1.00 20.00 +HETATM 30 H30 UNK 1 2.096 3.021 -5.798 1.00 20.00 +HETATM 31 H31 UNK 1 3.856 4.728 -5.568 1.00 20.00 +HETATM 32 H32 UNK 1 4.301 5.749 -3.372 1.00 20.00 +HETATM 33 H33 UNK 1 2.987 5.062 -1.406 1.00 20.00 +HETATM 34 H34 UNK 1 -0.991 3.372 2.159 1.00 20.00 +HETATM 35 H35 UNK 1 0.534 3.979 1.389 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 17 18 +CONECT 3 2 4 19 20 +CONECT 4 3 17 5 9 +CONECT 5 4 6 21 +CONECT 6 5 7 8 +CONECT 7 6 22 23 24 +CONECT 8 6 +CONECT 9 4 10 25 26 +CONECT 10 9 11 27 28 +CONECT 11 10 16 12 +CONECT 12 11 13 29 +CONECT 13 12 14 30 +CONECT 14 13 15 31 +CONECT 15 14 16 32 +CONECT 16 15 11 33 +CONECT 17 2 4 34 35 +CONECT 18 2 +CONECT 19 3 +CONECT 20 3 +CONECT 21 5 +CONECT 22 7 +CONECT 23 7 +CONECT 24 7 +CONECT 25 9 +CONECT 26 9 +CONECT 27 10 +CONECT 28 10 +CONECT 29 12 +CONECT 30 13 +CONECT 31 14 +CONECT 32 15 +CONECT 33 16 +CONECT 34 17 +CONECT 35 17 +END diff --git a/top/cgenff/SM29/SM29.mol2 b/top/cgenff/SM29/SM29.mol2 deleted file mode 120000 index d2550c0..0000000 --- a/top/cgenff/SM29/SM29.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM29/SM29.mol2 \ No newline at end of file diff --git a/top/cgenff/SM29/SM29.mol2 b/top/cgenff/SM29/SM29.mol2 new file mode 100644 index 0000000..ae01644 --- /dev/null +++ b/top/cgenff/SM29/SM29.mol2 @@ -0,0 +1,90 @@ +# Name: SM29 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 34 35 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 C1 0.7361 1.5316 2.8910 C.3 + 2 S2 1.1371 -0.1818 2.4504 S.o2 + 3 N3 -0.2036 -0.7261 1.6451 N.am + 4 C4 -0.5593 -0.1537 0.3443 C.3 + 5 C5 -0.6881 1.3813 0.3544 C.3 + 6 O6 0.7054 1.3876 -0.0153 O.3 + 7 C7 0.6460 0.0663 -0.5892 C.3 + 8 C8 -1.7359 -0.8680 -0.3238 C.3 + 9 C9 -1.5684 -2.3809 -0.1692 C.3 + 10 C10 -2.7272 -3.0845 -0.8273 C.ar + 11 C11 -3.8647 -3.3743 -0.0972 C.ar + 12 C12 -4.9296 -4.0153 -0.7021 C.ar + 13 C13 -4.8529 -4.3760 -2.0343 C.ar + 14 C14 -3.7134 -4.0909 -2.7631 C.ar + 15 C15 -2.6506 -3.4451 -2.1596 C.ar + 16 O16 1.2005 -0.9942 3.6145 O.2 + 17 O17 2.1701 -0.2172 1.4752 O.2 + 18 H18 -0.2316 1.5609 3.3918 H + 19 H19 1.5029 1.9240 3.5588 H + 20 H20 0.6959 2.1393 1.9870 H + 21 H21 -0.7533 -1.4239 2.0346 H + 22 H22 -1.3508 1.7733 -0.4171 H + 23 H23 -0.8845 1.8008 1.3411 H + 24 H24 1.5078 -0.5571 -0.3509 H + 25 H25 0.3911 0.0545 -1.6489 H + 26 H26 -2.6668 -0.5553 0.1492 H + 27 H27 -1.7625 -0.6117 -1.3829 H + 28 H28 -0.6375 -2.6936 -0.6422 H + 29 H29 -1.5417 -2.6371 0.8899 H + 30 H30 -3.9229 -3.0964 0.9449 H + 31 H31 -5.8198 -4.2384 -0.1326 H + 32 H32 -5.6832 -4.8808 -2.5058 H + 33 H33 -3.6534 -4.3729 -3.8039 H + 34 H34 -1.7601 -3.2227 -2.7288 H +@BOND + 1 1 2 1 + 2 1 18 1 + 3 1 19 1 + 4 1 20 1 + 5 2 3 am + 6 2 16 2 + 7 2 17 2 + 8 3 4 1 + 9 3 21 1 + 10 4 7 1 + 11 4 5 1 + 12 4 8 1 + 13 5 6 1 + 14 5 22 1 + 15 5 23 1 + 16 6 7 1 + 17 7 24 1 + 18 7 25 1 + 19 8 9 1 + 20 8 26 1 + 21 8 27 1 + 22 9 10 1 + 23 9 28 1 + 24 9 29 1 + 25 10 15 ar + 26 10 11 ar + 27 11 12 ar + 28 11 30 1 + 29 12 13 ar + 30 12 31 1 + 31 13 14 ar + 32 13 32 1 + 33 14 15 ar + 34 14 33 1 + 35 15 34 1 + +# End of record + diff --git a/top/cgenff/SM29/SM29.pdb b/top/cgenff/SM29/SM29.pdb deleted file mode 120000 index b808e75..0000000 --- a/top/cgenff/SM29/SM29.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM29/SM29.pdb \ No newline at end of file diff --git a/top/cgenff/SM29/SM29.pdb b/top/cgenff/SM29/SM29.pdb new file mode 100644 index 0000000..f50780d --- /dev/null +++ b/top/cgenff/SM29/SM29.pdb @@ -0,0 +1,72 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM29 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 0.736 1.532 2.891 1.00 20.00 +HETATM 2 S2 UNK 1 1.137 -0.182 2.450 1.00 20.00 +HETATM 3 N3 UNK 1 -0.204 -0.726 1.645 1.00 20.00 +HETATM 4 C4 UNK 1 -0.559 -0.154 0.344 1.00 20.00 +HETATM 5 C5 UNK 1 -0.688 1.381 0.354 1.00 20.00 +HETATM 6 O6 UNK 1 0.705 1.388 -0.015 1.00 20.00 +HETATM 7 C7 UNK 1 0.646 0.066 -0.589 1.00 20.00 +HETATM 8 C8 UNK 1 -1.736 -0.868 -0.324 1.00 20.00 +HETATM 9 C9 UNK 1 -1.568 -2.381 -0.169 1.00 20.00 +HETATM 10 C10 UNK 1 -2.727 -3.084 -0.827 1.00 20.00 +HETATM 11 C11 UNK 1 -3.865 -3.374 -0.097 1.00 20.00 +HETATM 12 C12 UNK 1 -4.930 -4.015 -0.702 1.00 20.00 +HETATM 13 C13 UNK 1 -4.853 -4.376 -2.034 1.00 20.00 +HETATM 14 C14 UNK 1 -3.713 -4.091 -2.763 1.00 20.00 +HETATM 15 C15 UNK 1 -2.651 -3.445 -2.160 1.00 20.00 +HETATM 16 O16 UNK 1 1.201 -0.994 3.615 1.00 20.00 +HETATM 17 O17 UNK 1 2.170 -0.217 1.475 1.00 20.00 +HETATM 18 H18 UNK 1 -0.232 1.561 3.392 1.00 20.00 +HETATM 19 H19 UNK 1 1.503 1.924 3.559 1.00 20.00 +HETATM 20 H20 UNK 1 0.696 2.139 1.987 1.00 20.00 +HETATM 21 H21 UNK 1 -0.753 -1.424 2.035 1.00 20.00 +HETATM 22 H22 UNK 1 -1.351 1.773 -0.417 1.00 20.00 +HETATM 23 H23 UNK 1 -0.885 1.801 1.341 1.00 20.00 +HETATM 24 H24 UNK 1 1.508 -0.557 -0.351 1.00 20.00 +HETATM 25 H25 UNK 1 0.391 0.055 -1.649 1.00 20.00 +HETATM 26 H26 UNK 1 -2.667 -0.555 0.149 1.00 20.00 +HETATM 27 H27 UNK 1 -1.763 -0.612 -1.383 1.00 20.00 +HETATM 28 H28 UNK 1 -0.637 -2.694 -0.642 1.00 20.00 +HETATM 29 H29 UNK 1 -1.542 -2.637 0.890 1.00 20.00 +HETATM 30 H30 UNK 1 -3.923 -3.096 0.945 1.00 20.00 +HETATM 31 H31 UNK 1 -5.820 -4.238 -0.133 1.00 20.00 +HETATM 32 H32 UNK 1 -5.683 -4.881 -2.506 1.00 20.00 +HETATM 33 H33 UNK 1 -3.653 -4.373 -3.804 1.00 20.00 +HETATM 34 H34 UNK 1 -1.760 -3.223 -2.729 1.00 20.00 +CONECT 1 2 18 19 20 +CONECT 2 1 3 16 17 +CONECT 3 2 4 21 +CONECT 4 3 7 5 8 +CONECT 5 4 6 22 23 +CONECT 6 5 7 +CONECT 7 6 4 24 25 +CONECT 8 4 9 26 27 +CONECT 9 8 10 28 29 +CONECT 10 9 15 11 +CONECT 11 10 12 30 +CONECT 12 11 13 31 +CONECT 13 12 14 32 +CONECT 14 13 15 33 +CONECT 15 14 10 34 +CONECT 16 2 +CONECT 17 2 +CONECT 18 1 +CONECT 19 1 +CONECT 20 1 +CONECT 21 3 +CONECT 22 5 +CONECT 23 5 +CONECT 24 7 +CONECT 25 7 +CONECT 26 8 +CONECT 27 8 +CONECT 28 9 +CONECT 29 9 +CONECT 30 11 +CONECT 31 12 +CONECT 32 13 +CONECT 33 14 +CONECT 34 15 +END diff --git a/top/cgenff/SM30/SM30.mol2 b/top/cgenff/SM30/SM30.mol2 deleted file mode 120000 index c3d1265..0000000 --- a/top/cgenff/SM30/SM30.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM30/SM30.mol2 \ No newline at end of file diff --git a/top/cgenff/SM30/SM30.mol2 b/top/cgenff/SM30/SM30.mol2 new file mode 100644 index 0000000..965bde8 --- /dev/null +++ b/top/cgenff/SM30/SM30.mol2 @@ -0,0 +1,105 @@ +# Name: SM30 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 41 43 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 1.1728 6.1240 0.4860 O.2 + 2 S2 -0.1340 5.7580 0.0647 S.o2 + 3 N3 -0.1809 5.9955 -1.5735 N.am + 4 C4 -1.4003 5.6856 -2.3240 C.3 + 5 C5 -2.6915 6.1776 -1.6434 C.3 + 6 O6 -2.7296 4.8742 -1.0283 O.3 + 7 C7 -1.9421 4.2659 -2.0717 C.3 + 8 C8 -1.3005 6.0545 -3.8055 C.3 + 9 C9 -0.6881 7.4498 -3.9435 C.3 + 10 C10 -0.5898 7.8131 -5.4027 C.ar + 11 C11 0.5513 7.5002 -6.1176 C.ar + 12 C12 0.6396 7.8292 -7.4573 C.ar + 13 C13 -0.4090 8.4805 -8.0796 C.ar + 14 C14 -1.5479 8.7981 -7.3635 C.ar + 15 C15 -1.6383 8.4644 -6.0250 C.ar + 16 C16 -1.2363 6.9241 0.7926 C.ar + 17 C17 -2.5132 6.5364 1.1531 C.ar + 18 C18 -3.3782 7.4514 1.7237 C.ar + 19 C19 -2.9658 8.7538 1.9346 C.ar + 20 C20 -1.6905 9.1427 1.5697 C.ar + 21 C21 -0.8243 8.2268 1.0027 C.ar + 22 O22 -0.6954 4.4740 0.3002 O.2 + 23 H23 0.5990 6.3398 -2.0362 H + 24 H24 -2.5348 6.9937 -0.9380 H + 25 H25 -3.5124 6.3624 -2.3363 H + 26 H26 -2.5341 3.8670 -2.8953 H + 27 H27 -1.1905 3.5652 -1.7081 H + 28 H28 -0.6700 5.3286 -4.3190 H + 29 H29 -2.2961 6.0491 -4.2492 H + 30 H30 -1.3186 8.1757 -3.4300 H + 31 H31 0.3075 7.4551 -3.4999 H + 32 H32 1.3723 6.9953 -5.6303 H + 33 H33 1.5295 7.5814 -8.0167 H + 34 H34 -0.3383 8.7415 -9.1252 H + 35 H35 -2.3670 9.3072 -7.8496 H + 36 H36 -2.5280 8.7129 -5.4655 H + 37 H37 -2.8353 5.5187 0.9886 H + 38 H38 -4.3759 7.1486 2.0050 H + 39 H39 -3.6416 9.4687 2.3805 H + 40 H40 -1.3699 10.1614 1.7304 H + 41 H41 0.1733 8.5298 0.7207 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 16 1 + 4 2 22 2 + 5 3 4 1 + 6 3 23 1 + 7 4 7 1 + 8 4 5 1 + 9 4 8 1 + 10 5 6 1 + 11 5 24 1 + 12 5 25 1 + 13 6 7 1 + 14 7 26 1 + 15 7 27 1 + 16 8 9 1 + 17 8 28 1 + 18 8 29 1 + 19 9 10 1 + 20 9 30 1 + 21 9 31 1 + 22 10 15 ar + 23 10 11 ar + 24 11 12 ar + 25 11 32 1 + 26 12 13 ar + 27 12 33 1 + 28 13 14 ar + 29 13 34 1 + 30 14 15 ar + 31 14 35 1 + 32 15 36 1 + 33 16 21 ar + 34 16 17 ar + 35 17 18 ar + 36 17 37 1 + 37 18 19 ar + 38 18 38 1 + 39 19 20 ar + 40 19 39 1 + 41 20 21 ar + 42 20 40 1 + 43 21 41 1 + +# End of record + diff --git a/top/cgenff/SM30/SM30.pdb b/top/cgenff/SM30/SM30.pdb deleted file mode 120000 index a1fc3b4..0000000 --- a/top/cgenff/SM30/SM30.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM30/SM30.pdb \ No newline at end of file diff --git a/top/cgenff/SM30/SM30.pdb b/top/cgenff/SM30/SM30.pdb new file mode 100644 index 0000000..f21c886 --- /dev/null +++ b/top/cgenff/SM30/SM30.pdb @@ -0,0 +1,86 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM30 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 1.173 6.124 0.486 1.00 20.00 +HETATM 2 S2 UNK 1 -0.134 5.758 0.065 1.00 20.00 +HETATM 3 N3 UNK 1 -0.181 5.995 -1.574 1.00 20.00 +HETATM 4 C4 UNK 1 -1.400 5.686 -2.324 1.00 20.00 +HETATM 5 C5 UNK 1 -2.692 6.178 -1.643 1.00 20.00 +HETATM 6 O6 UNK 1 -2.730 4.874 -1.028 1.00 20.00 +HETATM 7 C7 UNK 1 -1.942 4.266 -2.072 1.00 20.00 +HETATM 8 C8 UNK 1 -1.300 6.054 -3.806 1.00 20.00 +HETATM 9 C9 UNK 1 -0.688 7.450 -3.944 1.00 20.00 +HETATM 10 C10 UNK 1 -0.590 7.813 -5.403 1.00 20.00 +HETATM 11 C11 UNK 1 0.551 7.500 -6.118 1.00 20.00 +HETATM 12 C12 UNK 1 0.640 7.829 -7.457 1.00 20.00 +HETATM 13 C13 UNK 1 -0.409 8.480 -8.080 1.00 20.00 +HETATM 14 C14 UNK 1 -1.548 8.798 -7.363 1.00 20.00 +HETATM 15 C15 UNK 1 -1.638 8.464 -6.025 1.00 20.00 +HETATM 16 C16 UNK 1 -1.236 6.924 0.793 1.00 20.00 +HETATM 17 C17 UNK 1 -2.513 6.536 1.153 1.00 20.00 +HETATM 18 C18 UNK 1 -3.378 7.451 1.724 1.00 20.00 +HETATM 19 C19 UNK 1 -2.966 8.754 1.935 1.00 20.00 +HETATM 20 C20 UNK 1 -1.690 9.143 1.570 1.00 20.00 +HETATM 21 C21 UNK 1 -0.824 8.227 1.003 1.00 20.00 +HETATM 22 O22 UNK 1 -0.695 4.474 0.300 1.00 20.00 +HETATM 23 H23 UNK 1 0.599 6.340 -2.036 1.00 20.00 +HETATM 24 H24 UNK 1 -2.535 6.994 -0.938 1.00 20.00 +HETATM 25 H25 UNK 1 -3.512 6.362 -2.336 1.00 20.00 +HETATM 26 H26 UNK 1 -2.534 3.867 -2.895 1.00 20.00 +HETATM 27 H27 UNK 1 -1.190 3.565 -1.708 1.00 20.00 +HETATM 28 H28 UNK 1 -0.670 5.329 -4.319 1.00 20.00 +HETATM 29 H29 UNK 1 -2.296 6.049 -4.249 1.00 20.00 +HETATM 30 H30 UNK 1 -1.319 8.176 -3.430 1.00 20.00 +HETATM 31 H31 UNK 1 0.308 7.455 -3.500 1.00 20.00 +HETATM 32 H32 UNK 1 1.372 6.995 -5.630 1.00 20.00 +HETATM 33 H33 UNK 1 1.530 7.581 -8.017 1.00 20.00 +HETATM 34 H34 UNK 1 -0.338 8.741 -9.125 1.00 20.00 +HETATM 35 H35 UNK 1 -2.367 9.307 -7.850 1.00 20.00 +HETATM 36 H36 UNK 1 -2.528 8.713 -5.465 1.00 20.00 +HETATM 37 H37 UNK 1 -2.835 5.519 0.989 1.00 20.00 +HETATM 38 H38 UNK 1 -4.376 7.149 2.005 1.00 20.00 +HETATM 39 H39 UNK 1 -3.642 9.469 2.380 1.00 20.00 +HETATM 40 H40 UNK 1 -1.370 10.161 1.730 1.00 20.00 +HETATM 41 H41 UNK 1 0.173 8.530 0.721 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 16 22 +CONECT 3 2 4 23 +CONECT 4 3 7 5 8 +CONECT 5 4 6 24 25 +CONECT 6 5 7 +CONECT 7 6 4 26 27 +CONECT 8 4 9 28 29 +CONECT 9 8 10 30 31 +CONECT 10 9 15 11 +CONECT 11 10 12 32 +CONECT 12 11 13 33 +CONECT 13 12 14 34 +CONECT 14 13 15 35 +CONECT 15 14 10 36 +CONECT 16 2 21 17 +CONECT 17 16 18 37 +CONECT 18 17 19 38 +CONECT 19 18 20 39 +CONECT 20 19 21 40 +CONECT 21 20 16 41 +CONECT 22 2 +CONECT 23 3 +CONECT 24 5 +CONECT 25 5 +CONECT 26 7 +CONECT 27 7 +CONECT 28 8 +CONECT 29 8 +CONECT 30 9 +CONECT 31 9 +CONECT 32 11 +CONECT 33 12 +CONECT 34 13 +CONECT 35 14 +CONECT 36 15 +CONECT 37 17 +CONECT 38 18 +CONECT 39 19 +CONECT 40 20 +CONECT 41 21 +END diff --git a/top/cgenff/SM31/SM31.mol2 b/top/cgenff/SM31/SM31.mol2 deleted file mode 120000 index 0aa7445..0000000 --- a/top/cgenff/SM31/SM31.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM31/SM31.mol2 \ No newline at end of file diff --git a/top/cgenff/SM31/SM31.mol2 b/top/cgenff/SM31/SM31.mol2 new file mode 100644 index 0000000..e28e7bd --- /dev/null +++ b/top/cgenff/SM31/SM31.mol2 @@ -0,0 +1,100 @@ +# Name: SM31 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 39 40 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 0.1515 6.5053 2.6260 O.2 + 2 S2 0.4785 6.0091 1.3352 S.o2 + 3 N3 0.5808 4.3625 1.4793 N.am + 4 C4 1.2056 3.5716 0.4161 C.3 + 5 C5 0.4800 3.6636 -0.9395 C.3 + 6 O6 1.3761 4.7584 -1.2169 O.3 + 7 C7 2.3733 4.2882 -0.2878 C.3 + 8 C8 1.5294 2.1399 0.8477 C.3 + 9 C9 0.3072 1.5249 1.5326 C.3 + 10 C10 0.6261 0.1148 1.9577 C.ar + 11 C11 0.3793 -0.9390 1.0977 C.ar + 12 C12 0.6763 -2.2320 1.4858 C.ar + 13 C13 1.2105 -2.4724 2.7379 C.ar + 14 C14 1.4524 -1.4192 3.5999 C.ar + 15 C15 1.1603 -0.1256 3.2098 C.ar + 16 N16 -0.8229 6.3364 0.3649 N.am + 17 C17 -2.1785 6.2944 0.9188 C.3 + 18 C18 -0.6186 6.6679 -1.0474 C.3 + 19 O19 1.6310 6.4211 0.6133 O.2 + 20 H20 0.2270 3.9217 2.2676 H + 21 H21 0.6324 2.7956 -1.5810 H + 22 H22 -0.5662 3.9591 -0.8606 H + 23 H23 2.8288 5.0792 0.3080 H + 24 H24 3.1050 3.6110 -0.7284 H + 25 H25 2.3684 2.1511 1.5434 H + 26 H26 1.7917 1.5469 -0.0284 H + 27 H27 -0.5318 1.5137 0.8369 H + 28 H28 0.0448 2.1180 2.4087 H + 29 H29 -0.0421 -0.7516 0.1211 H + 30 H30 0.4869 -3.0549 0.8125 H + 31 H31 1.4384 -3.4831 3.0428 H + 32 H32 1.8694 -1.6070 4.5783 H + 33 H33 1.3490 0.6972 3.8834 H + 34 H34 -2.2634 7.0207 1.7271 H + 35 H35 -2.8983 6.5355 0.1366 H + 36 H36 -2.3825 5.2956 1.3049 H + 37 H37 -0.7371 5.7691 -1.6524 H + 38 H38 -1.3524 7.4127 -1.3555 H + 39 H39 0.3857 7.0687 -1.1849 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 16 am + 4 2 19 2 + 5 3 4 1 + 6 3 20 1 + 7 4 7 1 + 8 4 5 1 + 9 4 8 1 + 10 5 6 1 + 11 5 21 1 + 12 5 22 1 + 13 6 7 1 + 14 7 23 1 + 15 7 24 1 + 16 8 9 1 + 17 8 25 1 + 18 8 26 1 + 19 9 10 1 + 20 9 27 1 + 21 9 28 1 + 22 10 15 ar + 23 10 11 ar + 24 11 12 ar + 25 11 29 1 + 26 12 13 ar + 27 12 30 1 + 28 13 14 ar + 29 13 31 1 + 30 14 15 ar + 31 14 32 1 + 32 15 33 1 + 33 16 17 1 + 34 16 18 1 + 35 17 34 1 + 36 17 35 1 + 37 17 36 1 + 38 18 37 1 + 39 18 38 1 + 40 18 39 1 + +# End of record + diff --git a/top/cgenff/SM31/SM31.pdb b/top/cgenff/SM31/SM31.pdb deleted file mode 120000 index 7e40e39..0000000 --- a/top/cgenff/SM31/SM31.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM31/SM31.pdb \ No newline at end of file diff --git a/top/cgenff/SM31/SM31.pdb b/top/cgenff/SM31/SM31.pdb new file mode 100644 index 0000000..37a46d5 --- /dev/null +++ b/top/cgenff/SM31/SM31.pdb @@ -0,0 +1,82 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM31 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 0.151 6.505 2.626 1.00 20.00 +HETATM 2 S2 UNK 1 0.479 6.009 1.335 1.00 20.00 +HETATM 3 N3 UNK 1 0.581 4.363 1.479 1.00 20.00 +HETATM 4 C4 UNK 1 1.206 3.572 0.416 1.00 20.00 +HETATM 5 C5 UNK 1 0.480 3.664 -0.939 1.00 20.00 +HETATM 6 O6 UNK 1 1.376 4.758 -1.217 1.00 20.00 +HETATM 7 C7 UNK 1 2.373 4.288 -0.288 1.00 20.00 +HETATM 8 C8 UNK 1 1.529 2.140 0.848 1.00 20.00 +HETATM 9 C9 UNK 1 0.307 1.525 1.533 1.00 20.00 +HETATM 10 C10 UNK 1 0.626 0.115 1.958 1.00 20.00 +HETATM 11 C11 UNK 1 0.379 -0.939 1.098 1.00 20.00 +HETATM 12 C12 UNK 1 0.676 -2.232 1.486 1.00 20.00 +HETATM 13 C13 UNK 1 1.210 -2.472 2.738 1.00 20.00 +HETATM 14 C14 UNK 1 1.452 -1.419 3.600 1.00 20.00 +HETATM 15 C15 UNK 1 1.160 -0.126 3.210 1.00 20.00 +HETATM 16 N16 UNK 1 -0.823 6.336 0.365 1.00 20.00 +HETATM 17 C17 UNK 1 -2.179 6.294 0.919 1.00 20.00 +HETATM 18 C18 UNK 1 -0.619 6.668 -1.047 1.00 20.00 +HETATM 19 O19 UNK 1 1.631 6.421 0.613 1.00 20.00 +HETATM 20 H20 UNK 1 0.227 3.922 2.268 1.00 20.00 +HETATM 21 H21 UNK 1 0.632 2.796 -1.581 1.00 20.00 +HETATM 22 H22 UNK 1 -0.566 3.959 -0.861 1.00 20.00 +HETATM 23 H23 UNK 1 2.829 5.079 0.308 1.00 20.00 +HETATM 24 H24 UNK 1 3.105 3.611 -0.728 1.00 20.00 +HETATM 25 H25 UNK 1 2.368 2.151 1.543 1.00 20.00 +HETATM 26 H26 UNK 1 1.792 1.547 -0.028 1.00 20.00 +HETATM 27 H27 UNK 1 -0.532 1.514 0.837 1.00 20.00 +HETATM 28 H28 UNK 1 0.045 2.118 2.409 1.00 20.00 +HETATM 29 H29 UNK 1 -0.042 -0.752 0.121 1.00 20.00 +HETATM 30 H30 UNK 1 0.487 -3.055 0.812 1.00 20.00 +HETATM 31 H31 UNK 1 1.438 -3.483 3.043 1.00 20.00 +HETATM 32 H32 UNK 1 1.869 -1.607 4.578 1.00 20.00 +HETATM 33 H33 UNK 1 1.349 0.697 3.883 1.00 20.00 +HETATM 34 H34 UNK 1 -2.263 7.021 1.727 1.00 20.00 +HETATM 35 H35 UNK 1 -2.898 6.535 0.137 1.00 20.00 +HETATM 36 H36 UNK 1 -2.382 5.296 1.305 1.00 20.00 +HETATM 37 H37 UNK 1 -0.737 5.769 -1.652 1.00 20.00 +HETATM 38 H38 UNK 1 -1.352 7.413 -1.356 1.00 20.00 +HETATM 39 H39 UNK 1 0.386 7.069 -1.185 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 16 19 +CONECT 3 2 4 20 +CONECT 4 3 7 5 8 +CONECT 5 4 6 21 22 +CONECT 6 5 7 +CONECT 7 6 4 23 24 +CONECT 8 4 9 25 26 +CONECT 9 8 10 27 28 +CONECT 10 9 15 11 +CONECT 11 10 12 29 +CONECT 12 11 13 30 +CONECT 13 12 14 31 +CONECT 14 13 15 32 +CONECT 15 14 10 33 +CONECT 16 2 17 18 +CONECT 17 16 34 35 36 +CONECT 18 16 37 38 39 +CONECT 19 2 +CONECT 20 3 +CONECT 21 5 +CONECT 22 5 +CONECT 23 7 +CONECT 24 7 +CONECT 25 8 +CONECT 26 8 +CONECT 27 9 +CONECT 28 9 +CONECT 29 11 +CONECT 30 12 +CONECT 31 13 +CONECT 32 14 +CONECT 33 15 +CONECT 34 17 +CONECT 35 17 +CONECT 36 17 +CONECT 37 18 +CONECT 38 18 +CONECT 39 18 +END diff --git a/top/cgenff/SM32/SM32.mol2 b/top/cgenff/SM32/SM32.mol2 deleted file mode 120000 index ec118f9..0000000 --- a/top/cgenff/SM32/SM32.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM32/SM32.mol2 \ No newline at end of file diff --git a/top/cgenff/SM32/SM32.mol2 b/top/cgenff/SM32/SM32.mol2 new file mode 100644 index 0000000..164b8d1 --- /dev/null +++ b/top/cgenff/SM32/SM32.mol2 @@ -0,0 +1,90 @@ +# Name: SM32 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 34 35 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 C1 0.6902 -0.3709 0.4861 C.3 + 2 S2 0.0783 1.2878 0.0801 S.o2 + 3 N3 -0.1956 1.9985 1.5506 N.am + 4 C4 -1.2432 1.4773 2.4322 C.3 + 5 C5 -1.1876 -0.0429 2.5995 C.3 + 6 S6 -2.0894 -0.2441 1.0381 S.3 + 7 C7 -2.6023 1.3480 1.7407 C.3 + 8 C8 -1.3146 2.2277 3.7637 C.3 + 9 C9 0.0982 2.4146 4.3203 C.3 + 10 C10 0.0279 3.1537 5.6317 C.ar + 11 C11 0.0929 4.5344 5.6512 C.ar + 12 C12 0.0235 5.2126 6.8538 C.ar + 13 C13 -0.1005 4.5096 8.0376 C.ar + 14 C14 -0.1602 3.1287 8.0184 C.ar + 15 C15 -0.0961 2.4507 6.8155 C.ar + 16 O16 1.1112 2.0719 -0.5010 O.2 + 17 O17 -1.2086 1.2121 -0.5177 O.2 + 18 H18 1.4220 -0.3014 1.2909 H + 19 H19 -0.1427 -0.9974 0.8054 H + 20 H20 1.1590 -0.8108 -0.3942 H + 21 H21 0.3375 2.7598 1.8282 H + 22 H22 -0.1736 -0.4412 2.5631 H + 23 H23 -1.7453 -0.3994 3.4654 H + 24 H24 -3.4328 1.2596 2.4412 H + 25 H25 -2.7733 2.1147 0.9850 H + 26 H26 -1.7752 3.2031 3.6067 H + 27 H27 -1.9115 1.6539 4.4726 H + 28 H28 0.5589 1.4392 4.4772 H + 29 H29 0.6951 2.9884 3.6113 H + 30 H30 0.1941 5.0834 4.7267 H + 31 H31 0.0705 6.2915 6.8688 H + 32 H32 -0.1502 5.0393 8.9775 H + 33 H33 -0.2567 2.5795 8.9433 H + 34 H34 -0.1424 1.3718 6.8005 H +@BOND + 1 1 2 1 + 2 1 18 1 + 3 1 19 1 + 4 1 20 1 + 5 2 3 am + 6 2 16 2 + 7 2 17 2 + 8 3 4 1 + 9 3 21 1 + 10 4 7 1 + 11 4 5 1 + 12 4 8 1 + 13 5 6 1 + 14 5 22 1 + 15 5 23 1 + 16 6 7 1 + 17 7 24 1 + 18 7 25 1 + 19 8 9 1 + 20 8 26 1 + 21 8 27 1 + 22 9 10 1 + 23 9 28 1 + 24 9 29 1 + 25 10 15 ar + 26 10 11 ar + 27 11 12 ar + 28 11 30 1 + 29 12 13 ar + 30 12 31 1 + 31 13 14 ar + 32 13 32 1 + 33 14 15 ar + 34 14 33 1 + 35 15 34 1 + +# End of record + diff --git a/top/cgenff/SM32/SM32.pdb b/top/cgenff/SM32/SM32.pdb deleted file mode 120000 index 83bdf1d..0000000 --- a/top/cgenff/SM32/SM32.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM32/SM32.pdb \ No newline at end of file diff --git a/top/cgenff/SM32/SM32.pdb b/top/cgenff/SM32/SM32.pdb new file mode 100644 index 0000000..886e147 --- /dev/null +++ b/top/cgenff/SM32/SM32.pdb @@ -0,0 +1,72 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM32 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 0.690 -0.371 0.486 1.00 20.00 +HETATM 2 S2 UNK 1 0.078 1.288 0.080 1.00 20.00 +HETATM 3 N3 UNK 1 -0.196 1.998 1.551 1.00 20.00 +HETATM 4 C4 UNK 1 -1.243 1.477 2.432 1.00 20.00 +HETATM 5 C5 UNK 1 -1.188 -0.043 2.599 1.00 20.00 +HETATM 6 S6 UNK 1 -2.089 -0.244 1.038 1.00 20.00 +HETATM 7 C7 UNK 1 -2.602 1.348 1.741 1.00 20.00 +HETATM 8 C8 UNK 1 -1.315 2.228 3.764 1.00 20.00 +HETATM 9 C9 UNK 1 0.098 2.415 4.320 1.00 20.00 +HETATM 10 C10 UNK 1 0.028 3.154 5.632 1.00 20.00 +HETATM 11 C11 UNK 1 0.093 4.534 5.651 1.00 20.00 +HETATM 12 C12 UNK 1 0.023 5.213 6.854 1.00 20.00 +HETATM 13 C13 UNK 1 -0.100 4.510 8.038 1.00 20.00 +HETATM 14 C14 UNK 1 -0.160 3.129 8.018 1.00 20.00 +HETATM 15 C15 UNK 1 -0.096 2.451 6.815 1.00 20.00 +HETATM 16 O16 UNK 1 1.111 2.072 -0.501 1.00 20.00 +HETATM 17 O17 UNK 1 -1.209 1.212 -0.518 1.00 20.00 +HETATM 18 H18 UNK 1 1.422 -0.301 1.291 1.00 20.00 +HETATM 19 H19 UNK 1 -0.143 -0.997 0.805 1.00 20.00 +HETATM 20 H20 UNK 1 1.159 -0.811 -0.394 1.00 20.00 +HETATM 21 H21 UNK 1 0.338 2.760 1.828 1.00 20.00 +HETATM 22 H22 UNK 1 -0.174 -0.441 2.563 1.00 20.00 +HETATM 23 H23 UNK 1 -1.745 -0.399 3.465 1.00 20.00 +HETATM 24 H24 UNK 1 -3.433 1.260 2.441 1.00 20.00 +HETATM 25 H25 UNK 1 -2.773 2.115 0.985 1.00 20.00 +HETATM 26 H26 UNK 1 -1.775 3.203 3.607 1.00 20.00 +HETATM 27 H27 UNK 1 -1.911 1.654 4.473 1.00 20.00 +HETATM 28 H28 UNK 1 0.559 1.439 4.477 1.00 20.00 +HETATM 29 H29 UNK 1 0.695 2.988 3.611 1.00 20.00 +HETATM 30 H30 UNK 1 0.194 5.083 4.727 1.00 20.00 +HETATM 31 H31 UNK 1 0.071 6.291 6.869 1.00 20.00 +HETATM 32 H32 UNK 1 -0.150 5.039 8.977 1.00 20.00 +HETATM 33 H33 UNK 1 -0.257 2.579 8.943 1.00 20.00 +HETATM 34 H34 UNK 1 -0.142 1.372 6.801 1.00 20.00 +CONECT 1 2 18 19 20 +CONECT 2 1 3 16 17 +CONECT 3 2 4 21 +CONECT 4 3 7 5 8 +CONECT 5 4 6 22 23 +CONECT 6 5 7 +CONECT 7 6 4 24 25 +CONECT 8 4 9 26 27 +CONECT 9 8 10 28 29 +CONECT 10 9 15 11 +CONECT 11 10 12 30 +CONECT 12 11 13 31 +CONECT 13 12 14 32 +CONECT 14 13 15 33 +CONECT 15 14 10 34 +CONECT 16 2 +CONECT 17 2 +CONECT 18 1 +CONECT 19 1 +CONECT 20 1 +CONECT 21 3 +CONECT 22 5 +CONECT 23 5 +CONECT 24 7 +CONECT 25 7 +CONECT 26 8 +CONECT 27 8 +CONECT 28 9 +CONECT 29 9 +CONECT 30 11 +CONECT 31 12 +CONECT 32 13 +CONECT 33 14 +CONECT 34 15 +END diff --git a/top/cgenff/SM33/SM33.mol2 b/top/cgenff/SM33/SM33.mol2 deleted file mode 120000 index 560f200..0000000 --- a/top/cgenff/SM33/SM33.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM33/SM33.mol2 \ No newline at end of file diff --git a/top/cgenff/SM33/SM33.mol2 b/top/cgenff/SM33/SM33.mol2 new file mode 100644 index 0000000..3478f22 --- /dev/null +++ b/top/cgenff/SM33/SM33.mol2 @@ -0,0 +1,105 @@ +# Name: SM33 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 41 43 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -1.3938 6.4195 0.4770 O.2 + 2 S2 -0.1575 5.8351 0.0908 S.o2 + 3 N3 0.0291 6.1588 -1.5225 N.am + 4 C4 -1.0983 5.9798 -2.4407 C.3 + 5 C5 -2.4111 6.5513 -1.9002 C.3 + 6 S6 -2.6681 5.0378 -0.9335 S.3 + 7 C7 -1.6958 4.5716 -2.3926 C.3 + 8 C8 -0.7766 6.4486 -3.8611 C.3 + 9 C9 -0.0756 7.8073 -3.8033 C.3 + 10 C10 0.2412 8.2690 -5.2024 C.ar + 11 C11 1.4505 7.9353 -5.7831 C.ar + 12 C12 1.7391 8.3548 -7.0683 C.ar + 13 C13 0.8229 9.1168 -7.7688 C.ar + 14 C14 -0.3842 9.4549 -7.1861 C.ar + 15 C15 -0.6750 9.0310 -5.9029 C.ar + 16 C16 -0.3587 4.0922 0.2532 C.ar + 17 C17 0.6143 3.2362 -0.2279 C.ar + 18 C18 0.4569 1.8689 -0.0997 C.ar + 19 C19 -0.6734 1.3575 0.5100 C.ar + 20 C20 -1.6490 2.2132 0.9864 C.ar + 21 C21 -1.4895 3.5807 0.8621 C.ar + 22 O22 1.0807 6.1555 0.7102 O.2 + 23 H23 0.8849 6.4670 -1.8595 H + 24 H24 -2.2700 7.4368 -1.2804 H + 25 H25 -3.1649 6.6989 -2.6736 H + 26 H26 -2.3116 4.3376 -3.2609 H + 27 H27 -0.9555 3.7989 -2.1852 H + 28 H28 -0.1225 5.7225 -4.3439 H + 29 H29 -1.7010 6.5406 -4.4314 H + 30 H30 -0.7297 8.5333 -3.3204 H + 31 H31 0.8487 7.7153 -3.2330 H + 32 H32 2.1682 7.3437 -5.2341 H + 33 H33 2.6824 8.0910 -7.5234 H + 34 H34 1.0502 9.4482 -8.7712 H + 35 H35 -1.0999 10.0505 -7.7333 H + 36 H36 -1.6180 9.2954 -5.4475 H + 37 H37 1.4977 3.6358 -0.7036 H + 38 H38 1.2171 1.2002 -0.4756 H + 39 H39 -0.7965 0.2892 0.6102 H + 40 H40 -2.5341 1.8135 1.4587 H + 41 H41 -2.2495 4.2494 1.2383 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 16 1 + 4 2 22 2 + 5 3 4 1 + 6 3 23 1 + 7 4 7 1 + 8 4 5 1 + 9 4 8 1 + 10 5 6 1 + 11 5 24 1 + 12 5 25 1 + 13 6 7 1 + 14 7 26 1 + 15 7 27 1 + 16 8 9 1 + 17 8 28 1 + 18 8 29 1 + 19 9 10 1 + 20 9 30 1 + 21 9 31 1 + 22 10 15 ar + 23 10 11 ar + 24 11 12 ar + 25 11 32 1 + 26 12 13 ar + 27 12 33 1 + 28 13 14 ar + 29 13 34 1 + 30 14 15 ar + 31 14 35 1 + 32 15 36 1 + 33 16 21 ar + 34 16 17 ar + 35 17 18 ar + 36 17 37 1 + 37 18 19 ar + 38 18 38 1 + 39 19 20 ar + 40 19 39 1 + 41 20 21 ar + 42 20 40 1 + 43 21 41 1 + +# End of record + diff --git a/top/cgenff/SM33/SM33.pdb b/top/cgenff/SM33/SM33.pdb deleted file mode 120000 index d26e3c6..0000000 --- a/top/cgenff/SM33/SM33.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM33/SM33.pdb \ No newline at end of file diff --git a/top/cgenff/SM33/SM33.pdb b/top/cgenff/SM33/SM33.pdb new file mode 100644 index 0000000..307d504 --- /dev/null +++ b/top/cgenff/SM33/SM33.pdb @@ -0,0 +1,86 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM33 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -1.394 6.419 0.477 1.00 20.00 +HETATM 2 S2 UNK 1 -0.157 5.835 0.091 1.00 20.00 +HETATM 3 N3 UNK 1 0.029 6.159 -1.522 1.00 20.00 +HETATM 4 C4 UNK 1 -1.098 5.980 -2.441 1.00 20.00 +HETATM 5 C5 UNK 1 -2.411 6.551 -1.900 1.00 20.00 +HETATM 6 S6 UNK 1 -2.668 5.038 -0.933 1.00 20.00 +HETATM 7 C7 UNK 1 -1.696 4.572 -2.393 1.00 20.00 +HETATM 8 C8 UNK 1 -0.777 6.449 -3.861 1.00 20.00 +HETATM 9 C9 UNK 1 -0.076 7.807 -3.803 1.00 20.00 +HETATM 10 C10 UNK 1 0.241 8.269 -5.202 1.00 20.00 +HETATM 11 C11 UNK 1 1.450 7.935 -5.783 1.00 20.00 +HETATM 12 C12 UNK 1 1.739 8.355 -7.068 1.00 20.00 +HETATM 13 C13 UNK 1 0.823 9.117 -7.769 1.00 20.00 +HETATM 14 C14 UNK 1 -0.384 9.455 -7.186 1.00 20.00 +HETATM 15 C15 UNK 1 -0.675 9.031 -5.903 1.00 20.00 +HETATM 16 C16 UNK 1 -0.359 4.092 0.253 1.00 20.00 +HETATM 17 C17 UNK 1 0.614 3.236 -0.228 1.00 20.00 +HETATM 18 C18 UNK 1 0.457 1.869 -0.100 1.00 20.00 +HETATM 19 C19 UNK 1 -0.673 1.357 0.510 1.00 20.00 +HETATM 20 C20 UNK 1 -1.649 2.213 0.986 1.00 20.00 +HETATM 21 C21 UNK 1 -1.489 3.581 0.862 1.00 20.00 +HETATM 22 O22 UNK 1 1.081 6.155 0.710 1.00 20.00 +HETATM 23 H23 UNK 1 0.885 6.467 -1.860 1.00 20.00 +HETATM 24 H24 UNK 1 -2.270 7.437 -1.280 1.00 20.00 +HETATM 25 H25 UNK 1 -3.165 6.699 -2.674 1.00 20.00 +HETATM 26 H26 UNK 1 -2.312 4.338 -3.261 1.00 20.00 +HETATM 27 H27 UNK 1 -0.956 3.799 -2.185 1.00 20.00 +HETATM 28 H28 UNK 1 -0.123 5.723 -4.344 1.00 20.00 +HETATM 29 H29 UNK 1 -1.701 6.541 -4.431 1.00 20.00 +HETATM 30 H30 UNK 1 -0.730 8.533 -3.320 1.00 20.00 +HETATM 31 H31 UNK 1 0.849 7.715 -3.233 1.00 20.00 +HETATM 32 H32 UNK 1 2.168 7.344 -5.234 1.00 20.00 +HETATM 33 H33 UNK 1 2.682 8.091 -7.523 1.00 20.00 +HETATM 34 H34 UNK 1 1.050 9.448 -8.771 1.00 20.00 +HETATM 35 H35 UNK 1 -1.100 10.050 -7.733 1.00 20.00 +HETATM 36 H36 UNK 1 -1.618 9.295 -5.448 1.00 20.00 +HETATM 37 H37 UNK 1 1.498 3.636 -0.704 1.00 20.00 +HETATM 38 H38 UNK 1 1.217 1.200 -0.476 1.00 20.00 +HETATM 39 H39 UNK 1 -0.796 0.289 0.610 1.00 20.00 +HETATM 40 H40 UNK 1 -2.534 1.814 1.459 1.00 20.00 +HETATM 41 H41 UNK 1 -2.250 4.249 1.238 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 16 22 +CONECT 3 2 4 23 +CONECT 4 3 7 5 8 +CONECT 5 4 6 24 25 +CONECT 6 5 7 +CONECT 7 6 4 26 27 +CONECT 8 4 9 28 29 +CONECT 9 8 10 30 31 +CONECT 10 9 15 11 +CONECT 11 10 12 32 +CONECT 12 11 13 33 +CONECT 13 12 14 34 +CONECT 14 13 15 35 +CONECT 15 14 10 36 +CONECT 16 2 21 17 +CONECT 17 16 18 37 +CONECT 18 17 19 38 +CONECT 19 18 20 39 +CONECT 20 19 21 40 +CONECT 21 20 16 41 +CONECT 22 2 +CONECT 23 3 +CONECT 24 5 +CONECT 25 5 +CONECT 26 7 +CONECT 27 7 +CONECT 28 8 +CONECT 29 8 +CONECT 30 9 +CONECT 31 9 +CONECT 32 11 +CONECT 33 12 +CONECT 34 13 +CONECT 35 14 +CONECT 36 15 +CONECT 37 17 +CONECT 38 18 +CONECT 39 19 +CONECT 40 20 +CONECT 41 21 +END diff --git a/top/cgenff/SM34/SM34.mol2 b/top/cgenff/SM34/SM34.mol2 deleted file mode 120000 index 55116c0..0000000 --- a/top/cgenff/SM34/SM34.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM34/SM34.mol2 \ No newline at end of file diff --git a/top/cgenff/SM34/SM34.mol2 b/top/cgenff/SM34/SM34.mol2 new file mode 100644 index 0000000..665194a --- /dev/null +++ b/top/cgenff/SM34/SM34.mol2 @@ -0,0 +1,100 @@ +# Name: SM34 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 39 40 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -0.4388 0.6038 -3.9820 O.2 + 2 S2 0.3206 1.0225 -2.8562 S.o2 + 3 N3 1.5890 -0.0345 -2.7285 N.am + 4 C4 2.4894 0.0377 -1.5751 C.3 + 5 C5 1.6936 -0.0983 -0.2416 C.3 + 6 S6 1.7187 1.7306 -0.3217 S.3 + 7 C7 3.1275 1.4551 -1.4581 C.3 + 8 C8 3.5715 -1.0393 -1.6751 C.3 + 9 C9 4.3320 -0.8775 -2.9928 C.3 + 10 C10 5.3978 -1.9383 -3.0912 C.ar + 11 C11 6.6668 -1.6906 -2.6021 C.ar + 12 C12 7.6431 -2.6654 -2.6881 C.ar + 13 C13 7.3534 -3.8842 -3.2726 C.ar + 14 C14 6.0858 -4.1300 -3.7663 C.ar + 15 C15 5.1081 -3.1571 -3.6757 C.ar + 16 N16 0.9533 2.5031 -3.2434 N.am + 17 C17 1.5928 2.7086 -4.5453 C.3 + 18 C18 0.8736 3.6073 -2.2839 C.3 + 19 O19 -0.2287 1.1495 -1.5519 O.2 + 20 H20 1.7359 -0.7014 -3.4175 H + 21 H21 2.2672 -0.5205 0.5836 H + 22 H22 0.7032 -0.5400 -0.3517 H + 23 H23 3.0878 2.0435 -2.3748 H + 24 H24 4.1047 1.4702 -0.9754 H + 25 H25 4.2649 -0.9363 -0.8404 H + 26 H26 3.1072 -2.0250 -1.6422 H + 27 H27 3.6386 -0.9805 -3.8275 H + 28 H28 4.7963 0.1082 -3.0256 H + 29 H29 6.8944 -0.7368 -2.1495 H + 30 H30 8.6335 -2.4733 -2.3026 H + 31 H31 8.1174 -4.6442 -3.3437 H + 32 H32 5.8595 -5.0820 -4.2233 H + 33 H33 4.1179 -3.3490 -4.0618 H + 34 H34 0.8474 3.0415 -5.2677 H + 35 H35 2.3717 3.4654 -4.4521 H + 36 H36 2.0350 1.7720 -4.8849 H + 37 H37 0.2851 3.2967 -1.4206 H + 38 H38 1.8779 3.8802 -1.9598 H + 39 H39 0.3986 4.4665 -2.7574 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 16 am + 4 2 19 2 + 5 3 4 1 + 6 3 20 1 + 7 4 7 1 + 8 4 5 1 + 9 4 8 1 + 10 5 6 1 + 11 5 21 1 + 12 5 22 1 + 13 6 7 1 + 14 7 23 1 + 15 7 24 1 + 16 8 9 1 + 17 8 25 1 + 18 8 26 1 + 19 9 10 1 + 20 9 27 1 + 21 9 28 1 + 22 10 15 ar + 23 10 11 ar + 24 11 12 ar + 25 11 29 1 + 26 12 13 ar + 27 12 30 1 + 28 13 14 ar + 29 13 31 1 + 30 14 15 ar + 31 14 32 1 + 32 15 33 1 + 33 16 17 1 + 34 16 18 1 + 35 17 34 1 + 36 17 35 1 + 37 17 36 1 + 38 18 37 1 + 39 18 38 1 + 40 18 39 1 + +# End of record + diff --git a/top/cgenff/SM34/SM34.pdb b/top/cgenff/SM34/SM34.pdb deleted file mode 120000 index dff5ac3..0000000 --- a/top/cgenff/SM34/SM34.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM34/SM34.pdb \ No newline at end of file diff --git a/top/cgenff/SM34/SM34.pdb b/top/cgenff/SM34/SM34.pdb new file mode 100644 index 0000000..f1b5d5c --- /dev/null +++ b/top/cgenff/SM34/SM34.pdb @@ -0,0 +1,82 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM34 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -0.439 0.604 -3.982 1.00 20.00 +HETATM 2 S2 UNK 1 0.321 1.022 -2.856 1.00 20.00 +HETATM 3 N3 UNK 1 1.589 -0.034 -2.729 1.00 20.00 +HETATM 4 C4 UNK 1 2.489 0.038 -1.575 1.00 20.00 +HETATM 5 C5 UNK 1 1.694 -0.098 -0.242 1.00 20.00 +HETATM 6 S6 UNK 1 1.719 1.731 -0.322 1.00 20.00 +HETATM 7 C7 UNK 1 3.128 1.455 -1.458 1.00 20.00 +HETATM 8 C8 UNK 1 3.571 -1.039 -1.675 1.00 20.00 +HETATM 9 C9 UNK 1 4.332 -0.877 -2.993 1.00 20.00 +HETATM 10 C10 UNK 1 5.398 -1.938 -3.091 1.00 20.00 +HETATM 11 C11 UNK 1 6.667 -1.691 -2.602 1.00 20.00 +HETATM 12 C12 UNK 1 7.643 -2.665 -2.688 1.00 20.00 +HETATM 13 C13 UNK 1 7.353 -3.884 -3.273 1.00 20.00 +HETATM 14 C14 UNK 1 6.086 -4.130 -3.766 1.00 20.00 +HETATM 15 C15 UNK 1 5.108 -3.157 -3.676 1.00 20.00 +HETATM 16 N16 UNK 1 0.953 2.503 -3.243 1.00 20.00 +HETATM 17 C17 UNK 1 1.593 2.709 -4.545 1.00 20.00 +HETATM 18 C18 UNK 1 0.874 3.607 -2.284 1.00 20.00 +HETATM 19 O19 UNK 1 -0.229 1.149 -1.552 1.00 20.00 +HETATM 20 H20 UNK 1 1.736 -0.701 -3.417 1.00 20.00 +HETATM 21 H21 UNK 1 2.267 -0.520 0.584 1.00 20.00 +HETATM 22 H22 UNK 1 0.703 -0.540 -0.352 1.00 20.00 +HETATM 23 H23 UNK 1 3.088 2.044 -2.375 1.00 20.00 +HETATM 24 H24 UNK 1 4.105 1.470 -0.975 1.00 20.00 +HETATM 25 H25 UNK 1 4.265 -0.936 -0.840 1.00 20.00 +HETATM 26 H26 UNK 1 3.107 -2.025 -1.642 1.00 20.00 +HETATM 27 H27 UNK 1 3.639 -0.980 -3.827 1.00 20.00 +HETATM 28 H28 UNK 1 4.796 0.108 -3.026 1.00 20.00 +HETATM 29 H29 UNK 1 6.894 -0.737 -2.149 1.00 20.00 +HETATM 30 H30 UNK 1 8.634 -2.473 -2.303 1.00 20.00 +HETATM 31 H31 UNK 1 8.117 -4.644 -3.344 1.00 20.00 +HETATM 32 H32 UNK 1 5.860 -5.082 -4.223 1.00 20.00 +HETATM 33 H33 UNK 1 4.118 -3.349 -4.062 1.00 20.00 +HETATM 34 H34 UNK 1 0.847 3.041 -5.268 1.00 20.00 +HETATM 35 H35 UNK 1 2.372 3.465 -4.452 1.00 20.00 +HETATM 36 H36 UNK 1 2.035 1.772 -4.885 1.00 20.00 +HETATM 37 H37 UNK 1 0.285 3.297 -1.421 1.00 20.00 +HETATM 38 H38 UNK 1 1.878 3.880 -1.960 1.00 20.00 +HETATM 39 H39 UNK 1 0.399 4.466 -2.757 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 16 19 +CONECT 3 2 4 20 +CONECT 4 3 7 5 8 +CONECT 5 4 6 21 22 +CONECT 6 5 7 +CONECT 7 6 4 23 24 +CONECT 8 4 9 25 26 +CONECT 9 8 10 27 28 +CONECT 10 9 15 11 +CONECT 11 10 12 29 +CONECT 12 11 13 30 +CONECT 13 12 14 31 +CONECT 14 13 15 32 +CONECT 15 14 10 33 +CONECT 16 2 17 18 +CONECT 17 16 34 35 36 +CONECT 18 16 37 38 39 +CONECT 19 2 +CONECT 20 3 +CONECT 21 5 +CONECT 22 5 +CONECT 23 7 +CONECT 24 7 +CONECT 25 8 +CONECT 26 8 +CONECT 27 9 +CONECT 28 9 +CONECT 29 11 +CONECT 30 12 +CONECT 31 13 +CONECT 32 14 +CONECT 33 15 +CONECT 34 17 +CONECT 35 17 +CONECT 36 17 +CONECT 37 18 +CONECT 38 18 +CONECT 39 18 +END diff --git a/top/cgenff/SM35/SM35.mol2 b/top/cgenff/SM35/SM35.mol2 deleted file mode 120000 index 0091321..0000000 --- a/top/cgenff/SM35/SM35.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM35/SM35.mol2 \ No newline at end of file diff --git a/top/cgenff/SM35/SM35.mol2 b/top/cgenff/SM35/SM35.mol2 new file mode 100644 index 0000000..f12083c --- /dev/null +++ b/top/cgenff/SM35/SM35.mol2 @@ -0,0 +1,92 @@ +# Name: SM35 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 35 36 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 C1 -1.4668 -1.5581 -1.5447 C.3 + 2 S2 -2.5562 -0.1930 -2.0348 S.o2 + 3 N3 -2.3180 0.9632 -0.8735 N.am + 4 C4 -0.9959 1.5719 -0.7061 C.3 + 5 C5 0.0114 0.6443 -0.0227 C.3 + 6 S6 -0.6567 1.1155 1.5969 S.o + 7 O7 -2.0188 0.4366 1.6161 O.3 + 8 C8 -0.9201 2.5274 0.4870 C.3 + 9 C9 -0.4652 2.1848 -2.0036 C.3 + 10 C10 -1.5189 3.1253 -2.5918 C.3 + 11 C11 -0.9499 3.8248 -3.7992 C.ar + 12 C12 -0.2951 5.0334 -3.6531 C.ar + 13 C13 0.2310 5.6727 -4.7601 C.ar + 14 C14 0.0932 5.1086 -6.0145 C.ar + 15 C15 -0.5663 3.9025 -6.1613 C.ar + 16 C16 -1.0878 3.2607 -5.0537 C.ar + 17 O17 -3.9195 -0.5646 -1.8850 O.2 + 18 O18 -2.0892 0.4121 -3.2327 O.2 + 19 H19 -1.6485 -1.8109 -0.5001 H + 20 H20 -1.6703 -2.4277 -2.1696 H + 21 H21 -0.4270 -1.2561 -1.6698 H + 22 H22 -3.0538 1.2374 -0.3040 H + 23 H23 -0.1448 -0.4078 -0.2609 H + 24 H24 1.0462 0.9552 -0.1663 H + 25 H25 -0.0649 3.2017 0.4422 H + 26 H26 -1.8562 3.0530 0.6752 H + 27 H27 0.4460 2.7453 -1.7945 H + 28 H28 -0.2475 1.3909 -2.7180 H + 29 H29 -2.3965 2.5494 -2.8855 H + 30 H30 -1.8035 3.8653 -1.8437 H + 31 H31 -0.1912 5.4764 -2.6736 H + 32 H32 0.7459 6.6152 -4.6455 H + 33 H33 0.5003 5.6102 -6.8800 H + 34 H34 -0.6743 3.4620 -7.1414 H + 35 H35 -1.6033 2.3186 -5.1684 H +@BOND + 1 1 2 1 + 2 1 19 1 + 3 1 20 1 + 4 1 21 1 + 5 2 3 am + 6 2 17 2 + 7 2 18 2 + 8 3 4 1 + 9 3 22 1 + 10 4 8 1 + 11 4 5 1 + 12 4 9 1 + 13 5 6 1 + 14 5 23 1 + 15 5 24 1 + 16 6 7 1 + 17 6 8 1 + 18 8 25 1 + 19 8 26 1 + 20 9 10 1 + 21 9 27 1 + 22 9 28 1 + 23 10 11 1 + 24 10 29 1 + 25 10 30 1 + 26 11 16 ar + 27 11 12 ar + 28 12 13 ar + 29 12 31 1 + 30 13 14 ar + 31 13 32 1 + 32 14 15 ar + 33 14 33 1 + 34 15 16 ar + 35 15 34 1 + 36 16 35 1 + +# End of record + diff --git a/top/cgenff/SM35/SM35.pdb b/top/cgenff/SM35/SM35.pdb deleted file mode 120000 index 5100c72..0000000 --- a/top/cgenff/SM35/SM35.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM35/SM35.pdb \ No newline at end of file diff --git a/top/cgenff/SM35/SM35.pdb b/top/cgenff/SM35/SM35.pdb new file mode 100644 index 0000000..30b5e08 --- /dev/null +++ b/top/cgenff/SM35/SM35.pdb @@ -0,0 +1,74 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM35 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 -1.467 -1.558 -1.545 1.00 20.00 +HETATM 2 S2 UNK 1 -2.556 -0.193 -2.035 1.00 20.00 +HETATM 3 N3 UNK 1 -2.318 0.963 -0.873 1.00 20.00 +HETATM 4 C4 UNK 1 -0.996 1.572 -0.706 1.00 20.00 +HETATM 5 C5 UNK 1 0.011 0.644 -0.023 1.00 20.00 +HETATM 6 S6 UNK 1 -0.657 1.116 1.597 1.00 20.00 +HETATM 7 O7 UNK 1 -2.019 0.437 1.616 1.00 20.00 +HETATM 8 C8 UNK 1 -0.920 2.527 0.487 1.00 20.00 +HETATM 9 C9 UNK 1 -0.465 2.185 -2.004 1.00 20.00 +HETATM 10 C10 UNK 1 -1.519 3.125 -2.592 1.00 20.00 +HETATM 11 C11 UNK 1 -0.950 3.825 -3.799 1.00 20.00 +HETATM 12 C12 UNK 1 -0.295 5.033 -3.653 1.00 20.00 +HETATM 13 C13 UNK 1 0.231 5.673 -4.760 1.00 20.00 +HETATM 14 C14 UNK 1 0.093 5.109 -6.015 1.00 20.00 +HETATM 15 C15 UNK 1 -0.566 3.903 -6.161 1.00 20.00 +HETATM 16 C16 UNK 1 -1.088 3.261 -5.054 1.00 20.00 +HETATM 17 O17 UNK 1 -3.920 -0.565 -1.885 1.00 20.00 +HETATM 18 O18 UNK 1 -2.089 0.412 -3.233 1.00 20.00 +HETATM 19 H19 UNK 1 -1.649 -1.811 -0.500 1.00 20.00 +HETATM 20 H20 UNK 1 -1.670 -2.428 -2.170 1.00 20.00 +HETATM 21 H21 UNK 1 -0.427 -1.256 -1.670 1.00 20.00 +HETATM 22 H22 UNK 1 -3.054 1.237 -0.304 1.00 20.00 +HETATM 23 H23 UNK 1 -0.145 -0.408 -0.261 1.00 20.00 +HETATM 24 H24 UNK 1 1.046 0.955 -0.166 1.00 20.00 +HETATM 25 H25 UNK 1 -0.065 3.202 0.442 1.00 20.00 +HETATM 26 H26 UNK 1 -1.856 3.053 0.675 1.00 20.00 +HETATM 27 H27 UNK 1 0.446 2.745 -1.795 1.00 20.00 +HETATM 28 H28 UNK 1 -0.247 1.391 -2.718 1.00 20.00 +HETATM 29 H29 UNK 1 -2.397 2.549 -2.885 1.00 20.00 +HETATM 30 H30 UNK 1 -1.804 3.865 -1.844 1.00 20.00 +HETATM 31 H31 UNK 1 -0.191 5.476 -2.674 1.00 20.00 +HETATM 32 H32 UNK 1 0.746 6.615 -4.645 1.00 20.00 +HETATM 33 H33 UNK 1 0.500 5.610 -6.880 1.00 20.00 +HETATM 34 H34 UNK 1 -0.674 3.462 -7.141 1.00 20.00 +HETATM 35 H35 UNK 1 -1.603 2.319 -5.168 1.00 20.00 +CONECT 1 2 19 20 21 +CONECT 2 1 3 17 18 +CONECT 3 2 4 22 +CONECT 4 3 8 5 9 +CONECT 5 4 6 23 24 +CONECT 6 5 7 8 +CONECT 7 6 +CONECT 8 6 4 25 26 +CONECT 9 4 10 27 28 +CONECT 10 9 11 29 30 +CONECT 11 10 16 12 +CONECT 12 11 13 31 +CONECT 13 12 14 32 +CONECT 14 13 15 33 +CONECT 15 14 16 34 +CONECT 16 15 11 35 +CONECT 17 2 +CONECT 18 2 +CONECT 19 1 +CONECT 20 1 +CONECT 21 1 +CONECT 22 3 +CONECT 23 5 +CONECT 24 5 +CONECT 25 8 +CONECT 26 8 +CONECT 27 9 +CONECT 28 9 +CONECT 29 10 +CONECT 30 10 +CONECT 31 12 +CONECT 32 13 +CONECT 33 14 +CONECT 34 15 +CONECT 35 16 +END diff --git a/top/cgenff/SM36/SM36.mol2 b/top/cgenff/SM36/SM36.mol2 deleted file mode 120000 index 8451ff0..0000000 --- a/top/cgenff/SM36/SM36.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM36/SM36.mol2 \ No newline at end of file diff --git a/top/cgenff/SM36/SM36.mol2 b/top/cgenff/SM36/SM36.mol2 new file mode 100644 index 0000000..7429188 --- /dev/null +++ b/top/cgenff/SM36/SM36.mol2 @@ -0,0 +1,107 @@ +# Name: SM36 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 42 44 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 0.6047 1.8005 1.2454 O.2 + 2 S2 1.2791 0.5760 1.5007 S.o2 + 3 N3 0.1137 -0.5999 1.5420 N.am + 4 C4 -1.0987 -0.4019 2.3402 C.3 + 5 C5 -2.3393 -1.0494 1.7207 C.3 + 6 S6 -3.3721 0.2672 2.4235 S.o + 7 O7 -4.1649 0.7600 1.2214 O.3 + 8 C8 -1.7269 0.9803 2.1475 C.3 + 9 C9 -0.8980 -0.7717 3.8112 C.3 + 10 C10 -0.1582 -2.1077 3.9048 C.3 + 11 C11 0.0394 -2.4720 5.3537 C.ar + 12 C12 1.1799 -2.0638 6.0196 C.ar + 13 C13 1.3590 -2.3938 7.3500 C.ar + 14 C14 0.4024 -3.1410 8.0115 C.ar + 15 C15 -0.7356 -3.5537 7.3441 C.ar + 16 C16 -0.9171 -3.2192 6.0152 C.ar + 17 C17 1.9472 0.7054 3.1259 C.ar + 18 C18 1.3851 1.5802 4.0367 C.ar + 19 C19 1.9063 1.6782 5.3133 C.ar + 20 C20 2.9961 0.9090 5.6758 C.ar + 21 C21 3.5616 0.0380 4.7634 C.ar + 22 C22 3.0371 -0.0638 3.4884 C.ar + 23 O23 2.3233 0.0772 0.6761 O.2 + 24 H24 0.2338 -1.4197 1.0376 H + 25 H25 -2.3250 -1.0471 0.6308 H + 26 H26 -2.5600 -2.0340 2.1332 H + 27 H27 -1.4349 1.6947 2.9172 H + 28 H28 -1.5937 1.3749 1.1402 H + 29 H29 -0.3115 0.0037 4.3040 H + 30 H30 -1.8686 -0.8588 4.2996 H + 31 H31 -0.7447 -2.8831 3.4119 H + 32 H32 0.8123 -2.0206 3.4164 H + 33 H33 1.9293 -1.4838 5.5015 H + 34 H34 2.2483 -2.0717 7.8713 H + 35 H35 0.5444 -3.4026 9.0497 H + 36 H36 -1.4828 -4.1377 7.8609 H + 37 H37 -1.8061 -3.5419 5.4937 H + 38 H38 0.5363 2.1844 3.7521 H + 39 H39 1.4647 2.3589 6.0261 H + 40 H40 3.4061 0.9888 6.6718 H + 41 H41 4.4133 -0.5627 5.0465 H + 42 H42 3.4791 -0.7441 2.7754 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 17 1 + 4 2 23 2 + 5 3 4 1 + 6 3 24 1 + 7 4 8 1 + 8 4 5 1 + 9 4 9 1 + 10 5 6 1 + 11 5 25 1 + 12 5 26 1 + 13 6 7 1 + 14 6 8 1 + 15 8 27 1 + 16 8 28 1 + 17 9 10 1 + 18 9 29 1 + 19 9 30 1 + 20 10 11 1 + 21 10 31 1 + 22 10 32 1 + 23 11 16 ar + 24 11 12 ar + 25 12 13 ar + 26 12 33 1 + 27 13 14 ar + 28 13 34 1 + 29 14 15 ar + 30 14 35 1 + 31 15 16 ar + 32 15 36 1 + 33 16 37 1 + 34 17 22 ar + 35 17 18 ar + 36 18 19 ar + 37 18 38 1 + 38 19 20 ar + 39 19 39 1 + 40 20 21 ar + 41 20 40 1 + 42 21 22 ar + 43 21 41 1 + 44 22 42 1 + +# End of record + diff --git a/top/cgenff/SM36/SM36.pdb b/top/cgenff/SM36/SM36.pdb deleted file mode 120000 index c020172..0000000 --- a/top/cgenff/SM36/SM36.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM36/SM36.pdb \ No newline at end of file diff --git a/top/cgenff/SM36/SM36.pdb b/top/cgenff/SM36/SM36.pdb new file mode 100644 index 0000000..c68065a --- /dev/null +++ b/top/cgenff/SM36/SM36.pdb @@ -0,0 +1,88 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM36 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 0.605 1.800 1.245 1.00 20.00 +HETATM 2 S2 UNK 1 1.279 0.576 1.501 1.00 20.00 +HETATM 3 N3 UNK 1 0.114 -0.600 1.542 1.00 20.00 +HETATM 4 C4 UNK 1 -1.099 -0.402 2.340 1.00 20.00 +HETATM 5 C5 UNK 1 -2.339 -1.049 1.721 1.00 20.00 +HETATM 6 S6 UNK 1 -3.372 0.267 2.424 1.00 20.00 +HETATM 7 O7 UNK 1 -4.165 0.760 1.221 1.00 20.00 +HETATM 8 C8 UNK 1 -1.727 0.980 2.148 1.00 20.00 +HETATM 9 C9 UNK 1 -0.898 -0.772 3.811 1.00 20.00 +HETATM 10 C10 UNK 1 -0.158 -2.108 3.905 1.00 20.00 +HETATM 11 C11 UNK 1 0.039 -2.472 5.354 1.00 20.00 +HETATM 12 C12 UNK 1 1.180 -2.064 6.020 1.00 20.00 +HETATM 13 C13 UNK 1 1.359 -2.394 7.350 1.00 20.00 +HETATM 14 C14 UNK 1 0.402 -3.141 8.012 1.00 20.00 +HETATM 15 C15 UNK 1 -0.736 -3.554 7.344 1.00 20.00 +HETATM 16 C16 UNK 1 -0.917 -3.219 6.015 1.00 20.00 +HETATM 17 C17 UNK 1 1.947 0.705 3.126 1.00 20.00 +HETATM 18 C18 UNK 1 1.385 1.580 4.037 1.00 20.00 +HETATM 19 C19 UNK 1 1.906 1.678 5.313 1.00 20.00 +HETATM 20 C20 UNK 1 2.996 0.909 5.676 1.00 20.00 +HETATM 21 C21 UNK 1 3.562 0.038 4.763 1.00 20.00 +HETATM 22 C22 UNK 1 3.037 -0.064 3.488 1.00 20.00 +HETATM 23 O23 UNK 1 2.323 0.077 0.676 1.00 20.00 +HETATM 24 H24 UNK 1 0.234 -1.420 1.038 1.00 20.00 +HETATM 25 H25 UNK 1 -2.325 -1.047 0.631 1.00 20.00 +HETATM 26 H26 UNK 1 -2.560 -2.034 2.133 1.00 20.00 +HETATM 27 H27 UNK 1 -1.435 1.695 2.917 1.00 20.00 +HETATM 28 H28 UNK 1 -1.594 1.375 1.140 1.00 20.00 +HETATM 29 H29 UNK 1 -0.312 0.004 4.304 1.00 20.00 +HETATM 30 H30 UNK 1 -1.869 -0.859 4.300 1.00 20.00 +HETATM 31 H31 UNK 1 -0.745 -2.883 3.412 1.00 20.00 +HETATM 32 H32 UNK 1 0.812 -2.021 3.416 1.00 20.00 +HETATM 33 H33 UNK 1 1.929 -1.484 5.502 1.00 20.00 +HETATM 34 H34 UNK 1 2.248 -2.072 7.871 1.00 20.00 +HETATM 35 H35 UNK 1 0.544 -3.403 9.050 1.00 20.00 +HETATM 36 H36 UNK 1 -1.483 -4.138 7.861 1.00 20.00 +HETATM 37 H37 UNK 1 -1.806 -3.542 5.494 1.00 20.00 +HETATM 38 H38 UNK 1 0.536 2.184 3.752 1.00 20.00 +HETATM 39 H39 UNK 1 1.465 2.359 6.026 1.00 20.00 +HETATM 40 H40 UNK 1 3.406 0.989 6.672 1.00 20.00 +HETATM 41 H41 UNK 1 4.413 -0.563 5.046 1.00 20.00 +HETATM 42 H42 UNK 1 3.479 -0.744 2.775 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 17 23 +CONECT 3 2 4 24 +CONECT 4 3 8 5 9 +CONECT 5 4 6 25 26 +CONECT 6 5 7 8 +CONECT 7 6 +CONECT 8 6 4 27 28 +CONECT 9 4 10 29 30 +CONECT 10 9 11 31 32 +CONECT 11 10 16 12 +CONECT 12 11 13 33 +CONECT 13 12 14 34 +CONECT 14 13 15 35 +CONECT 15 14 16 36 +CONECT 16 15 11 37 +CONECT 17 2 22 18 +CONECT 18 17 19 38 +CONECT 19 18 20 39 +CONECT 20 19 21 40 +CONECT 21 20 22 41 +CONECT 22 21 17 42 +CONECT 23 2 +CONECT 24 3 +CONECT 25 5 +CONECT 26 5 +CONECT 27 8 +CONECT 28 8 +CONECT 29 9 +CONECT 30 9 +CONECT 31 10 +CONECT 32 10 +CONECT 33 12 +CONECT 34 13 +CONECT 35 14 +CONECT 36 15 +CONECT 37 16 +CONECT 38 18 +CONECT 39 19 +CONECT 40 20 +CONECT 41 21 +CONECT 42 22 +END diff --git a/top/cgenff/SM37/SM37.mol2 b/top/cgenff/SM37/SM37.mol2 deleted file mode 120000 index ab2e8d5..0000000 --- a/top/cgenff/SM37/SM37.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM37/SM37.mol2 \ No newline at end of file diff --git a/top/cgenff/SM37/SM37.mol2 b/top/cgenff/SM37/SM37.mol2 new file mode 100644 index 0000000..b675f83 --- /dev/null +++ b/top/cgenff/SM37/SM37.mol2 @@ -0,0 +1,102 @@ +# Name: SM37 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 40 41 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -3.0677 -1.6105 -2.4976 O.2 + 2 S2 -1.9084 -0.8634 -2.1555 S.o2 + 3 N3 -2.4411 0.6199 -1.6472 N.am + 4 C4 -1.4824 1.6158 -1.1622 C.3 + 5 C5 -0.8180 1.2184 0.1580 C.3 + 6 S6 -2.2599 1.8386 1.0678 S.o + 7 O7 -3.3353 0.8103 0.7472 O.3 + 8 C8 -2.1486 2.8042 -0.4651 C.3 + 9 C9 -0.4788 2.0350 -2.2384 C.3 + 10 C10 -1.2299 2.4130 -3.5166 C.3 + 11 C11 -0.2415 2.8259 -4.5766 C.ar + 12 C12 0.1376 4.1504 -4.6898 C.ar + 13 C13 1.0480 4.5283 -5.6590 C.ar + 14 C14 1.5712 3.5835 -6.5217 C.ar + 15 C15 1.1881 2.2598 -6.4119 C.ar + 16 C16 0.2818 1.8810 -5.4393 C.ar + 17 N17 -1.2356 -1.6185 -0.8442 N.am + 18 C18 -2.0957 -2.2682 0.1480 C.3 + 19 C19 0.2196 -1.6367 -0.6763 C.3 + 20 O20 -0.8455 -0.6176 -3.0661 O.2 + 21 H21 -3.3879 0.8293 -1.6706 H + 22 H22 -0.6773 0.1424 0.2600 H + 23 H23 0.0932 1.7796 0.3651 H + 24 H24 -1.4942 3.6716 -0.3777 H + 25 H25 -3.1220 3.0569 -0.8854 H + 26 H26 0.0942 2.8928 -1.8864 H + 27 H27 0.1982 1.2064 -2.4464 H + 28 H28 -1.8030 1.5552 -3.8685 H + 29 H29 -1.9069 3.2416 -3.3086 H + 30 H30 -0.2745 4.8893 -4.0186 H + 31 H31 1.3470 5.5625 -5.7450 H + 32 H32 2.2791 3.8795 -7.2818 H + 33 H33 1.5967 1.5217 -7.0861 H + 34 H34 -0.0178 0.8469 -5.3537 H + 35 H35 -2.2587 -3.3074 -0.1374 H + 36 H36 -1.6150 -2.2309 1.1255 H + 37 H37 -3.0533 -1.7495 0.1940 H + 38 H38 0.6825 -1.0264 -1.4518 H + 39 H39 0.4773 -1.2356 0.3039 H + 40 H40 0.5817 -2.6617 -0.7561 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 17 am + 4 2 20 2 + 5 3 4 1 + 6 3 21 1 + 7 4 8 1 + 8 4 5 1 + 9 4 9 1 + 10 5 6 1 + 11 5 22 1 + 12 5 23 1 + 13 6 7 1 + 14 6 8 1 + 15 8 24 1 + 16 8 25 1 + 17 9 10 1 + 18 9 26 1 + 19 9 27 1 + 20 10 11 1 + 21 10 28 1 + 22 10 29 1 + 23 11 16 ar + 24 11 12 ar + 25 12 13 ar + 26 12 30 1 + 27 13 14 ar + 28 13 31 1 + 29 14 15 ar + 30 14 32 1 + 31 15 16 ar + 32 15 33 1 + 33 16 34 1 + 34 17 18 1 + 35 17 19 1 + 36 18 35 1 + 37 18 36 1 + 38 18 37 1 + 39 19 38 1 + 40 19 39 1 + 41 19 40 1 + +# End of record + diff --git a/top/cgenff/SM37/SM37.pdb b/top/cgenff/SM37/SM37.pdb deleted file mode 120000 index 2f5c362..0000000 --- a/top/cgenff/SM37/SM37.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM37/SM37.pdb \ No newline at end of file diff --git a/top/cgenff/SM37/SM37.pdb b/top/cgenff/SM37/SM37.pdb new file mode 100644 index 0000000..3265a77 --- /dev/null +++ b/top/cgenff/SM37/SM37.pdb @@ -0,0 +1,84 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM37 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -3.068 -1.610 -2.498 1.00 20.00 +HETATM 2 S2 UNK 1 -1.908 -0.863 -2.156 1.00 20.00 +HETATM 3 N3 UNK 1 -2.441 0.620 -1.647 1.00 20.00 +HETATM 4 C4 UNK 1 -1.482 1.616 -1.162 1.00 20.00 +HETATM 5 C5 UNK 1 -0.818 1.218 0.158 1.00 20.00 +HETATM 6 S6 UNK 1 -2.260 1.839 1.068 1.00 20.00 +HETATM 7 O7 UNK 1 -3.335 0.810 0.747 1.00 20.00 +HETATM 8 C8 UNK 1 -2.149 2.804 -0.465 1.00 20.00 +HETATM 9 C9 UNK 1 -0.479 2.035 -2.238 1.00 20.00 +HETATM 10 C10 UNK 1 -1.230 2.413 -3.517 1.00 20.00 +HETATM 11 C11 UNK 1 -0.241 2.826 -4.577 1.00 20.00 +HETATM 12 C12 UNK 1 0.138 4.150 -4.690 1.00 20.00 +HETATM 13 C13 UNK 1 1.048 4.528 -5.659 1.00 20.00 +HETATM 14 C14 UNK 1 1.571 3.583 -6.522 1.00 20.00 +HETATM 15 C15 UNK 1 1.188 2.260 -6.412 1.00 20.00 +HETATM 16 C16 UNK 1 0.282 1.881 -5.439 1.00 20.00 +HETATM 17 N17 UNK 1 -1.236 -1.618 -0.844 1.00 20.00 +HETATM 18 C18 UNK 1 -2.096 -2.268 0.148 1.00 20.00 +HETATM 19 C19 UNK 1 0.220 -1.637 -0.676 1.00 20.00 +HETATM 20 O20 UNK 1 -0.846 -0.618 -3.066 1.00 20.00 +HETATM 21 H21 UNK 1 -3.388 0.829 -1.671 1.00 20.00 +HETATM 22 H22 UNK 1 -0.677 0.142 0.260 1.00 20.00 +HETATM 23 H23 UNK 1 0.093 1.780 0.365 1.00 20.00 +HETATM 24 H24 UNK 1 -1.494 3.672 -0.378 1.00 20.00 +HETATM 25 H25 UNK 1 -3.122 3.057 -0.885 1.00 20.00 +HETATM 26 H26 UNK 1 0.094 2.893 -1.886 1.00 20.00 +HETATM 27 H27 UNK 1 0.198 1.206 -2.446 1.00 20.00 +HETATM 28 H28 UNK 1 -1.803 1.555 -3.868 1.00 20.00 +HETATM 29 H29 UNK 1 -1.907 3.242 -3.309 1.00 20.00 +HETATM 30 H30 UNK 1 -0.275 4.889 -4.019 1.00 20.00 +HETATM 31 H31 UNK 1 1.347 5.563 -5.745 1.00 20.00 +HETATM 32 H32 UNK 1 2.279 3.879 -7.282 1.00 20.00 +HETATM 33 H33 UNK 1 1.597 1.522 -7.086 1.00 20.00 +HETATM 34 H34 UNK 1 -0.018 0.847 -5.354 1.00 20.00 +HETATM 35 H35 UNK 1 -2.259 -3.307 -0.137 1.00 20.00 +HETATM 36 H36 UNK 1 -1.615 -2.231 1.126 1.00 20.00 +HETATM 37 H37 UNK 1 -3.053 -1.750 0.194 1.00 20.00 +HETATM 38 H38 UNK 1 0.683 -1.026 -1.452 1.00 20.00 +HETATM 39 H39 UNK 1 0.477 -1.236 0.304 1.00 20.00 +HETATM 40 H40 UNK 1 0.582 -2.662 -0.756 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 17 20 +CONECT 3 2 4 21 +CONECT 4 3 8 5 9 +CONECT 5 4 6 22 23 +CONECT 6 5 7 8 +CONECT 7 6 +CONECT 8 6 4 24 25 +CONECT 9 4 10 26 27 +CONECT 10 9 11 28 29 +CONECT 11 10 16 12 +CONECT 12 11 13 30 +CONECT 13 12 14 31 +CONECT 14 13 15 32 +CONECT 15 14 16 33 +CONECT 16 15 11 34 +CONECT 17 2 18 19 +CONECT 18 17 35 36 37 +CONECT 19 17 38 39 40 +CONECT 20 2 +CONECT 21 3 +CONECT 22 5 +CONECT 23 5 +CONECT 24 8 +CONECT 25 8 +CONECT 26 9 +CONECT 27 9 +CONECT 28 10 +CONECT 29 10 +CONECT 30 12 +CONECT 31 13 +CONECT 32 14 +CONECT 33 15 +CONECT 34 16 +CONECT 35 18 +CONECT 36 18 +CONECT 37 18 +CONECT 38 19 +CONECT 39 19 +CONECT 40 19 +END diff --git a/top/cgenff/SM38/SM38.mol2 b/top/cgenff/SM38/SM38.mol2 deleted file mode 120000 index a710ac8..0000000 --- a/top/cgenff/SM38/SM38.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM38/SM38.mol2 \ No newline at end of file diff --git a/top/cgenff/SM38/SM38.mol2 b/top/cgenff/SM38/SM38.mol2 new file mode 100644 index 0000000..d939314 --- /dev/null +++ b/top/cgenff/SM38/SM38.mol2 @@ -0,0 +1,94 @@ +# Name: SM38 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 36 37 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 C1 1.1665 0.0871 -2.7901 C.3 + 2 S2 -0.3339 -0.4110 -1.9004 S.o2 + 3 N3 -0.0566 0.0475 -0.3335 N.am + 4 C4 0.1352 1.4628 -0.0074 C.3 + 5 C5 -0.3702 1.8324 1.3891 C.3 + 6 S6 -0.7943 3.4928 0.7914 S.o2 + 7 C7 -0.9261 2.3729 -0.6298 C.3 + 8 O8 0.3347 4.3521 0.7111 O.2 + 9 O9 -2.0598 3.9408 1.2574 O.2 + 10 C10 1.5653 1.9364 -0.2744 C.3 + 11 C11 2.5493 1.0343 0.4732 C.3 + 12 C12 3.9602 1.4272 0.1183 C.ar + 13 C13 4.5948 0.8301 -0.9549 C.ar + 14 C14 5.8873 1.1939 -1.2834 C.ar + 15 C15 6.5490 2.1473 -0.5323 C.ar + 16 C16 5.9163 2.7406 0.5441 C.ar + 17 C17 4.6219 2.3805 0.8694 C.ar + 18 O18 -0.4303 -1.8274 -1.8393 O.2 + 19 O19 -1.4410 0.3818 -2.3069 O.2 + 20 H20 2.0289 -0.4246 -2.3629 H + 21 H21 1.0703 -0.1796 -3.8425 H + 22 H22 1.3018 1.1649 -2.6993 H + 23 H23 -0.0212 -0.6211 0.3684 H + 24 H24 -1.2404 1.2527 1.6971 H + 25 H25 0.4172 1.8359 2.1427 H + 26 H26 -0.6040 2.8288 -1.5660 H + 27 H27 -1.9036 1.8976 -0.7116 H + 28 H28 1.7699 1.8894 -1.3440 H + 29 H29 1.6786 2.9636 0.0724 H + 30 H30 2.4004 1.1456 1.5472 H + 31 H31 2.3787 -0.0039 0.1884 H + 32 H32 4.0794 0.0820 -1.5390 H + 33 H33 6.3818 0.7302 -2.1241 H + 34 H34 7.5604 2.4284 -0.7862 H + 35 H35 6.4334 3.4852 1.1312 H + 36 H36 4.1277 2.8438 1.7106 H +@BOND + 1 1 2 1 + 2 1 20 1 + 3 1 21 1 + 4 1 22 1 + 5 2 3 am + 6 2 18 2 + 7 2 19 2 + 8 3 4 1 + 9 3 23 1 + 10 4 7 1 + 11 4 5 1 + 12 4 10 1 + 13 5 6 1 + 14 5 24 1 + 15 5 25 1 + 16 6 7 1 + 17 6 8 2 + 18 6 9 2 + 19 7 26 1 + 20 7 27 1 + 21 10 11 1 + 22 10 28 1 + 23 10 29 1 + 24 11 12 1 + 25 11 30 1 + 26 11 31 1 + 27 12 17 ar + 28 12 13 ar + 29 13 14 ar + 30 13 32 1 + 31 14 15 ar + 32 14 33 1 + 33 15 16 ar + 34 15 34 1 + 35 16 17 ar + 36 16 35 1 + 37 17 36 1 + +# End of record + diff --git a/top/cgenff/SM38/SM38.pdb b/top/cgenff/SM38/SM38.pdb deleted file mode 120000 index ae03c48..0000000 --- a/top/cgenff/SM38/SM38.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM38/SM38.pdb \ No newline at end of file diff --git a/top/cgenff/SM38/SM38.pdb b/top/cgenff/SM38/SM38.pdb new file mode 100644 index 0000000..bc57bbf --- /dev/null +++ b/top/cgenff/SM38/SM38.pdb @@ -0,0 +1,76 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM38 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 1.166 0.087 -2.790 1.00 20.00 +HETATM 2 S2 UNK 1 -0.334 -0.411 -1.900 1.00 20.00 +HETATM 3 N3 UNK 1 -0.057 0.047 -0.334 1.00 20.00 +HETATM 4 C4 UNK 1 0.135 1.463 -0.007 1.00 20.00 +HETATM 5 C5 UNK 1 -0.370 1.832 1.389 1.00 20.00 +HETATM 6 S6 UNK 1 -0.794 3.493 0.791 1.00 20.00 +HETATM 7 C7 UNK 1 -0.926 2.373 -0.630 1.00 20.00 +HETATM 8 O8 UNK 1 0.335 4.352 0.711 1.00 20.00 +HETATM 9 O9 UNK 1 -2.060 3.941 1.257 1.00 20.00 +HETATM 10 C10 UNK 1 1.565 1.936 -0.274 1.00 20.00 +HETATM 11 C11 UNK 1 2.549 1.034 0.473 1.00 20.00 +HETATM 12 C12 UNK 1 3.960 1.427 0.118 1.00 20.00 +HETATM 13 C13 UNK 1 4.595 0.830 -0.955 1.00 20.00 +HETATM 14 C14 UNK 1 5.887 1.194 -1.283 1.00 20.00 +HETATM 15 C15 UNK 1 6.549 2.147 -0.532 1.00 20.00 +HETATM 16 C16 UNK 1 5.916 2.741 0.544 1.00 20.00 +HETATM 17 C17 UNK 1 4.622 2.381 0.869 1.00 20.00 +HETATM 18 O18 UNK 1 -0.430 -1.827 -1.839 1.00 20.00 +HETATM 19 O19 UNK 1 -1.441 0.382 -2.307 1.00 20.00 +HETATM 20 H20 UNK 1 2.029 -0.425 -2.363 1.00 20.00 +HETATM 21 H21 UNK 1 1.070 -0.180 -3.843 1.00 20.00 +HETATM 22 H22 UNK 1 1.302 1.165 -2.699 1.00 20.00 +HETATM 23 H23 UNK 1 -0.021 -0.621 0.368 1.00 20.00 +HETATM 24 H24 UNK 1 -1.240 1.253 1.697 1.00 20.00 +HETATM 25 H25 UNK 1 0.417 1.836 2.143 1.00 20.00 +HETATM 26 H26 UNK 1 -0.604 2.829 -1.566 1.00 20.00 +HETATM 27 H27 UNK 1 -1.904 1.898 -0.712 1.00 20.00 +HETATM 28 H28 UNK 1 1.770 1.889 -1.344 1.00 20.00 +HETATM 29 H29 UNK 1 1.679 2.964 0.072 1.00 20.00 +HETATM 30 H30 UNK 1 2.400 1.146 1.547 1.00 20.00 +HETATM 31 H31 UNK 1 2.379 -0.004 0.188 1.00 20.00 +HETATM 32 H32 UNK 1 4.079 0.082 -1.539 1.00 20.00 +HETATM 33 H33 UNK 1 6.382 0.730 -2.124 1.00 20.00 +HETATM 34 H34 UNK 1 7.560 2.428 -0.786 1.00 20.00 +HETATM 35 H35 UNK 1 6.433 3.485 1.131 1.00 20.00 +HETATM 36 H36 UNK 1 4.128 2.844 1.711 1.00 20.00 +CONECT 1 2 20 21 22 +CONECT 2 1 3 18 19 +CONECT 3 2 4 23 +CONECT 4 3 7 5 10 +CONECT 5 4 6 24 25 +CONECT 6 5 7 8 9 +CONECT 7 6 4 26 27 +CONECT 8 6 +CONECT 9 6 +CONECT 10 4 11 28 29 +CONECT 11 10 12 30 31 +CONECT 12 11 17 13 +CONECT 13 12 14 32 +CONECT 14 13 15 33 +CONECT 15 14 16 34 +CONECT 16 15 17 35 +CONECT 17 16 12 36 +CONECT 18 2 +CONECT 19 2 +CONECT 20 1 +CONECT 21 1 +CONECT 22 1 +CONECT 23 3 +CONECT 24 5 +CONECT 25 5 +CONECT 26 7 +CONECT 27 7 +CONECT 28 10 +CONECT 29 10 +CONECT 30 11 +CONECT 31 11 +CONECT 32 13 +CONECT 33 14 +CONECT 34 15 +CONECT 35 16 +CONECT 36 17 +END diff --git a/top/cgenff/SM39/SM39.mol2 b/top/cgenff/SM39/SM39.mol2 deleted file mode 120000 index 74b8b55..0000000 --- a/top/cgenff/SM39/SM39.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM39/SM39.mol2 \ No newline at end of file diff --git a/top/cgenff/SM39/SM39.mol2 b/top/cgenff/SM39/SM39.mol2 new file mode 100644 index 0000000..487ec68 --- /dev/null +++ b/top/cgenff/SM39/SM39.mol2 @@ -0,0 +1,109 @@ +# Name: SM39 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 43 45 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 0.5370 7.7981 -3.4612 O.2 + 2 S2 0.4485 7.8090 -2.0430 S.o2 + 3 N3 -0.0324 6.2897 -1.5928 N.am + 4 C4 -1.1748 5.6563 -2.2561 C.3 + 5 C5 -1.0831 4.1289 -2.2847 C.3 + 6 S6 -1.9677 4.1098 -3.8694 S.o2 + 7 C7 -1.0777 5.6884 -3.7831 C.3 + 8 O8 -3.3722 4.2616 -3.7158 O.2 + 9 O9 -1.3981 3.2084 -4.8087 O.2 + 10 C10 -2.5162 6.1686 -1.7278 C.3 + 11 C11 -2.6392 5.8349 -0.2397 C.3 + 12 C12 -4.0108 6.2220 0.2502 C.ar + 13 C13 -4.2314 7.4885 0.7583 C.ar + 14 C14 -5.4907 7.8451 1.2032 C.ar + 15 C15 -6.5269 6.9317 1.1497 C.ar + 16 C16 -6.3052 5.6635 0.6464 C.ar + 17 C17 -5.0471 5.3086 0.1966 C.ar + 18 C18 -0.8624 8.9133 -1.6348 C.ar + 19 C19 -0.9680 9.4164 -0.3516 C.ar + 20 C20 -1.9967 10.2825 -0.0312 C.ar + 21 C21 -2.9198 10.6454 -0.9941 C.ar + 22 C22 -2.8173 10.1381 -2.2759 C.ar + 23 C23 -1.7855 9.2763 -2.5977 C.ar + 24 O24 1.5391 8.1513 -1.1988 O.2 + 25 H25 0.4424 5.8190 -0.8900 H + 26 H26 -0.0594 3.7625 -2.3611 H + 27 H27 -1.6385 3.6511 -1.4777 H + 28 H28 -1.6286 6.5159 -4.2302 H + 29 H29 -0.0529 5.6231 -4.1488 H + 30 H30 -2.5718 7.2486 -1.8638 H + 31 H31 -3.3287 5.6912 -2.2755 H + 32 H32 -2.4897 4.7652 -0.0936 H + 33 H33 -1.8843 6.3871 0.3201 H + 34 H34 -3.4207 8.2006 0.8043 H + 35 H35 -5.6639 8.8358 1.5968 H + 36 H36 -7.5097 7.2089 1.5013 H + 37 H37 -7.1147 4.9498 0.6048 H + 38 H38 -4.8737 4.3177 -0.1963 H + 39 H39 -0.2470 9.1326 0.4007 H + 40 H40 -2.0795 10.6752 0.9714 H + 41 H41 -3.7237 11.3217 -0.7437 H + 42 H42 -3.5411 10.4182 -3.0270 H + 43 H43 -1.7032 8.8829 -3.6001 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 18 1 + 4 2 24 2 + 5 3 4 1 + 6 3 25 1 + 7 4 7 1 + 8 4 5 1 + 9 4 10 1 + 10 5 6 1 + 11 5 26 1 + 12 5 27 1 + 13 6 7 1 + 14 6 8 2 + 15 6 9 2 + 16 7 28 1 + 17 7 29 1 + 18 10 11 1 + 19 10 30 1 + 20 10 31 1 + 21 11 12 1 + 22 11 32 1 + 23 11 33 1 + 24 12 17 ar + 25 12 13 ar + 26 13 14 ar + 27 13 34 1 + 28 14 15 ar + 29 14 35 1 + 30 15 16 ar + 31 15 36 1 + 32 16 17 ar + 33 16 37 1 + 34 17 38 1 + 35 18 23 ar + 36 18 19 ar + 37 19 20 ar + 38 19 39 1 + 39 20 21 ar + 40 20 40 1 + 41 21 22 ar + 42 21 41 1 + 43 22 23 ar + 44 22 42 1 + 45 23 43 1 + +# End of record + diff --git a/top/cgenff/SM39/SM39.pdb b/top/cgenff/SM39/SM39.pdb deleted file mode 120000 index fef13ed..0000000 --- a/top/cgenff/SM39/SM39.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM39/SM39.pdb \ No newline at end of file diff --git a/top/cgenff/SM39/SM39.pdb b/top/cgenff/SM39/SM39.pdb new file mode 100644 index 0000000..5e5d97d --- /dev/null +++ b/top/cgenff/SM39/SM39.pdb @@ -0,0 +1,90 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM39 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 0.537 7.798 -3.461 1.00 20.00 +HETATM 2 S2 UNK 1 0.448 7.809 -2.043 1.00 20.00 +HETATM 3 N3 UNK 1 -0.032 6.290 -1.593 1.00 20.00 +HETATM 4 C4 UNK 1 -1.175 5.656 -2.256 1.00 20.00 +HETATM 5 C5 UNK 1 -1.083 4.129 -2.285 1.00 20.00 +HETATM 6 S6 UNK 1 -1.968 4.110 -3.869 1.00 20.00 +HETATM 7 C7 UNK 1 -1.078 5.688 -3.783 1.00 20.00 +HETATM 8 O8 UNK 1 -3.372 4.262 -3.716 1.00 20.00 +HETATM 9 O9 UNK 1 -1.398 3.208 -4.809 1.00 20.00 +HETATM 10 C10 UNK 1 -2.516 6.169 -1.728 1.00 20.00 +HETATM 11 C11 UNK 1 -2.639 5.835 -0.240 1.00 20.00 +HETATM 12 C12 UNK 1 -4.011 6.222 0.250 1.00 20.00 +HETATM 13 C13 UNK 1 -4.231 7.488 0.758 1.00 20.00 +HETATM 14 C14 UNK 1 -5.491 7.845 1.203 1.00 20.00 +HETATM 15 C15 UNK 1 -6.527 6.932 1.150 1.00 20.00 +HETATM 16 C16 UNK 1 -6.305 5.663 0.646 1.00 20.00 +HETATM 17 C17 UNK 1 -5.047 5.309 0.197 1.00 20.00 +HETATM 18 C18 UNK 1 -0.862 8.913 -1.635 1.00 20.00 +HETATM 19 C19 UNK 1 -0.968 9.416 -0.352 1.00 20.00 +HETATM 20 C20 UNK 1 -1.997 10.282 -0.031 1.00 20.00 +HETATM 21 C21 UNK 1 -2.920 10.645 -0.994 1.00 20.00 +HETATM 22 C22 UNK 1 -2.817 10.138 -2.276 1.00 20.00 +HETATM 23 C23 UNK 1 -1.786 9.276 -2.598 1.00 20.00 +HETATM 24 O24 UNK 1 1.539 8.151 -1.199 1.00 20.00 +HETATM 25 H25 UNK 1 0.442 5.819 -0.890 1.00 20.00 +HETATM 26 H26 UNK 1 -0.059 3.763 -2.361 1.00 20.00 +HETATM 27 H27 UNK 1 -1.638 3.651 -1.478 1.00 20.00 +HETATM 28 H28 UNK 1 -1.629 6.516 -4.230 1.00 20.00 +HETATM 29 H29 UNK 1 -0.053 5.623 -4.149 1.00 20.00 +HETATM 30 H30 UNK 1 -2.572 7.249 -1.864 1.00 20.00 +HETATM 31 H31 UNK 1 -3.329 5.691 -2.276 1.00 20.00 +HETATM 32 H32 UNK 1 -2.490 4.765 -0.094 1.00 20.00 +HETATM 33 H33 UNK 1 -1.884 6.387 0.320 1.00 20.00 +HETATM 34 H34 UNK 1 -3.421 8.201 0.804 1.00 20.00 +HETATM 35 H35 UNK 1 -5.664 8.836 1.597 1.00 20.00 +HETATM 36 H36 UNK 1 -7.510 7.209 1.501 1.00 20.00 +HETATM 37 H37 UNK 1 -7.115 4.950 0.605 1.00 20.00 +HETATM 38 H38 UNK 1 -4.874 4.318 -0.196 1.00 20.00 +HETATM 39 H39 UNK 1 -0.247 9.133 0.401 1.00 20.00 +HETATM 40 H40 UNK 1 -2.079 10.675 0.971 1.00 20.00 +HETATM 41 H41 UNK 1 -3.724 11.322 -0.744 1.00 20.00 +HETATM 42 H42 UNK 1 -3.541 10.418 -3.027 1.00 20.00 +HETATM 43 H43 UNK 1 -1.703 8.883 -3.600 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 18 24 +CONECT 3 2 4 25 +CONECT 4 3 7 5 10 +CONECT 5 4 6 26 27 +CONECT 6 5 7 8 9 +CONECT 7 6 4 28 29 +CONECT 8 6 +CONECT 9 6 +CONECT 10 4 11 30 31 +CONECT 11 10 12 32 33 +CONECT 12 11 17 13 +CONECT 13 12 14 34 +CONECT 14 13 15 35 +CONECT 15 14 16 36 +CONECT 16 15 17 37 +CONECT 17 16 12 38 +CONECT 18 2 23 19 +CONECT 19 18 20 39 +CONECT 20 19 21 40 +CONECT 21 20 22 41 +CONECT 22 21 23 42 +CONECT 23 22 18 43 +CONECT 24 2 +CONECT 25 3 +CONECT 26 5 +CONECT 27 5 +CONECT 28 7 +CONECT 29 7 +CONECT 30 10 +CONECT 31 10 +CONECT 32 11 +CONECT 33 11 +CONECT 34 13 +CONECT 35 14 +CONECT 36 15 +CONECT 37 16 +CONECT 38 17 +CONECT 39 19 +CONECT 40 20 +CONECT 41 21 +CONECT 42 22 +CONECT 43 23 +END diff --git a/top/cgenff/SM40/SM40.mol2 b/top/cgenff/SM40/SM40.mol2 deleted file mode 120000 index fe669eb..0000000 --- a/top/cgenff/SM40/SM40.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM40/SM40.mol2 \ No newline at end of file diff --git a/top/cgenff/SM40/SM40.mol2 b/top/cgenff/SM40/SM40.mol2 new file mode 100644 index 0000000..56ea1f3 --- /dev/null +++ b/top/cgenff/SM40/SM40.mol2 @@ -0,0 +1,104 @@ +# Name: SM40 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 41 42 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -0.9745 -1.8878 -1.8995 O.2 + 2 S2 -0.6777 -0.4981 -1.8950 S.o2 + 3 N3 -0.1691 -0.1336 -0.3618 N.am + 4 C4 0.3322 1.2086 -0.0561 C.3 + 5 C5 0.0297 1.6519 1.3772 C.3 + 6 S6 -0.0967 3.3726 0.8137 S.o2 + 7 C7 -0.5703 2.3239 -0.5889 C.3 + 8 O8 1.1725 3.9867 0.6369 O.2 + 9 O9 -1.2019 4.0602 1.3837 O.2 + 10 C10 1.8015 1.3871 -0.4435 C.3 + 11 C11 2.6429 0.3039 0.2345 C.3 + 12 C12 4.1030 0.5565 -0.0402 C.ar + 13 C13 4.7045 -0.0046 -1.1511 C.ar + 14 C14 6.0426 0.2311 -1.4057 C.ar + 15 C15 6.7817 1.0194 -0.5437 C.ar + 16 C16 6.1815 1.5763 0.5701 C.ar + 17 C17 4.8421 1.3448 0.8218 C.ar + 18 N18 0.6198 -0.2937 -2.9035 N.am + 19 C19 1.6299 -1.3483 -3.0203 C.3 + 20 C20 0.7574 0.9417 -3.6788 C.3 + 21 O21 -1.6243 0.4999 -2.2517 O.2 + 22 H22 -0.2031 -0.8087 0.3339 H + 23 H23 -0.9113 1.2557 1.7587 H + 24 H24 0.8612 1.4848 2.0619 H + 25 H25 -0.2411 2.7192 -1.5499 H + 26 H26 -1.6273 2.0574 -0.5870 H + 27 H27 1.9047 1.3033 -1.5254 H + 28 H28 2.1456 2.3696 -0.1207 H + 29 H29 2.4663 0.3265 1.3098 H + 30 H30 2.3629 -0.6732 -0.1592 H + 31 H31 4.1280 -0.6241 -1.8223 H + 32 H32 6.5116 -0.2043 -2.2757 H + 33 H33 7.8282 1.1999 -0.7401 H + 34 H34 6.7591 2.1919 1.2438 H + 35 H35 4.3732 1.7796 1.6922 H + 36 H36 1.3486 -2.0340 -3.8196 H + 37 H37 2.5973 -0.9010 -3.2490 H + 38 H38 1.6955 -1.8945 -2.0793 H + 39 H39 1.3822 1.6469 -3.1306 H + 40 H40 1.2198 0.7177 -4.6401 H + 41 H41 -0.2272 1.3796 -3.8424 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 18 am + 4 2 21 2 + 5 3 4 1 + 6 3 22 1 + 7 4 7 1 + 8 4 5 1 + 9 4 10 1 + 10 5 6 1 + 11 5 23 1 + 12 5 24 1 + 13 6 7 1 + 14 6 8 2 + 15 6 9 2 + 16 7 25 1 + 17 7 26 1 + 18 10 11 1 + 19 10 27 1 + 20 10 28 1 + 21 11 12 1 + 22 11 29 1 + 23 11 30 1 + 24 12 17 ar + 25 12 13 ar + 26 13 14 ar + 27 13 31 1 + 28 14 15 ar + 29 14 32 1 + 30 15 16 ar + 31 15 33 1 + 32 16 17 ar + 33 16 34 1 + 34 17 35 1 + 35 18 19 1 + 36 18 20 1 + 37 19 36 1 + 38 19 37 1 + 39 19 38 1 + 40 20 39 1 + 41 20 40 1 + 42 20 41 1 + +# End of record + diff --git a/top/cgenff/SM40/SM40.pdb b/top/cgenff/SM40/SM40.pdb deleted file mode 120000 index 897712f..0000000 --- a/top/cgenff/SM40/SM40.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM40/SM40.pdb \ No newline at end of file diff --git a/top/cgenff/SM40/SM40.pdb b/top/cgenff/SM40/SM40.pdb new file mode 100644 index 0000000..99daa83 --- /dev/null +++ b/top/cgenff/SM40/SM40.pdb @@ -0,0 +1,86 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM40 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -0.974 -1.888 -1.900 1.00 20.00 +HETATM 2 S2 UNK 1 -0.678 -0.498 -1.895 1.00 20.00 +HETATM 3 N3 UNK 1 -0.169 -0.134 -0.362 1.00 20.00 +HETATM 4 C4 UNK 1 0.332 1.209 -0.056 1.00 20.00 +HETATM 5 C5 UNK 1 0.030 1.652 1.377 1.00 20.00 +HETATM 6 S6 UNK 1 -0.097 3.373 0.814 1.00 20.00 +HETATM 7 C7 UNK 1 -0.570 2.324 -0.589 1.00 20.00 +HETATM 8 O8 UNK 1 1.172 3.987 0.637 1.00 20.00 +HETATM 9 O9 UNK 1 -1.202 4.060 1.384 1.00 20.00 +HETATM 10 C10 UNK 1 1.802 1.387 -0.444 1.00 20.00 +HETATM 11 C11 UNK 1 2.643 0.304 0.234 1.00 20.00 +HETATM 12 C12 UNK 1 4.103 0.557 -0.040 1.00 20.00 +HETATM 13 C13 UNK 1 4.704 -0.005 -1.151 1.00 20.00 +HETATM 14 C14 UNK 1 6.043 0.231 -1.406 1.00 20.00 +HETATM 15 C15 UNK 1 6.782 1.019 -0.544 1.00 20.00 +HETATM 16 C16 UNK 1 6.181 1.576 0.570 1.00 20.00 +HETATM 17 C17 UNK 1 4.842 1.345 0.822 1.00 20.00 +HETATM 18 N18 UNK 1 0.620 -0.294 -2.903 1.00 20.00 +HETATM 19 C19 UNK 1 1.630 -1.348 -3.020 1.00 20.00 +HETATM 20 C20 UNK 1 0.757 0.942 -3.679 1.00 20.00 +HETATM 21 O21 UNK 1 -1.624 0.500 -2.252 1.00 20.00 +HETATM 22 H22 UNK 1 -0.203 -0.809 0.334 1.00 20.00 +HETATM 23 H23 UNK 1 -0.911 1.256 1.759 1.00 20.00 +HETATM 24 H24 UNK 1 0.861 1.485 2.062 1.00 20.00 +HETATM 25 H25 UNK 1 -0.241 2.719 -1.550 1.00 20.00 +HETATM 26 H26 UNK 1 -1.627 2.057 -0.587 1.00 20.00 +HETATM 27 H27 UNK 1 1.905 1.303 -1.525 1.00 20.00 +HETATM 28 H28 UNK 1 2.146 2.370 -0.121 1.00 20.00 +HETATM 29 H29 UNK 1 2.466 0.327 1.310 1.00 20.00 +HETATM 30 H30 UNK 1 2.363 -0.673 -0.159 1.00 20.00 +HETATM 31 H31 UNK 1 4.128 -0.624 -1.822 1.00 20.00 +HETATM 32 H32 UNK 1 6.512 -0.204 -2.276 1.00 20.00 +HETATM 33 H33 UNK 1 7.828 1.200 -0.740 1.00 20.00 +HETATM 34 H34 UNK 1 6.759 2.192 1.244 1.00 20.00 +HETATM 35 H35 UNK 1 4.373 1.780 1.692 1.00 20.00 +HETATM 36 H36 UNK 1 1.349 -2.034 -3.820 1.00 20.00 +HETATM 37 H37 UNK 1 2.597 -0.901 -3.249 1.00 20.00 +HETATM 38 H38 UNK 1 1.696 -1.894 -2.079 1.00 20.00 +HETATM 39 H39 UNK 1 1.382 1.647 -3.131 1.00 20.00 +HETATM 40 H40 UNK 1 1.220 0.718 -4.640 1.00 20.00 +HETATM 41 H41 UNK 1 -0.227 1.380 -3.842 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 18 21 +CONECT 3 2 4 22 +CONECT 4 3 7 5 10 +CONECT 5 4 6 23 24 +CONECT 6 5 7 8 9 +CONECT 7 6 4 25 26 +CONECT 8 6 +CONECT 9 6 +CONECT 10 4 11 27 28 +CONECT 11 10 12 29 30 +CONECT 12 11 17 13 +CONECT 13 12 14 31 +CONECT 14 13 15 32 +CONECT 15 14 16 33 +CONECT 16 15 17 34 +CONECT 17 16 12 35 +CONECT 18 2 19 20 +CONECT 19 18 36 37 38 +CONECT 20 18 39 40 41 +CONECT 21 2 +CONECT 22 3 +CONECT 23 5 +CONECT 24 5 +CONECT 25 7 +CONECT 26 7 +CONECT 27 10 +CONECT 28 10 +CONECT 29 11 +CONECT 30 11 +CONECT 31 13 +CONECT 32 14 +CONECT 33 15 +CONECT 34 16 +CONECT 35 17 +CONECT 36 19 +CONECT 37 19 +CONECT 38 19 +CONECT 39 20 +CONECT 40 20 +CONECT 41 20 +END diff --git a/top/cgenff/SM41/SM41.mol2 b/top/cgenff/SM41/SM41.mol2 deleted file mode 120000 index 3715ab2..0000000 --- a/top/cgenff/SM41/SM41.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM41/SM41.mol2 \ No newline at end of file diff --git a/top/cgenff/SM41/SM41.mol2 b/top/cgenff/SM41/SM41.mol2 new file mode 100644 index 0000000..9f4054f --- /dev/null +++ b/top/cgenff/SM41/SM41.mol2 @@ -0,0 +1,74 @@ +# Name: SM41 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 26 27 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -2.4342 0.7435 0.0434 O.2 + 2 S2 -1.4563 1.7742 0.0186 S.o2 + 3 N3 -0.0111 0.9658 0.0074 N.am + 4 C4 1.1844 1.6779 -0.0002 C.2 + 5 N5 1.3219 2.9792 0.0059 N.2 + 6 O6 2.4853 3.3075 -0.0032 O.3 + 7 C7 3.3026 2.2389 -0.0169 C.2 + 8 C8 4.7812 2.2538 -0.0308 C.ar + 9 C9 5.4940 1.0541 -0.0379 C.ar + 10 C10 6.8734 1.0750 -0.0552 C.ar + 11 C11 7.5501 2.2818 -0.0557 C.ar + 12 C12 6.8493 3.4746 -0.0433 C.ar + 13 C13 5.4698 3.4676 -0.0309 C.ar + 14 C14 2.4948 1.1375 -0.0099 C.2 + 15 C15 -1.4964 2.6518 -1.5685 C.3 + 16 O16 -1.3346 2.6947 1.0943 O.2 + 17 H17 0.0021 -0.0041 0.0020 H + 18 H18 4.9670 0.1115 -0.0337 H + 19 H19 7.4263 0.1473 -0.0645 H + 20 H20 8.6300 2.2926 -0.0654 H + 21 H21 7.3834 4.4133 -0.0438 H + 22 H22 4.9239 4.3995 -0.0216 H + 23 H23 2.7864 0.0976 -0.0129 H + 24 H24 -1.4399 1.9306 -2.3839 H + 25 H25 -2.4248 3.2175 -1.6475 H + 26 H26 -0.6488 3.3344 -1.6278 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 1 + 4 2 16 2 + 5 3 4 1 + 6 3 17 1 + 7 4 14 1 + 8 4 5 2 + 9 5 6 1 + 10 6 7 1 + 11 7 8 1 + 12 7 14 2 + 13 8 13 ar + 14 8 9 ar + 15 9 10 ar + 16 9 18 1 + 17 10 11 ar + 18 10 19 1 + 19 11 12 ar + 20 11 20 1 + 21 12 13 ar + 22 12 21 1 + 23 13 22 1 + 24 14 23 1 + 25 15 24 1 + 26 15 25 1 + 27 15 26 1 + +# End of record + diff --git a/top/cgenff/SM41/SM41.pdb b/top/cgenff/SM41/SM41.pdb deleted file mode 120000 index 4842c9c..0000000 --- a/top/cgenff/SM41/SM41.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM41/SM41.pdb \ No newline at end of file diff --git a/top/cgenff/SM41/SM41.pdb b/top/cgenff/SM41/SM41.pdb new file mode 100644 index 0000000..fcdf663 --- /dev/null +++ b/top/cgenff/SM41/SM41.pdb @@ -0,0 +1,56 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM41 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.434 0.744 0.043 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 4 C4 UNK 1 1.184 1.678 -0.000 1.00 20.00 +HETATM 5 N5 UNK 1 1.322 2.979 0.006 1.00 20.00 +HETATM 6 O6 UNK 1 2.485 3.307 -0.003 1.00 20.00 +HETATM 7 C7 UNK 1 3.303 2.239 -0.017 1.00 20.00 +HETATM 8 C8 UNK 1 4.781 2.254 -0.031 1.00 20.00 +HETATM 9 C9 UNK 1 5.494 1.054 -0.038 1.00 20.00 +HETATM 10 C10 UNK 1 6.873 1.075 -0.055 1.00 20.00 +HETATM 11 C11 UNK 1 7.550 2.282 -0.056 1.00 20.00 +HETATM 12 C12 UNK 1 6.849 3.475 -0.043 1.00 20.00 +HETATM 13 C13 UNK 1 5.470 3.468 -0.031 1.00 20.00 +HETATM 14 C14 UNK 1 2.495 1.137 -0.010 1.00 20.00 +HETATM 15 C15 UNK 1 -1.496 2.652 -1.569 1.00 20.00 +HETATM 16 O16 UNK 1 -1.335 2.695 1.094 1.00 20.00 +HETATM 17 H17 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 18 H18 UNK 1 4.967 0.111 -0.034 1.00 20.00 +HETATM 19 H19 UNK 1 7.426 0.147 -0.065 1.00 20.00 +HETATM 20 H20 UNK 1 8.630 2.293 -0.065 1.00 20.00 +HETATM 21 H21 UNK 1 7.383 4.413 -0.044 1.00 20.00 +HETATM 22 H22 UNK 1 4.924 4.399 -0.022 1.00 20.00 +HETATM 23 H23 UNK 1 2.786 0.098 -0.013 1.00 20.00 +HETATM 24 H24 UNK 1 -1.440 1.931 -2.384 1.00 20.00 +HETATM 25 H25 UNK 1 -2.425 3.217 -1.648 1.00 20.00 +HETATM 26 H26 UNK 1 -0.649 3.334 -1.628 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 16 +CONECT 3 2 4 17 +CONECT 4 3 14 5 +CONECT 5 4 6 +CONECT 6 5 7 +CONECT 7 6 8 14 +CONECT 8 7 13 9 +CONECT 9 8 10 18 +CONECT 10 9 11 19 +CONECT 11 10 12 20 +CONECT 12 11 13 21 +CONECT 13 12 8 22 +CONECT 14 7 4 23 +CONECT 15 2 24 25 26 +CONECT 16 2 +CONECT 17 3 +CONECT 18 9 +CONECT 19 10 +CONECT 20 11 +CONECT 21 12 +CONECT 22 13 +CONECT 23 14 +CONECT 24 15 +CONECT 25 15 +CONECT 26 15 +END diff --git a/top/cgenff/SM42/SM42.mol2 b/top/cgenff/SM42/SM42.mol2 deleted file mode 120000 index b323809..0000000 --- a/top/cgenff/SM42/SM42.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM42/SM42.mol2 \ No newline at end of file diff --git a/top/cgenff/SM42/SM42.mol2 b/top/cgenff/SM42/SM42.mol2 new file mode 100644 index 0000000..57f0bc8 --- /dev/null +++ b/top/cgenff/SM42/SM42.mol2 @@ -0,0 +1,89 @@ +# Name: SM42 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 33 35 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 1.1325 -2.1978 0.0147 O.2 + 2 S2 1.4473 -0.8125 -0.0155 S.o2 + 3 N3 0.0021 -0.0041 0.0020 N.am + 4 C4 -0.0168 1.3873 0.0097 C.2 + 5 N5 1.0201 2.1855 0.0041 N.2 + 6 O6 0.6910 3.3487 0.0135 O.3 + 7 C7 -0.6473 3.4859 0.0270 C.2 + 8 C8 -1.4084 4.7536 0.0406 C.ar + 9 C9 -2.8037 4.7332 0.0476 C.ar + 10 C10 -3.5079 5.9195 0.0662 C.ar + 11 C11 -2.8337 7.1276 0.0668 C.ar + 12 C12 -1.4505 7.1548 0.0537 C.ar + 13 C13 -0.7344 5.9756 0.0408 C.ar + 14 C14 -1.1631 2.2211 0.0189 C.2 + 15 C15 2.2636 -0.4545 1.5044 C.ar + 16 C16 3.1132 0.6323 1.5934 C.ar + 17 C17 3.7499 0.9159 2.7872 C.ar + 18 C18 3.5451 0.1067 3.8890 C.ar + 19 C19 2.6995 -0.9831 3.7986 C.ar + 20 C20 2.0587 -1.2637 2.6063 C.ar + 21 O21 2.2287 -0.2152 -1.0411 O.2 + 22 H22 -0.8313 -0.5004 0.0069 H + 23 H23 -3.3312 3.7908 0.0430 H + 24 H24 -4.5877 5.9051 0.0765 H + 25 H25 -3.3895 8.0535 0.0772 H + 26 H26 -0.9301 8.1012 0.0538 H + 27 H27 0.3453 5.9981 0.0313 H + 28 H28 -2.2018 1.9253 0.0212 H + 29 H29 3.2767 1.2619 0.7313 H + 30 H30 4.4108 1.7671 2.8577 H + 31 H31 4.0459 0.3257 4.8205 H + 32 H32 2.5397 -1.6156 4.6593 H + 33 H33 1.3983 -2.1154 2.5355 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 1 + 4 2 21 2 + 5 3 4 1 + 6 3 22 1 + 7 4 14 1 + 8 4 5 2 + 9 5 6 1 + 10 6 7 1 + 11 7 8 1 + 12 7 14 2 + 13 8 13 ar + 14 8 9 ar + 15 9 10 ar + 16 9 23 1 + 17 10 11 ar + 18 10 24 1 + 19 11 12 ar + 20 11 25 1 + 21 12 13 ar + 22 12 26 1 + 23 13 27 1 + 24 14 28 1 + 25 15 20 ar + 26 15 16 ar + 27 16 17 ar + 28 16 29 1 + 29 17 18 ar + 30 17 30 1 + 31 18 19 ar + 32 18 31 1 + 33 19 20 ar + 34 19 32 1 + 35 20 33 1 + +# End of record + diff --git a/top/cgenff/SM42/SM42.pdb b/top/cgenff/SM42/SM42.pdb deleted file mode 120000 index 34b9acc..0000000 --- a/top/cgenff/SM42/SM42.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM42/SM42.pdb \ No newline at end of file diff --git a/top/cgenff/SM42/SM42.pdb b/top/cgenff/SM42/SM42.pdb new file mode 100644 index 0000000..a8b42d2 --- /dev/null +++ b/top/cgenff/SM42/SM42.pdb @@ -0,0 +1,70 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM42 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 1.132 -2.198 0.015 1.00 20.00 +HETATM 2 S2 UNK 1 1.447 -0.812 -0.016 1.00 20.00 +HETATM 3 N3 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 4 C4 UNK 1 -0.017 1.387 0.010 1.00 20.00 +HETATM 5 N5 UNK 1 1.020 2.186 0.004 1.00 20.00 +HETATM 6 O6 UNK 1 0.691 3.349 0.013 1.00 20.00 +HETATM 7 C7 UNK 1 -0.647 3.486 0.027 1.00 20.00 +HETATM 8 C8 UNK 1 -1.408 4.754 0.041 1.00 20.00 +HETATM 9 C9 UNK 1 -2.804 4.733 0.048 1.00 20.00 +HETATM 10 C10 UNK 1 -3.508 5.919 0.066 1.00 20.00 +HETATM 11 C11 UNK 1 -2.834 7.128 0.067 1.00 20.00 +HETATM 12 C12 UNK 1 -1.450 7.155 0.054 1.00 20.00 +HETATM 13 C13 UNK 1 -0.734 5.976 0.041 1.00 20.00 +HETATM 14 C14 UNK 1 -1.163 2.221 0.019 1.00 20.00 +HETATM 15 C15 UNK 1 2.264 -0.455 1.504 1.00 20.00 +HETATM 16 C16 UNK 1 3.113 0.632 1.593 1.00 20.00 +HETATM 17 C17 UNK 1 3.750 0.916 2.787 1.00 20.00 +HETATM 18 C18 UNK 1 3.545 0.107 3.889 1.00 20.00 +HETATM 19 C19 UNK 1 2.699 -0.983 3.799 1.00 20.00 +HETATM 20 C20 UNK 1 2.059 -1.264 2.606 1.00 20.00 +HETATM 21 O21 UNK 1 2.229 -0.215 -1.041 1.00 20.00 +HETATM 22 H22 UNK 1 -0.831 -0.500 0.007 1.00 20.00 +HETATM 23 H23 UNK 1 -3.331 3.791 0.043 1.00 20.00 +HETATM 24 H24 UNK 1 -4.588 5.905 0.076 1.00 20.00 +HETATM 25 H25 UNK 1 -3.390 8.054 0.077 1.00 20.00 +HETATM 26 H26 UNK 1 -0.930 8.101 0.054 1.00 20.00 +HETATM 27 H27 UNK 1 0.345 5.998 0.031 1.00 20.00 +HETATM 28 H28 UNK 1 -2.202 1.925 0.021 1.00 20.00 +HETATM 29 H29 UNK 1 3.277 1.262 0.731 1.00 20.00 +HETATM 30 H30 UNK 1 4.411 1.767 2.858 1.00 20.00 +HETATM 31 H31 UNK 1 4.046 0.326 4.820 1.00 20.00 +HETATM 32 H32 UNK 1 2.540 -1.616 4.659 1.00 20.00 +HETATM 33 H33 UNK 1 1.398 -2.115 2.536 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 21 +CONECT 3 2 4 22 +CONECT 4 3 14 5 +CONECT 5 4 6 +CONECT 6 5 7 +CONECT 7 6 8 14 +CONECT 8 7 13 9 +CONECT 9 8 10 23 +CONECT 10 9 11 24 +CONECT 11 10 12 25 +CONECT 12 11 13 26 +CONECT 13 12 8 27 +CONECT 14 7 4 28 +CONECT 15 2 20 16 +CONECT 16 15 17 29 +CONECT 17 16 18 30 +CONECT 18 17 19 31 +CONECT 19 18 20 32 +CONECT 20 19 15 33 +CONECT 21 2 +CONECT 22 3 +CONECT 23 9 +CONECT 24 10 +CONECT 25 11 +CONECT 26 12 +CONECT 27 13 +CONECT 28 14 +CONECT 29 16 +CONECT 30 17 +CONECT 31 18 +CONECT 32 19 +CONECT 33 20 +END diff --git a/top/cgenff/SM43/SM43.mol2 b/top/cgenff/SM43/SM43.mol2 deleted file mode 120000 index b1f6700..0000000 --- a/top/cgenff/SM43/SM43.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM43/SM43.mol2 \ No newline at end of file diff --git a/top/cgenff/SM43/SM43.mol2 b/top/cgenff/SM43/SM43.mol2 new file mode 100644 index 0000000..bfeece4 --- /dev/null +++ b/top/cgenff/SM43/SM43.mol2 @@ -0,0 +1,84 @@ +# Name: SM43 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 31 32 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -2.4719 0.7810 -0.0167 O.2 + 2 S2 -1.4563 1.7742 0.0186 S.o2 + 3 N3 -0.0111 0.9658 0.0074 N.am + 4 C4 1.1844 1.6779 -0.0002 C.2 + 5 N5 1.3219 2.9792 0.0059 N.2 + 6 O6 2.4853 3.3075 -0.0032 O.3 + 7 C7 3.3026 2.2389 -0.0169 C.2 + 8 C8 4.7812 2.2538 -0.0308 C.ar + 9 C9 5.4940 1.0541 -0.0379 C.ar + 10 C10 6.8734 1.0750 -0.0552 C.ar + 11 C11 7.5501 2.2818 -0.0557 C.ar + 12 C12 6.8493 3.4746 -0.0433 C.ar + 13 C13 5.4698 3.4676 -0.0309 C.ar + 14 C14 2.4948 1.1375 -0.0099 C.2 + 15 N15 -1.5645 2.6048 -1.4100 N.am + 16 C16 -2.1763 1.9715 -2.5809 C.3 + 17 C17 -1.0485 3.9727 -1.5029 C.3 + 18 O18 -1.3610 2.7523 1.0451 O.2 + 19 H19 0.0021 -0.0041 0.0020 H + 20 H20 4.9670 0.1115 -0.0337 H + 21 H21 7.4263 0.1473 -0.0645 H + 22 H22 8.6300 2.2926 -0.0654 H + 23 H23 7.3834 4.4133 -0.0438 H + 24 H24 4.9239 4.3995 -0.0216 H + 25 H25 2.7864 0.0976 -0.0129 H + 26 H26 -3.2462 2.1800 -2.5892 H + 27 H27 -1.7216 2.3692 -3.4882 H + 28 H28 -2.0164 0.8942 -2.5364 H + 29 H29 -0.0024 3.9465 -1.8080 H + 30 H30 -1.6278 4.5303 -2.2389 H + 31 H31 -1.1314 4.4591 -0.5310 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 am + 4 2 18 2 + 5 3 4 1 + 6 3 19 1 + 7 4 14 1 + 8 4 5 2 + 9 5 6 1 + 10 6 7 1 + 11 7 8 1 + 12 7 14 2 + 13 8 13 ar + 14 8 9 ar + 15 9 10 ar + 16 9 20 1 + 17 10 11 ar + 18 10 21 1 + 19 11 12 ar + 20 11 22 1 + 21 12 13 ar + 22 12 23 1 + 23 13 24 1 + 24 14 25 1 + 25 15 16 1 + 26 15 17 1 + 27 16 26 1 + 28 16 27 1 + 29 16 28 1 + 30 17 29 1 + 31 17 30 1 + 32 17 31 1 + +# End of record + diff --git a/top/cgenff/SM43/SM43.pdb b/top/cgenff/SM43/SM43.pdb deleted file mode 120000 index 0995fe1..0000000 --- a/top/cgenff/SM43/SM43.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM43/SM43.pdb \ No newline at end of file diff --git a/top/cgenff/SM43/SM43.pdb b/top/cgenff/SM43/SM43.pdb new file mode 100644 index 0000000..b985f25 --- /dev/null +++ b/top/cgenff/SM43/SM43.pdb @@ -0,0 +1,66 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM43 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.472 0.781 -0.017 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 4 C4 UNK 1 1.184 1.678 -0.000 1.00 20.00 +HETATM 5 N5 UNK 1 1.322 2.979 0.006 1.00 20.00 +HETATM 6 O6 UNK 1 2.485 3.307 -0.003 1.00 20.00 +HETATM 7 C7 UNK 1 3.303 2.239 -0.017 1.00 20.00 +HETATM 8 C8 UNK 1 4.781 2.254 -0.031 1.00 20.00 +HETATM 9 C9 UNK 1 5.494 1.054 -0.038 1.00 20.00 +HETATM 10 C10 UNK 1 6.873 1.075 -0.055 1.00 20.00 +HETATM 11 C11 UNK 1 7.550 2.282 -0.056 1.00 20.00 +HETATM 12 C12 UNK 1 6.849 3.475 -0.043 1.00 20.00 +HETATM 13 C13 UNK 1 5.470 3.468 -0.031 1.00 20.00 +HETATM 14 C14 UNK 1 2.495 1.137 -0.010 1.00 20.00 +HETATM 15 N15 UNK 1 -1.565 2.605 -1.410 1.00 20.00 +HETATM 16 C16 UNK 1 -2.176 1.972 -2.581 1.00 20.00 +HETATM 17 C17 UNK 1 -1.049 3.973 -1.503 1.00 20.00 +HETATM 18 O18 UNK 1 -1.361 2.752 1.045 1.00 20.00 +HETATM 19 H19 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 20 H20 UNK 1 4.967 0.111 -0.034 1.00 20.00 +HETATM 21 H21 UNK 1 7.426 0.147 -0.065 1.00 20.00 +HETATM 22 H22 UNK 1 8.630 2.293 -0.065 1.00 20.00 +HETATM 23 H23 UNK 1 7.383 4.413 -0.044 1.00 20.00 +HETATM 24 H24 UNK 1 4.924 4.399 -0.022 1.00 20.00 +HETATM 25 H25 UNK 1 2.786 0.098 -0.013 1.00 20.00 +HETATM 26 H26 UNK 1 -3.246 2.180 -2.589 1.00 20.00 +HETATM 27 H27 UNK 1 -1.722 2.369 -3.488 1.00 20.00 +HETATM 28 H28 UNK 1 -2.016 0.894 -2.536 1.00 20.00 +HETATM 29 H29 UNK 1 -0.002 3.946 -1.808 1.00 20.00 +HETATM 30 H30 UNK 1 -1.628 4.530 -2.239 1.00 20.00 +HETATM 31 H31 UNK 1 -1.131 4.459 -0.531 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 18 +CONECT 3 2 4 19 +CONECT 4 3 14 5 +CONECT 5 4 6 +CONECT 6 5 7 +CONECT 7 6 8 14 +CONECT 8 7 13 9 +CONECT 9 8 10 20 +CONECT 10 9 11 21 +CONECT 11 10 12 22 +CONECT 12 11 13 23 +CONECT 13 12 8 24 +CONECT 14 7 4 25 +CONECT 15 2 16 17 +CONECT 16 15 26 27 28 +CONECT 17 15 29 30 31 +CONECT 18 2 +CONECT 19 3 +CONECT 20 9 +CONECT 21 10 +CONECT 22 11 +CONECT 23 12 +CONECT 24 13 +CONECT 25 14 +CONECT 26 16 +CONECT 27 16 +CONECT 28 16 +CONECT 29 17 +CONECT 30 17 +CONECT 31 17 +END diff --git a/top/cgenff/SM44/SM44.mol2 b/top/cgenff/SM44/SM44.mol2 deleted file mode 120000 index f557a72..0000000 --- a/top/cgenff/SM44/SM44.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM44/SM44.mol2 \ No newline at end of file diff --git a/top/cgenff/SM44/SM44.mol2 b/top/cgenff/SM44/SM44.mol2 new file mode 100644 index 0000000..595043c --- /dev/null +++ b/top/cgenff/SM44/SM44.mol2 @@ -0,0 +1,74 @@ +# Name: SM44 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 26 27 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -2.4342 0.7435 0.0434 O.2 + 2 S2 -1.4563 1.7742 0.0186 S.o2 + 3 N3 -0.0111 0.9658 0.0074 N.am + 4 C4 1.1952 1.6843 -0.0003 C.2 + 5 N5 1.3355 3.0174 0.0060 N.2 + 6 N6 2.5876 3.3093 -0.0046 N.2 + 7 C7 2.4511 1.1657 -0.0096 C.2 + 8 N8 3.2983 2.2362 -0.0177 N.pl3 + 9 C9 4.6992 2.1771 -0.0325 C.ar + 10 C10 5.3434 0.9473 -0.0405 C.ar + 11 C11 6.7233 0.8922 -0.0613 C.ar + 12 C12 7.4633 2.0604 -0.0616 C.ar + 13 C13 6.8246 3.2867 -0.0479 C.ar + 14 C14 5.4448 3.3481 -0.0333 C.ar + 15 C15 -1.4964 2.6518 -1.5685 C.3 + 16 O16 -1.3346 2.6947 1.0943 O.2 + 17 H17 0.0021 -0.0041 0.0020 H + 18 H18 2.7234 0.1206 -0.0120 H + 19 H19 4.7660 0.0346 -0.0350 H + 20 H20 7.2250 -0.0641 -0.0724 H + 21 H21 8.5423 2.0148 -0.0730 H + 22 H22 7.4052 4.1974 -0.0489 H + 23 H23 4.9465 4.3062 -0.0229 H + 24 H24 -1.4399 1.9306 -2.3839 H + 25 H25 -2.4248 3.2175 -1.6475 H + 26 H26 -0.6488 3.3344 -1.6278 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 1 + 4 2 16 2 + 5 3 4 1 + 6 3 17 1 + 7 4 5 1 + 8 4 7 2 + 9 5 6 2 + 10 6 8 1 + 11 7 8 1 + 12 7 18 1 + 13 8 9 1 + 14 9 14 ar + 15 9 10 ar + 16 10 11 ar + 17 10 19 1 + 18 11 12 ar + 19 11 20 1 + 20 12 13 ar + 21 12 21 1 + 22 13 14 ar + 23 13 22 1 + 24 14 23 1 + 25 15 24 1 + 26 15 25 1 + 27 15 26 1 + +# End of record + diff --git a/top/cgenff/SM44/SM44.pdb b/top/cgenff/SM44/SM44.pdb deleted file mode 120000 index f0df9cb..0000000 --- a/top/cgenff/SM44/SM44.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM44/SM44.pdb \ No newline at end of file diff --git a/top/cgenff/SM44/SM44.pdb b/top/cgenff/SM44/SM44.pdb new file mode 100644 index 0000000..3173888 --- /dev/null +++ b/top/cgenff/SM44/SM44.pdb @@ -0,0 +1,56 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM44 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.434 0.744 0.043 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 4 C4 UNK 1 1.195 1.684 -0.000 1.00 20.00 +HETATM 5 N5 UNK 1 1.335 3.017 0.006 1.00 20.00 +HETATM 6 N6 UNK 1 2.588 3.309 -0.005 1.00 20.00 +HETATM 7 C7 UNK 1 2.451 1.166 -0.010 1.00 20.00 +HETATM 8 N8 UNK 1 3.298 2.236 -0.018 1.00 20.00 +HETATM 9 C9 UNK 1 4.699 2.177 -0.032 1.00 20.00 +HETATM 10 C10 UNK 1 5.343 0.947 -0.041 1.00 20.00 +HETATM 11 C11 UNK 1 6.723 0.892 -0.061 1.00 20.00 +HETATM 12 C12 UNK 1 7.463 2.060 -0.062 1.00 20.00 +HETATM 13 C13 UNK 1 6.825 3.287 -0.048 1.00 20.00 +HETATM 14 C14 UNK 1 5.445 3.348 -0.033 1.00 20.00 +HETATM 15 C15 UNK 1 -1.496 2.652 -1.569 1.00 20.00 +HETATM 16 O16 UNK 1 -1.335 2.695 1.094 1.00 20.00 +HETATM 17 H17 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 18 H18 UNK 1 2.723 0.121 -0.012 1.00 20.00 +HETATM 19 H19 UNK 1 4.766 0.035 -0.035 1.00 20.00 +HETATM 20 H20 UNK 1 7.225 -0.064 -0.072 1.00 20.00 +HETATM 21 H21 UNK 1 8.542 2.015 -0.073 1.00 20.00 +HETATM 22 H22 UNK 1 7.405 4.197 -0.049 1.00 20.00 +HETATM 23 H23 UNK 1 4.947 4.306 -0.023 1.00 20.00 +HETATM 24 H24 UNK 1 -1.440 1.931 -2.384 1.00 20.00 +HETATM 25 H25 UNK 1 -2.425 3.217 -1.648 1.00 20.00 +HETATM 26 H26 UNK 1 -0.649 3.334 -1.628 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 16 +CONECT 3 2 4 17 +CONECT 4 3 5 7 +CONECT 5 4 6 +CONECT 6 5 8 +CONECT 7 4 8 18 +CONECT 8 7 6 9 +CONECT 9 8 14 10 +CONECT 10 9 11 19 +CONECT 11 10 12 20 +CONECT 12 11 13 21 +CONECT 13 12 14 22 +CONECT 14 13 9 23 +CONECT 15 2 24 25 26 +CONECT 16 2 +CONECT 17 3 +CONECT 18 7 +CONECT 19 10 +CONECT 20 11 +CONECT 21 12 +CONECT 22 13 +CONECT 23 14 +CONECT 24 15 +CONECT 25 15 +CONECT 26 15 +END diff --git a/top/cgenff/SM45/SM45.mol2 b/top/cgenff/SM45/SM45.mol2 deleted file mode 120000 index cdccb43..0000000 --- a/top/cgenff/SM45/SM45.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM45/SM45.mol2 \ No newline at end of file diff --git a/top/cgenff/SM45/SM45.mol2 b/top/cgenff/SM45/SM45.mol2 new file mode 100644 index 0000000..62b30d3 --- /dev/null +++ b/top/cgenff/SM45/SM45.mol2 @@ -0,0 +1,89 @@ +# Name: SM45 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 33 35 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 9.4313 -1.9481 -0.1315 O.2 + 2 S2 8.0779 -2.3787 -0.0863 S.o2 + 3 N3 7.1509 -1.0066 -0.0704 N.am + 4 C4 5.7504 -1.1056 -0.0577 C.2 + 5 N5 5.0254 -2.2331 -0.0571 N.2 + 6 N6 3.7758 -1.9304 -0.0440 N.2 + 7 C7 4.8620 -0.0774 -0.0499 C.2 + 8 N8 3.6239 -0.6523 -0.0357 N.pl3 + 9 C9 2.3994 0.0308 -0.0208 C.ar + 10 C10 1.2067 -0.6797 -0.0132 C.ar + 11 C11 0.0021 -0.0041 0.0020 C.ar + 12 C12 -0.0167 1.3786 0.0096 C.ar + 13 C13 1.1697 2.0889 0.0021 C.ar + 14 C14 2.3774 1.4188 -0.0131 C.ar + 15 C15 7.7661 -3.2012 -1.6130 C.ar + 16 C16 6.7532 -4.1379 -1.6992 C.ar + 17 C17 6.5054 -4.7797 -2.8982 C.ar + 18 C18 7.2773 -4.4923 -4.0084 C.ar + 19 C19 8.2936 -3.5593 -3.9208 C.ar + 20 C20 8.5380 -2.9138 -2.7232 C.ar + 21 O21 7.5643 -3.2218 0.9359 O.2 + 22 H22 7.5755 -0.1344 -0.0699 H + 23 H23 5.0890 0.9785 -0.0522 H + 24 H24 1.2207 -1.7596 -0.0195 H + 25 H25 -0.9261 -0.5562 0.0083 H + 26 H26 -0.9598 1.9047 0.0170 H + 27 H27 1.1519 3.1688 0.0078 H + 28 H28 3.3036 1.9742 -0.0194 H + 29 H29 6.1529 -4.3657 -0.8307 H + 30 H30 5.7117 -5.5088 -2.9665 H + 31 H31 7.0867 -4.9969 -4.9440 H + 32 H32 8.8970 -3.3350 -4.7881 H + 33 H33 9.3322 -2.1851 -2.6547 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 1 + 4 2 21 2 + 5 3 4 1 + 6 3 22 1 + 7 4 5 1 + 8 4 7 2 + 9 5 6 2 + 10 6 8 1 + 11 7 8 1 + 12 7 23 1 + 13 8 9 1 + 14 9 14 ar + 15 9 10 ar + 16 10 11 ar + 17 10 24 1 + 18 11 12 ar + 19 11 25 1 + 20 12 13 ar + 21 12 26 1 + 22 13 14 ar + 23 13 27 1 + 24 14 28 1 + 25 15 20 ar + 26 15 16 ar + 27 16 17 ar + 28 16 29 1 + 29 17 18 ar + 30 17 30 1 + 31 18 19 ar + 32 18 31 1 + 33 19 20 ar + 34 19 32 1 + 35 20 33 1 + +# End of record + diff --git a/top/cgenff/SM45/SM45.pdb b/top/cgenff/SM45/SM45.pdb deleted file mode 120000 index 7fe071d..0000000 --- a/top/cgenff/SM45/SM45.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM45/SM45.pdb \ No newline at end of file diff --git a/top/cgenff/SM45/SM45.pdb b/top/cgenff/SM45/SM45.pdb new file mode 100644 index 0000000..c6488e8 --- /dev/null +++ b/top/cgenff/SM45/SM45.pdb @@ -0,0 +1,70 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM45 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 9.431 -1.948 -0.132 1.00 20.00 +HETATM 2 S2 UNK 1 8.078 -2.379 -0.086 1.00 20.00 +HETATM 3 N3 UNK 1 7.151 -1.007 -0.070 1.00 20.00 +HETATM 4 C4 UNK 1 5.750 -1.106 -0.058 1.00 20.00 +HETATM 5 N5 UNK 1 5.025 -2.233 -0.057 1.00 20.00 +HETATM 6 N6 UNK 1 3.776 -1.930 -0.044 1.00 20.00 +HETATM 7 C7 UNK 1 4.862 -0.077 -0.050 1.00 20.00 +HETATM 8 N8 UNK 1 3.624 -0.652 -0.036 1.00 20.00 +HETATM 9 C9 UNK 1 2.399 0.031 -0.021 1.00 20.00 +HETATM 10 C10 UNK 1 1.207 -0.680 -0.013 1.00 20.00 +HETATM 11 C11 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 12 C12 UNK 1 -0.017 1.379 0.010 1.00 20.00 +HETATM 13 C13 UNK 1 1.170 2.089 0.002 1.00 20.00 +HETATM 14 C14 UNK 1 2.377 1.419 -0.013 1.00 20.00 +HETATM 15 C15 UNK 1 7.766 -3.201 -1.613 1.00 20.00 +HETATM 16 C16 UNK 1 6.753 -4.138 -1.699 1.00 20.00 +HETATM 17 C17 UNK 1 6.505 -4.780 -2.898 1.00 20.00 +HETATM 18 C18 UNK 1 7.277 -4.492 -4.008 1.00 20.00 +HETATM 19 C19 UNK 1 8.294 -3.559 -3.921 1.00 20.00 +HETATM 20 C20 UNK 1 8.538 -2.914 -2.723 1.00 20.00 +HETATM 21 O21 UNK 1 7.564 -3.222 0.936 1.00 20.00 +HETATM 22 H22 UNK 1 7.575 -0.134 -0.070 1.00 20.00 +HETATM 23 H23 UNK 1 5.089 0.979 -0.052 1.00 20.00 +HETATM 24 H24 UNK 1 1.221 -1.760 -0.019 1.00 20.00 +HETATM 25 H25 UNK 1 -0.926 -0.556 0.008 1.00 20.00 +HETATM 26 H26 UNK 1 -0.960 1.905 0.017 1.00 20.00 +HETATM 27 H27 UNK 1 1.152 3.169 0.008 1.00 20.00 +HETATM 28 H28 UNK 1 3.304 1.974 -0.019 1.00 20.00 +HETATM 29 H29 UNK 1 6.153 -4.366 -0.831 1.00 20.00 +HETATM 30 H30 UNK 1 5.712 -5.509 -2.967 1.00 20.00 +HETATM 31 H31 UNK 1 7.087 -4.997 -4.944 1.00 20.00 +HETATM 32 H32 UNK 1 8.897 -3.335 -4.788 1.00 20.00 +HETATM 33 H33 UNK 1 9.332 -2.185 -2.655 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 21 +CONECT 3 2 4 22 +CONECT 4 3 5 7 +CONECT 5 4 6 +CONECT 6 5 8 +CONECT 7 4 8 23 +CONECT 8 7 6 9 +CONECT 9 8 14 10 +CONECT 10 9 11 24 +CONECT 11 10 12 25 +CONECT 12 11 13 26 +CONECT 13 12 14 27 +CONECT 14 13 9 28 +CONECT 15 2 20 16 +CONECT 16 15 17 29 +CONECT 17 16 18 30 +CONECT 18 17 19 31 +CONECT 19 18 20 32 +CONECT 20 19 15 33 +CONECT 21 2 +CONECT 22 3 +CONECT 23 7 +CONECT 24 10 +CONECT 25 11 +CONECT 26 12 +CONECT 27 13 +CONECT 28 14 +CONECT 29 16 +CONECT 30 17 +CONECT 31 18 +CONECT 32 19 +CONECT 33 20 +END diff --git a/top/cgenff/SM46/SM46.mol2 b/top/cgenff/SM46/SM46.mol2 deleted file mode 120000 index 1db1800..0000000 --- a/top/cgenff/SM46/SM46.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM46/SM46.mol2 \ No newline at end of file diff --git a/top/cgenff/SM46/SM46.mol2 b/top/cgenff/SM46/SM46.mol2 new file mode 100644 index 0000000..87821bd --- /dev/null +++ b/top/cgenff/SM46/SM46.mol2 @@ -0,0 +1,84 @@ +# Name: SM46 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 31 32 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -2.4719 0.7810 -0.0167 O.2 + 2 S2 -1.4563 1.7742 0.0186 S.o2 + 3 N3 -0.0111 0.9658 0.0074 N.am + 4 C4 1.1952 1.6843 -0.0003 C.2 + 5 N5 1.3355 3.0174 0.0060 N.2 + 6 N6 2.5876 3.3093 -0.0046 N.2 + 7 C7 2.4511 1.1657 -0.0096 C.2 + 8 N8 3.2983 2.2362 -0.0177 N.pl3 + 9 C9 4.6992 2.1771 -0.0325 C.ar + 10 C10 5.3434 0.9473 -0.0405 C.ar + 11 C11 6.7233 0.8922 -0.0613 C.ar + 12 C12 7.4633 2.0604 -0.0616 C.ar + 13 C13 6.8246 3.2867 -0.0479 C.ar + 14 C14 5.4448 3.3481 -0.0333 C.ar + 15 N15 -1.5645 2.6048 -1.4100 N.am + 16 C16 -2.1763 1.9715 -2.5809 C.3 + 17 C17 -1.0485 3.9727 -1.5029 C.3 + 18 O18 -1.3610 2.7523 1.0451 O.2 + 19 H19 0.0021 -0.0041 0.0020 H + 20 H20 2.7234 0.1206 -0.0120 H + 21 H21 4.7660 0.0346 -0.0350 H + 22 H22 7.2250 -0.0641 -0.0724 H + 23 H23 8.5423 2.0148 -0.0730 H + 24 H24 7.4052 4.1974 -0.0489 H + 25 H25 4.9465 4.3062 -0.0229 H + 26 H26 -3.2462 2.1800 -2.5892 H + 27 H27 -1.7216 2.3692 -3.4882 H + 28 H28 -2.0164 0.8942 -2.5364 H + 29 H29 -0.0024 3.9465 -1.8080 H + 30 H30 -1.6278 4.5303 -2.2389 H + 31 H31 -1.1314 4.4591 -0.5310 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 am + 4 2 18 2 + 5 3 4 1 + 6 3 19 1 + 7 4 5 1 + 8 4 7 2 + 9 5 6 2 + 10 6 8 1 + 11 7 8 1 + 12 7 20 1 + 13 8 9 1 + 14 9 14 ar + 15 9 10 ar + 16 10 11 ar + 17 10 21 1 + 18 11 12 ar + 19 11 22 1 + 20 12 13 ar + 21 12 23 1 + 22 13 14 ar + 23 13 24 1 + 24 14 25 1 + 25 15 16 1 + 26 15 17 1 + 27 16 26 1 + 28 16 27 1 + 29 16 28 1 + 30 17 29 1 + 31 17 30 1 + 32 17 31 1 + +# End of record + diff --git a/top/cgenff/SM46/SM46.pdb b/top/cgenff/SM46/SM46.pdb deleted file mode 120000 index a13f689..0000000 --- a/top/cgenff/SM46/SM46.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM46/SM46.pdb \ No newline at end of file diff --git a/top/cgenff/SM46/SM46.pdb b/top/cgenff/SM46/SM46.pdb new file mode 100644 index 0000000..4bf16c3 --- /dev/null +++ b/top/cgenff/SM46/SM46.pdb @@ -0,0 +1,66 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM46 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.472 0.781 -0.017 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 4 C4 UNK 1 1.195 1.684 -0.000 1.00 20.00 +HETATM 5 N5 UNK 1 1.335 3.017 0.006 1.00 20.00 +HETATM 6 N6 UNK 1 2.588 3.309 -0.005 1.00 20.00 +HETATM 7 C7 UNK 1 2.451 1.166 -0.010 1.00 20.00 +HETATM 8 N8 UNK 1 3.298 2.236 -0.018 1.00 20.00 +HETATM 9 C9 UNK 1 4.699 2.177 -0.032 1.00 20.00 +HETATM 10 C10 UNK 1 5.343 0.947 -0.041 1.00 20.00 +HETATM 11 C11 UNK 1 6.723 0.892 -0.061 1.00 20.00 +HETATM 12 C12 UNK 1 7.463 2.060 -0.062 1.00 20.00 +HETATM 13 C13 UNK 1 6.825 3.287 -0.048 1.00 20.00 +HETATM 14 C14 UNK 1 5.445 3.348 -0.033 1.00 20.00 +HETATM 15 N15 UNK 1 -1.565 2.605 -1.410 1.00 20.00 +HETATM 16 C16 UNK 1 -2.176 1.972 -2.581 1.00 20.00 +HETATM 17 C17 UNK 1 -1.049 3.973 -1.503 1.00 20.00 +HETATM 18 O18 UNK 1 -1.361 2.752 1.045 1.00 20.00 +HETATM 19 H19 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 20 H20 UNK 1 2.723 0.121 -0.012 1.00 20.00 +HETATM 21 H21 UNK 1 4.766 0.035 -0.035 1.00 20.00 +HETATM 22 H22 UNK 1 7.225 -0.064 -0.072 1.00 20.00 +HETATM 23 H23 UNK 1 8.542 2.015 -0.073 1.00 20.00 +HETATM 24 H24 UNK 1 7.405 4.197 -0.049 1.00 20.00 +HETATM 25 H25 UNK 1 4.947 4.306 -0.023 1.00 20.00 +HETATM 26 H26 UNK 1 -3.246 2.180 -2.589 1.00 20.00 +HETATM 27 H27 UNK 1 -1.722 2.369 -3.488 1.00 20.00 +HETATM 28 H28 UNK 1 -2.016 0.894 -2.536 1.00 20.00 +HETATM 29 H29 UNK 1 -0.002 3.946 -1.808 1.00 20.00 +HETATM 30 H30 UNK 1 -1.628 4.530 -2.239 1.00 20.00 +HETATM 31 H31 UNK 1 -1.131 4.459 -0.531 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 18 +CONECT 3 2 4 19 +CONECT 4 3 5 7 +CONECT 5 4 6 +CONECT 6 5 8 +CONECT 7 4 8 20 +CONECT 8 7 6 9 +CONECT 9 8 14 10 +CONECT 10 9 11 21 +CONECT 11 10 12 22 +CONECT 12 11 13 23 +CONECT 13 12 14 24 +CONECT 14 13 9 25 +CONECT 15 2 16 17 +CONECT 16 15 26 27 28 +CONECT 17 15 29 30 31 +CONECT 18 2 +CONECT 19 3 +CONECT 20 7 +CONECT 21 10 +CONECT 22 11 +CONECT 23 12 +CONECT 24 13 +CONECT 25 14 +CONECT 26 16 +CONECT 27 16 +CONECT 28 16 +CONECT 29 17 +CONECT 30 17 +CONECT 31 17 +END diff --git a/top/cgenff/refCMC26/refCMC26.mol2 b/top/cgenff/refCMC26/refCMC26.mol2 deleted file mode 120000 index 5f11c96..0000000 --- a/top/cgenff/refCMC26/refCMC26.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/refCMC26/refCMC26.mol2 \ No newline at end of file diff --git a/top/cgenff/refCMC26/refCMC26.mol2 b/top/cgenff/refCMC26/refCMC26.mol2 new file mode 100644 index 0000000..e976d4e --- /dev/null +++ b/top/cgenff/refCMC26/refCMC26.mol2 @@ -0,0 +1,80 @@ +# Name: UNK +# Creating user name: iorga +# Creation time: 10. 07. 2020 09:50 + +# Modifying user name: iorga +# Modification time: 10. 07. 2020 09:50 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 29 30 0 0 0 +SMALL +NO_CHARGES + + +@ATOM + 1 O1 -2.3285 -0.1731 0.0243 O.2 + 2 C2 -1.2662 -0.7638 0.0105 C.2 + 3 C3 0.0021 -0.0041 0.0020 C.ar + 4 C4 -0.0169 1.3915 0.0097 C.ar + 5 C5 1.1702 2.0945 0.0021 C.ar + 6 C6 2.3776 1.4190 -0.0130 C.ar + 7 C7 2.4034 0.0357 -0.0207 C.ar + 8 C8 1.2235 -0.6793 -0.0133 C.ar + 9 N9 -1.2445 -2.1114 0.0031 N.am + 10 S10 -2.6651 -2.9624 0.0126 S.o2 + 11 C11 -3.4932 -2.6121 -1.5027 C.ar + 12 C12 -4.3747 -1.5501 -1.5791 C.ar + 13 C13 -5.0207 -1.2723 -2.7693 C.ar + 14 C14 -4.7930 -2.0629 -3.8802 C.ar + 15 C15 -3.9154 -3.1281 -3.8023 C.ar + 16 C16 -3.2655 -3.4027 -2.6136 C.ar + 17 O17 -2.3095 -4.3374 -0.0330 O.2 + 18 O18 -3.4629 -2.3999 1.0452 O.2 + 19 H19 -0.9587 1.9200 0.0170 H + 20 H20 1.1570 3.1744 0.0081 H + 21 H21 3.3041 1.9740 -0.0192 H + 22 H22 3.3492 -0.4856 -0.0329 H + 23 H23 1.2450 -1.7591 -0.0196 H + 24 H24 -0.3968 -2.5828 -0.0079 H + 25 H25 -4.5559 -0.9351 -0.7100 H + 26 H26 -5.7066 -0.4403 -2.8300 H + 27 H27 -5.3011 -1.8486 -4.8088 H + 28 H28 -3.7378 -3.7460 -4.6701 H + 29 H29 -2.5801 -4.2351 -2.5526 H +@BOND + 1 1 2 2 + 2 2 3 1 + 3 2 9 am + 4 3 8 ar + 5 3 4 ar + 6 4 5 ar + 7 4 19 1 + 8 5 6 ar + 9 5 20 1 + 10 6 7 ar + 11 6 21 1 + 12 7 8 ar + 13 7 22 1 + 14 8 23 1 + 15 9 10 am + 16 9 24 1 + 17 10 11 1 + 18 10 17 2 + 19 10 18 2 + 20 11 16 ar + 21 11 12 ar + 22 12 13 ar + 23 12 25 1 + 24 13 14 ar + 25 13 26 1 + 26 14 15 ar + 27 14 27 1 + 28 15 16 ar + 29 15 28 1 + 30 16 29 1 + +# End of record + diff --git a/top/cgenff/refCMC26/refCMC26.pdb b/top/cgenff/refCMC26/refCMC26.pdb new file mode 100644 index 0000000..aec9e69 --- /dev/null +++ b/top/cgenff/refCMC26/refCMC26.pdb @@ -0,0 +1,62 @@ +HEADER UNK 20-07-10 1UNK +COMPND refCMC26 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.328 -0.173 0.024 1.00 20.00 +HETATM 2 C2 UNK 1 -1.266 -0.764 0.011 1.00 20.00 +HETATM 3 C3 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 4 C4 UNK 1 -0.017 1.392 0.010 1.00 20.00 +HETATM 5 C5 UNK 1 1.170 2.094 0.002 1.00 20.00 +HETATM 6 C6 UNK 1 2.378 1.419 -0.013 1.00 20.00 +HETATM 7 C7 UNK 1 2.403 0.036 -0.021 1.00 20.00 +HETATM 8 C8 UNK 1 1.224 -0.679 -0.013 1.00 20.00 +HETATM 9 N9 UNK 1 -1.245 -2.111 0.003 1.00 20.00 +HETATM 10 S10 UNK 1 -2.665 -2.962 0.013 1.00 20.00 +HETATM 11 C11 UNK 1 -3.493 -2.612 -1.503 1.00 20.00 +HETATM 12 C12 UNK 1 -4.375 -1.550 -1.579 1.00 20.00 +HETATM 13 C13 UNK 1 -5.021 -1.272 -2.769 1.00 20.00 +HETATM 14 C14 UNK 1 -4.793 -2.063 -3.880 1.00 20.00 +HETATM 15 C15 UNK 1 -3.915 -3.128 -3.802 1.00 20.00 +HETATM 16 C16 UNK 1 -3.265 -3.403 -2.614 1.00 20.00 +HETATM 17 O17 UNK 1 -2.309 -4.337 -0.033 1.00 20.00 +HETATM 18 O18 UNK 1 -3.463 -2.400 1.045 1.00 20.00 +HETATM 19 H19 UNK 1 -0.959 1.920 0.017 1.00 20.00 +HETATM 20 H20 UNK 1 1.157 3.174 0.008 1.00 20.00 +HETATM 21 H21 UNK 1 3.304 1.974 -0.019 1.00 20.00 +HETATM 22 H22 UNK 1 3.349 -0.486 -0.033 1.00 20.00 +HETATM 23 H23 UNK 1 1.245 -1.759 -0.020 1.00 20.00 +HETATM 24 H24 UNK 1 -0.397 -2.583 -0.008 1.00 20.00 +HETATM 25 H25 UNK 1 -4.556 -0.935 -0.710 1.00 20.00 +HETATM 26 H26 UNK 1 -5.707 -0.440 -2.830 1.00 20.00 +HETATM 27 H27 UNK 1 -5.301 -1.849 -4.809 1.00 20.00 +HETATM 28 H28 UNK 1 -3.738 -3.746 -4.670 1.00 20.00 +HETATM 29 H29 UNK 1 -2.580 -4.235 -2.553 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 9 +CONECT 3 2 8 4 +CONECT 4 3 5 19 +CONECT 5 4 6 20 +CONECT 6 5 7 21 +CONECT 7 6 8 22 +CONECT 8 7 3 23 +CONECT 9 2 10 24 +CONECT 10 9 11 17 18 +CONECT 11 10 16 12 +CONECT 12 11 13 25 +CONECT 13 12 14 26 +CONECT 14 13 15 27 +CONECT 15 14 16 28 +CONECT 16 15 11 29 +CONECT 17 10 +CONECT 18 10 +CONECT 19 4 +CONECT 20 5 +CONECT 21 6 +CONECT 22 7 +CONECT 23 8 +CONECT 24 9 +CONECT 25 12 +CONECT 26 13 +CONECT 27 14 +CONECT 28 15 +CONECT 29 16 +END diff --git a/top/cgenff/refJMC11/refJMC11.mol2 b/top/cgenff/refJMC11/refJMC11.mol2 deleted file mode 120000 index 6642f23..0000000 --- a/top/cgenff/refJMC11/refJMC11.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/refJMC11/refJMC11.mol2 \ No newline at end of file diff --git a/top/cgenff/refJMC11/refJMC11.mol2 b/top/cgenff/refJMC11/refJMC11.mol2 new file mode 100644 index 0000000..846c4b7 --- /dev/null +++ b/top/cgenff/refJMC11/refJMC11.mol2 @@ -0,0 +1,79 @@ +# Name: UNK +# Creating user name: iorga +# Creation time: 10. 07. 2020 09:43 + +# Modifying user name: iorga +# Modification time: 10. 07. 2020 09:43 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 29 29 0 0 0 +SMALL +NO_CHARGES + + +@ATOM + 1 C1 0.8091 10.4291 -2.3116 C.3 + 2 S2 -0.5250 9.4710 -3.0816 S.o2 + 3 O3 -0.4641 9.5797 -4.4971 O.2 + 4 O4 -1.7471 9.6677 -2.3837 O.2 + 5 N5 -0.1296 7.8923 -2.7758 N.am + 6 C6 -0.1109 7.3956 -1.3976 C.3 + 7 C7 -0.0901 5.8658 -1.4071 C.3 + 8 C8 -0.0705 5.3471 0.0321 C.3 + 9 C9 -0.0501 3.8402 0.0228 C.ar + 10 C10 1.1563 3.1654 0.0081 C.ar + 11 C11 1.1750 1.7832 0.0004 C.ar + 12 C12 -0.0126 1.0758 0.0080 C.ar + 13 C13 -1.2190 1.7506 0.0173 C.ar + 14 C14 -1.2377 3.1328 0.0294 C.ar + 15 H15 1.7619 10.1533 -2.7635 H + 16 H16 0.6282 11.4928 -2.4658 H + 17 H17 0.8388 10.2167 -1.2429 H + 18 H18 0.0895 7.2964 -3.5091 H + 19 H19 -1.0011 7.7436 -0.8738 H + 20 H20 0.7786 7.7679 -0.8894 H + 21 H21 0.8001 5.5177 -1.9309 H + 22 H22 -0.9796 5.4935 -1.9154 H + 23 H23 -0.9608 5.6951 0.5560 H + 24 H24 0.8190 5.7193 0.5404 H + 25 H25 2.0842 3.7181 0.0029 H + 26 H26 2.1175 1.2560 -0.0111 H + 27 H27 0.0021 -0.0041 0.0020 H + 28 H28 -2.1469 1.1980 0.0188 H + 29 H29 -2.1802 3.6600 0.0413 H +@BOND + 1 1 2 1 + 2 1 15 1 + 3 1 16 1 + 4 1 17 1 + 5 2 3 2 + 6 2 4 2 + 7 2 5 am + 8 5 6 1 + 9 5 18 1 + 10 6 7 1 + 11 6 19 1 + 12 6 20 1 + 13 7 8 1 + 14 7 21 1 + 15 7 22 1 + 16 8 9 1 + 17 8 23 1 + 18 8 24 1 + 19 9 14 ar + 20 9 10 ar + 21 10 11 ar + 22 10 25 1 + 23 11 12 ar + 24 11 26 1 + 25 12 13 ar + 26 12 27 1 + 27 13 14 ar + 28 13 28 1 + 29 14 29 1 + +# End of record + diff --git a/top/cgenff/refJMC11/refJMC11.pdb b/top/cgenff/refJMC11/refJMC11.pdb new file mode 100644 index 0000000..1615dd4 --- /dev/null +++ b/top/cgenff/refJMC11/refJMC11.pdb @@ -0,0 +1,62 @@ +HEADER UNK 20-07-10 1UNK +COMPND refJMC11 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 0.809 10.429 -2.312 1.00 20.00 +HETATM 2 S2 UNK 1 -0.525 9.471 -3.082 1.00 20.00 +HETATM 3 O3 UNK 1 -0.464 9.580 -4.497 1.00 20.00 +HETATM 4 O4 UNK 1 -1.747 9.668 -2.384 1.00 20.00 +HETATM 5 N5 UNK 1 -0.130 7.892 -2.776 1.00 20.00 +HETATM 6 C6 UNK 1 -0.111 7.396 -1.398 1.00 20.00 +HETATM 7 C7 UNK 1 -0.090 5.866 -1.407 1.00 20.00 +HETATM 8 C8 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 9 C9 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 10 C10 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 11 C11 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 12 C12 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 13 C13 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 14 C14 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 15 H15 UNK 1 1.762 10.153 -2.763 1.00 20.00 +HETATM 16 H16 UNK 1 0.628 11.493 -2.466 1.00 20.00 +HETATM 17 H17 UNK 1 0.839 10.217 -1.243 1.00 20.00 +HETATM 18 H18 UNK 1 0.090 7.296 -3.509 1.00 20.00 +HETATM 19 H19 UNK 1 -1.001 7.744 -0.874 1.00 20.00 +HETATM 20 H20 UNK 1 0.779 7.768 -0.889 1.00 20.00 +HETATM 21 H21 UNK 1 0.800 5.518 -1.931 1.00 20.00 +HETATM 22 H22 UNK 1 -0.980 5.493 -1.915 1.00 20.00 +HETATM 23 H23 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 24 H24 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 25 H25 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 26 H26 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 27 H27 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 28 H28 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 29 H29 UNK 1 -2.180 3.660 0.041 1.00 20.00 +CONECT 1 2 15 16 17 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 18 +CONECT 6 5 7 19 20 +CONECT 7 6 8 21 22 +CONECT 8 7 9 23 24 +CONECT 9 8 14 10 +CONECT 10 9 11 25 +CONECT 11 10 12 26 +CONECT 12 11 13 27 +CONECT 13 12 14 28 +CONECT 14 13 9 29 +CONECT 15 1 +CONECT 16 1 +CONECT 17 1 +CONECT 18 5 +CONECT 19 6 +CONECT 20 6 +CONECT 21 7 +CONECT 22 7 +CONECT 23 8 +CONECT 24 8 +CONECT 25 10 +CONECT 26 11 +CONECT 27 12 +CONECT 28 13 +CONECT 29 14 +END diff --git a/top/cgenff/refJMC12/refJMC12.mol2 b/top/cgenff/refJMC12/refJMC12.mol2 deleted file mode 120000 index 21545a4..0000000 --- a/top/cgenff/refJMC12/refJMC12.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/refJMC12/refJMC12.mol2 \ No newline at end of file diff --git a/top/cgenff/refJMC12/refJMC12.mol2 b/top/cgenff/refJMC12/refJMC12.mol2 new file mode 100644 index 0000000..b35aa8f --- /dev/null +++ b/top/cgenff/refJMC12/refJMC12.mol2 @@ -0,0 +1,77 @@ +# Name: UNK +# Creating user name: iorga +# Creation time: 10. 07. 2020 09:44 + +# Modifying user name: iorga +# Modification time: 10. 07. 2020 09:44 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 28 28 0 0 0 +SMALL +NO_CHARGES + + +@ATOM + 1 C1 1.4398 10.1791 -1.8192 C.3 + 2 S2 -0.1524 9.7093 -2.5505 S.o2 + 3 O3 -0.1950 10.0677 -3.9249 O.2 + 4 O4 -1.2207 10.0399 -1.6737 O.2 + 5 N5 -0.1300 8.0535 -2.5607 N.am + 6 C6 -0.1105 7.3726 -1.3978 C.2 + 7 O7 -0.1095 7.9725 -0.3438 O.2 + 8 C8 -0.0901 5.8658 -1.4071 C.3 + 9 C9 -0.0705 5.3471 0.0321 C.3 + 10 C10 -0.0501 3.8402 0.0228 C.ar + 11 C11 1.1563 3.1654 0.0081 C.ar + 12 C12 1.1750 1.7832 0.0004 C.ar + 13 C13 -0.0126 1.0758 0.0080 C.ar + 14 C14 -1.2190 1.7506 0.0173 C.ar + 15 C15 -1.2377 3.1328 0.0294 C.ar + 16 H16 2.2511 9.7869 -2.4325 H + 17 H17 1.5119 11.2657 -1.7729 H + 18 H18 1.5132 9.7668 -0.8128 H + 19 H19 -0.1308 7.5737 -3.4037 H + 20 H20 0.8001 5.5177 -1.9309 H + 21 H21 -0.9796 5.4935 -1.9154 H + 22 H22 -0.9608 5.6951 0.5560 H + 23 H23 0.8190 5.7193 0.5404 H + 24 H24 2.0842 3.7181 0.0029 H + 25 H25 2.1175 1.2560 -0.0111 H + 26 H26 0.0021 -0.0041 0.0020 H + 27 H27 -2.1469 1.1980 0.0188 H + 28 H28 -2.1802 3.6600 0.0413 H +@BOND + 1 1 2 1 + 2 1 16 1 + 3 1 17 1 + 4 1 18 1 + 5 2 3 2 + 6 2 4 2 + 7 2 5 am + 8 5 6 am + 9 5 19 1 + 10 6 7 2 + 11 6 8 1 + 12 8 9 1 + 13 8 20 1 + 14 8 21 1 + 15 9 10 1 + 16 9 22 1 + 17 9 23 1 + 18 10 15 ar + 19 10 11 ar + 20 11 12 ar + 21 11 24 1 + 22 12 13 ar + 23 12 25 1 + 24 13 14 ar + 25 13 26 1 + 26 14 15 ar + 27 14 27 1 + 28 15 28 1 + +# End of record + diff --git a/top/cgenff/refJMC12/refJMC12.pdb b/top/cgenff/refJMC12/refJMC12.pdb new file mode 100644 index 0000000..beddbac --- /dev/null +++ b/top/cgenff/refJMC12/refJMC12.pdb @@ -0,0 +1,60 @@ +HEADER UNK 20-07-10 1UNK +COMPND refJMC12 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 1.440 10.179 -1.819 1.00 20.00 +HETATM 2 S2 UNK 1 -0.152 9.709 -2.550 1.00 20.00 +HETATM 3 O3 UNK 1 -0.195 10.068 -3.925 1.00 20.00 +HETATM 4 O4 UNK 1 -1.221 10.040 -1.674 1.00 20.00 +HETATM 5 N5 UNK 1 -0.130 8.053 -2.561 1.00 20.00 +HETATM 6 C6 UNK 1 -0.111 7.373 -1.398 1.00 20.00 +HETATM 7 O7 UNK 1 -0.110 7.973 -0.344 1.00 20.00 +HETATM 8 C8 UNK 1 -0.090 5.866 -1.407 1.00 20.00 +HETATM 9 C9 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 10 C10 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 11 C11 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 12 C12 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 13 C13 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 14 C14 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 15 C15 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 16 H16 UNK 1 2.251 9.787 -2.433 1.00 20.00 +HETATM 17 H17 UNK 1 1.512 11.266 -1.773 1.00 20.00 +HETATM 18 H18 UNK 1 1.513 9.767 -0.813 1.00 20.00 +HETATM 19 H19 UNK 1 -0.131 7.574 -3.404 1.00 20.00 +HETATM 20 H20 UNK 1 0.800 5.518 -1.931 1.00 20.00 +HETATM 21 H21 UNK 1 -0.980 5.493 -1.915 1.00 20.00 +HETATM 22 H22 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 23 H23 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 24 H24 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 25 H25 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 26 H26 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 27 H27 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 28 H28 UNK 1 -2.180 3.660 0.041 1.00 20.00 +CONECT 1 2 16 17 18 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 19 +CONECT 6 5 7 8 +CONECT 7 6 +CONECT 8 6 9 20 21 +CONECT 9 8 10 22 23 +CONECT 10 9 15 11 +CONECT 11 10 12 24 +CONECT 12 11 13 25 +CONECT 13 12 14 26 +CONECT 14 13 15 27 +CONECT 15 14 10 28 +CONECT 16 1 +CONECT 17 1 +CONECT 18 1 +CONECT 19 5 +CONECT 20 8 +CONECT 21 8 +CONECT 22 9 +CONECT 23 9 +CONECT 24 11 +CONECT 25 12 +CONECT 26 13 +CONECT 27 14 +CONECT 28 15 +END diff --git a/top/cgenff/refJMC13/refJMC13.mol2 b/top/cgenff/refJMC13/refJMC13.mol2 deleted file mode 120000 index c4a8af9..0000000 --- a/top/cgenff/refJMC13/refJMC13.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/refJMC13/refJMC13.mol2 \ No newline at end of file diff --git a/top/cgenff/refJMC13/refJMC13.mol2 b/top/cgenff/refJMC13/refJMC13.mol2 new file mode 100644 index 0000000..58481ca --- /dev/null +++ b/top/cgenff/refJMC13/refJMC13.mol2 @@ -0,0 +1,87 @@ +# Name: UNK +# Creating user name: iorga +# Creation time: 10. 07. 2020 09:45 + +# Modifying user name: iorga +# Modification time: 10. 07. 2020 09:45 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 33 33 0 0 0 +SMALL +NO_CHARGES + + +@ATOM + 1 C1 2.4399 10.4528 -2.7545 C.3 + 2 N2 1.2802 10.2149 -1.8915 N.am + 3 C3 1.3880 10.4242 -0.4455 C.3 + 4 S4 -0.1524 9.7093 -2.5505 S.o2 + 5 O5 -0.1351 10.1193 -3.9109 O.2 + 6 O6 -1.1713 10.0911 -1.6366 O.2 + 7 N7 -0.1300 8.0535 -2.5607 N.am + 8 C8 -0.1105 7.3726 -1.3978 C.2 + 9 O9 -0.1095 7.9725 -0.3438 O.2 + 10 C10 -0.0901 5.8658 -1.4071 C.3 + 11 C11 -0.0705 5.3471 0.0321 C.3 + 12 C12 -0.0501 3.8402 0.0228 C.ar + 13 C13 1.1563 3.1654 0.0081 C.ar + 14 C14 1.1750 1.7832 0.0004 C.ar + 15 C15 -0.0126 1.0758 0.0080 C.ar + 16 C16 -1.2190 1.7506 0.0173 C.ar + 17 C17 -1.2377 3.1328 0.0294 C.ar + 18 H18 2.4374 11.4903 -3.0886 H + 19 H19 3.3549 10.2529 -2.1969 H + 20 H20 2.3903 9.7923 -3.6201 H + 21 H21 0.4317 10.1987 0.0265 H + 22 H22 2.1574 9.7675 -0.0397 H + 23 H23 1.6549 11.4623 -0.2476 H + 24 H24 -0.1308 7.5737 -3.4037 H + 25 H25 0.8001 5.5177 -1.9309 H + 26 H26 -0.9796 5.4935 -1.9154 H + 27 H27 -0.9608 5.6951 0.5560 H + 28 H28 0.8190 5.7193 0.5404 H + 29 H29 2.0842 3.7181 0.0029 H + 30 H30 2.1175 1.2560 -0.0111 H + 31 H31 0.0021 -0.0041 0.0020 H + 32 H32 -2.1469 1.1980 0.0188 H + 33 H33 -2.1802 3.6600 0.0413 H +@BOND + 1 1 2 1 + 2 1 18 1 + 3 1 19 1 + 4 1 20 1 + 5 2 3 1 + 6 2 4 am + 7 3 21 1 + 8 3 22 1 + 9 3 23 1 + 10 4 5 2 + 11 4 6 2 + 12 4 7 am + 13 7 8 am + 14 7 24 1 + 15 8 9 2 + 16 8 10 1 + 17 10 11 1 + 18 10 25 1 + 19 10 26 1 + 20 11 12 1 + 21 11 27 1 + 22 11 28 1 + 23 12 17 ar + 24 12 13 ar + 25 13 14 ar + 26 13 29 1 + 27 14 15 ar + 28 14 30 1 + 29 15 16 ar + 30 15 31 1 + 31 16 17 ar + 32 16 32 1 + 33 17 33 1 + +# End of record + diff --git a/top/cgenff/refJMC13/refJMC13.pdb b/top/cgenff/refJMC13/refJMC13.pdb new file mode 100644 index 0000000..27d2939 --- /dev/null +++ b/top/cgenff/refJMC13/refJMC13.pdb @@ -0,0 +1,70 @@ +HEADER UNK 20-07-10 1UNK +COMPND refJMC13 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 2.440 10.453 -2.754 1.00 20.00 +HETATM 2 N2 UNK 1 1.280 10.215 -1.891 1.00 20.00 +HETATM 3 C3 UNK 1 1.388 10.424 -0.446 1.00 20.00 +HETATM 4 S4 UNK 1 -0.152 9.709 -2.550 1.00 20.00 +HETATM 5 O5 UNK 1 -0.135 10.119 -3.911 1.00 20.00 +HETATM 6 O6 UNK 1 -1.171 10.091 -1.637 1.00 20.00 +HETATM 7 N7 UNK 1 -0.130 8.053 -2.561 1.00 20.00 +HETATM 8 C8 UNK 1 -0.111 7.373 -1.398 1.00 20.00 +HETATM 9 O9 UNK 1 -0.110 7.973 -0.344 1.00 20.00 +HETATM 10 C10 UNK 1 -0.090 5.866 -1.407 1.00 20.00 +HETATM 11 C11 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 12 C12 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 13 C13 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 14 C14 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 15 C15 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 16 C16 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 17 C17 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 18 H18 UNK 1 2.437 11.490 -3.089 1.00 20.00 +HETATM 19 H19 UNK 1 3.355 10.253 -2.197 1.00 20.00 +HETATM 20 H20 UNK 1 2.390 9.792 -3.620 1.00 20.00 +HETATM 21 H21 UNK 1 0.432 10.199 0.026 1.00 20.00 +HETATM 22 H22 UNK 1 2.157 9.767 -0.040 1.00 20.00 +HETATM 23 H23 UNK 1 1.655 11.462 -0.248 1.00 20.00 +HETATM 24 H24 UNK 1 -0.131 7.574 -3.404 1.00 20.00 +HETATM 25 H25 UNK 1 0.800 5.518 -1.931 1.00 20.00 +HETATM 26 H26 UNK 1 -0.980 5.493 -1.915 1.00 20.00 +HETATM 27 H27 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 28 H28 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 29 H29 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 30 H30 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 31 H31 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 32 H32 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 33 H33 UNK 1 -2.180 3.660 0.041 1.00 20.00 +CONECT 1 2 18 19 20 +CONECT 2 1 3 4 +CONECT 3 2 21 22 23 +CONECT 4 2 5 6 7 +CONECT 5 4 +CONECT 6 4 +CONECT 7 4 8 24 +CONECT 8 7 9 10 +CONECT 9 8 +CONECT 10 8 11 25 26 +CONECT 11 10 12 27 28 +CONECT 12 11 17 13 +CONECT 13 12 14 29 +CONECT 14 13 15 30 +CONECT 15 14 16 31 +CONECT 16 15 17 32 +CONECT 17 16 12 33 +CONECT 18 1 +CONECT 19 1 +CONECT 20 1 +CONECT 21 3 +CONECT 22 3 +CONECT 23 3 +CONECT 24 7 +CONECT 25 10 +CONECT 26 10 +CONECT 27 11 +CONECT 28 11 +CONECT 29 13 +CONECT 30 14 +CONECT 31 15 +CONECT 32 16 +CONECT 33 17 +END diff --git a/top/cgenff/refJMC14/refJMC14.mol2 b/top/cgenff/refJMC14/refJMC14.mol2 deleted file mode 120000 index 20a8e3c..0000000 --- a/top/cgenff/refJMC14/refJMC14.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/refJMC14/refJMC14.mol2 \ No newline at end of file diff --git a/top/cgenff/refJMC14/refJMC14.mol2 b/top/cgenff/refJMC14/refJMC14.mol2 new file mode 100644 index 0000000..c97b808 --- /dev/null +++ b/top/cgenff/refJMC14/refJMC14.mol2 @@ -0,0 +1,75 @@ +# Name: UNK +# Creating user name: iorga +# Creation time: 10. 07. 2020 09:46 + +# Modifying user name: iorga +# Modification time: 10. 07. 2020 09:46 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 27 27 0 0 0 +SMALL +NO_CHARGES + + +@ATOM + 1 C1 1.4382 9.8552 -2.5075 C.3 + 2 S2 -0.1514 9.2568 -3.1443 S.o2 + 3 O3 -0.1909 9.3580 -4.5612 O.2 + 4 O4 -1.2225 9.7401 -2.3452 O.2 + 5 N5 -0.1267 7.6271 -2.8519 N.am + 6 C6 -0.1094 7.1701 -1.5840 C.2 + 7 O7 -0.1120 7.9545 -0.6550 O.2 + 8 N8 -0.0893 5.8437 -1.3460 N.am + 9 C9 -0.0705 5.3471 0.0321 C.3 + 10 C10 -0.0501 3.8402 0.0228 C.ar + 11 C11 1.1563 3.1654 0.0081 C.ar + 12 C12 1.1750 1.7832 0.0004 C.ar + 13 C13 -0.0126 1.0758 0.0080 C.ar + 14 C14 -1.2190 1.7506 0.0173 C.ar + 15 C15 -1.2377 3.1328 0.0294 C.ar + 16 H16 2.2517 9.3591 -3.0369 H + 17 H17 1.5087 10.9321 -2.6604 H + 18 H18 1.5095 9.6339 -1.4426 H + 19 H19 -0.1246 7.0013 -3.5930 H + 20 H20 -0.0872 5.2179 -2.0871 H + 21 H21 -0.9608 5.6951 0.5560 H + 22 H22 0.8190 5.7193 0.5404 H + 23 H23 2.0842 3.7181 0.0029 H + 24 H24 2.1175 1.2560 -0.0111 H + 25 H25 0.0021 -0.0041 0.0020 H + 26 H26 -2.1469 1.1980 0.0188 H + 27 H27 -2.1802 3.6600 0.0413 H +@BOND + 1 1 2 1 + 2 1 16 1 + 3 1 17 1 + 4 1 18 1 + 5 2 3 2 + 6 2 4 2 + 7 2 5 am + 8 5 6 am + 9 5 19 1 + 10 6 7 2 + 11 6 8 am + 12 8 9 1 + 13 8 20 1 + 14 9 10 1 + 15 9 21 1 + 16 9 22 1 + 17 10 15 ar + 18 10 11 ar + 19 11 12 ar + 20 11 23 1 + 21 12 13 ar + 22 12 24 1 + 23 13 14 ar + 24 13 25 1 + 25 14 15 ar + 26 14 26 1 + 27 15 27 1 + +# End of record + diff --git a/top/cgenff/refJMC14/refJMC14.pdb b/top/cgenff/refJMC14/refJMC14.pdb new file mode 100644 index 0000000..e80353d --- /dev/null +++ b/top/cgenff/refJMC14/refJMC14.pdb @@ -0,0 +1,58 @@ +HEADER UNK 20-07-10 1UNK +COMPND refJMC14 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 1.438 9.855 -2.508 1.00 20.00 +HETATM 2 S2 UNK 1 -0.151 9.257 -3.144 1.00 20.00 +HETATM 3 O3 UNK 1 -0.191 9.358 -4.561 1.00 20.00 +HETATM 4 O4 UNK 1 -1.222 9.740 -2.345 1.00 20.00 +HETATM 5 N5 UNK 1 -0.127 7.627 -2.852 1.00 20.00 +HETATM 6 C6 UNK 1 -0.109 7.170 -1.584 1.00 20.00 +HETATM 7 O7 UNK 1 -0.112 7.955 -0.655 1.00 20.00 +HETATM 8 N8 UNK 1 -0.089 5.844 -1.346 1.00 20.00 +HETATM 9 C9 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 10 C10 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 11 C11 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 12 C12 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 13 C13 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 14 C14 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 15 C15 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 16 H16 UNK 1 2.252 9.359 -3.037 1.00 20.00 +HETATM 17 H17 UNK 1 1.509 10.932 -2.660 1.00 20.00 +HETATM 18 H18 UNK 1 1.510 9.634 -1.443 1.00 20.00 +HETATM 19 H19 UNK 1 -0.125 7.001 -3.593 1.00 20.00 +HETATM 20 H20 UNK 1 -0.087 5.218 -2.087 1.00 20.00 +HETATM 21 H21 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 22 H22 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 23 H23 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 24 H24 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 25 H25 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 26 H26 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 27 H27 UNK 1 -2.180 3.660 0.041 1.00 20.00 +CONECT 1 2 16 17 18 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 19 +CONECT 6 5 7 8 +CONECT 7 6 +CONECT 8 6 9 20 +CONECT 9 8 10 21 22 +CONECT 10 9 15 11 +CONECT 11 10 12 23 +CONECT 12 11 13 24 +CONECT 13 12 14 25 +CONECT 14 13 15 26 +CONECT 15 14 10 27 +CONECT 16 1 +CONECT 17 1 +CONECT 18 1 +CONECT 19 5 +CONECT 20 8 +CONECT 21 9 +CONECT 22 9 +CONECT 23 11 +CONECT 24 12 +CONECT 25 13 +CONECT 26 14 +CONECT 27 15 +END diff --git a/top/gaff/SM25/SM25.pdb b/top/gaff/SM25/SM25.pdb deleted file mode 120000 index d725256..0000000 --- a/top/gaff/SM25/SM25.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM25/SM25.pdb \ No newline at end of file diff --git a/top/gaff/SM25/SM25.pdb b/top/gaff/SM25/SM25.pdb new file mode 100644 index 0000000..e6cb765 --- /dev/null +++ b/top/gaff/SM25/SM25.pdb @@ -0,0 +1,74 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM25 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.095 5.200 -1.876 1.00 20.00 +HETATM 2 C2 UNK 1 -1.156 5.819 -2.329 1.00 20.00 +HETATM 3 N3 UNK 1 -0.095 6.101 -1.547 1.00 20.00 +HETATM 4 S4 UNK 1 -0.074 5.602 0.032 1.00 20.00 +HETATM 5 C5 UNK 1 -0.050 3.840 0.022 1.00 20.00 +HETATM 6 C6 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 7 C7 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 8 C8 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 9 C9 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 10 C10 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 11 O11 UNK 1 -1.324 5.983 0.590 1.00 20.00 +HETATM 12 O12 UNK 1 1.175 6.017 0.568 1.00 20.00 +HETATM 13 C13 UNK 1 -1.174 6.273 -3.766 1.00 20.00 +HETATM 14 C14 UNK 1 -2.481 5.827 -4.424 1.00 20.00 +HETATM 15 C15 UNK 1 -2.500 6.281 -5.861 1.00 20.00 +HETATM 16 C16 UNK 1 -3.031 7.515 -6.190 1.00 20.00 +HETATM 17 C17 UNK 1 -3.044 7.933 -7.507 1.00 20.00 +HETATM 18 C18 UNK 1 -2.535 7.113 -8.497 1.00 20.00 +HETATM 19 C19 UNK 1 -2.009 5.878 -8.170 1.00 20.00 +HETATM 20 C20 UNK 1 -1.992 5.462 -6.852 1.00 20.00 +HETATM 21 H21 UNK 1 0.657 6.596 -1.909 1.00 20.00 +HETATM 22 H22 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 23 H23 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 24 H24 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 25 H25 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 26 H26 UNK 1 -2.180 3.660 0.041 1.00 20.00 +HETATM 27 H27 UNK 1 -1.100 7.360 -3.805 1.00 20.00 +HETATM 28 H28 UNK 1 -0.331 5.832 -4.297 1.00 20.00 +HETATM 29 H29 UNK 1 -2.556 4.741 -4.386 1.00 20.00 +HETATM 30 H30 UNK 1 -3.325 6.268 -3.893 1.00 20.00 +HETATM 31 H31 UNK 1 -3.432 8.153 -5.416 1.00 20.00 +HETATM 32 H32 UNK 1 -3.455 8.898 -7.763 1.00 20.00 +HETATM 33 H33 UNK 1 -2.549 7.438 -9.527 1.00 20.00 +HETATM 34 H34 UNK 1 -1.612 5.237 -8.943 1.00 20.00 +HETATM 35 H35 UNK 1 -1.581 4.496 -6.595 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 13 +CONECT 3 2 4 21 +CONECT 4 3 5 11 12 +CONECT 5 4 10 6 +CONECT 6 5 7 22 +CONECT 7 6 8 23 +CONECT 8 7 9 24 +CONECT 9 8 10 25 +CONECT 10 9 5 26 +CONECT 11 4 +CONECT 12 4 +CONECT 13 2 14 27 28 +CONECT 14 13 15 29 30 +CONECT 15 14 20 16 +CONECT 16 15 17 31 +CONECT 17 16 18 32 +CONECT 18 17 19 33 +CONECT 19 18 20 34 +CONECT 20 19 15 35 +CONECT 21 3 +CONECT 22 6 +CONECT 23 7 +CONECT 24 8 +CONECT 25 9 +CONECT 26 10 +CONECT 27 13 +CONECT 28 13 +CONECT 29 14 +CONECT 30 14 +CONECT 31 16 +CONECT 32 17 +CONECT 33 18 +CONECT 34 19 +CONECT 35 20 +END diff --git a/top/gaff/SM26/SM26.pdb b/top/gaff/SM26/SM26.pdb deleted file mode 120000 index 09329c9..0000000 --- a/top/gaff/SM26/SM26.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM26/SM26.pdb \ No newline at end of file diff --git a/top/gaff/SM26/SM26.pdb b/top/gaff/SM26/SM26.pdb new file mode 100644 index 0000000..5776ab0 --- /dev/null +++ b/top/gaff/SM26/SM26.pdb @@ -0,0 +1,60 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM26 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -1.354 8.158 -0.892 1.00 20.00 +HETATM 2 S2 UNK 1 -0.115 7.680 -1.396 1.00 20.00 +HETATM 3 C3 UNK 1 -0.090 5.866 -1.407 1.00 20.00 +HETATM 4 C4 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 5 C5 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 6 C6 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 7 C7 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 8 C8 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 9 C9 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 10 C10 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 11 N11 UNK 1 -0.134 8.102 -2.997 1.00 20.00 +HETATM 12 C12 UNK 1 -1.195 7.783 -3.765 1.00 20.00 +HETATM 13 C13 UNK 1 -1.213 8.168 -5.222 1.00 20.00 +HETATM 14 O14 UNK 1 -2.134 7.186 -3.284 1.00 20.00 +HETATM 15 O15 UNK 1 1.120 8.192 -0.913 1.00 20.00 +HETATM 16 H16 UNK 1 0.800 5.518 -1.931 1.00 20.00 +HETATM 17 H17 UNK 1 -0.980 5.493 -1.915 1.00 20.00 +HETATM 18 H18 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 19 H19 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 20 H20 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 21 H21 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 22 H22 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 23 H23 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 24 H24 UNK 1 -2.180 3.660 0.041 1.00 20.00 +HETATM 25 H25 UNK 1 0.617 8.580 -3.382 1.00 20.00 +HETATM 26 H26 UNK 1 -0.369 7.703 -5.731 1.00 20.00 +HETATM 27 H27 UNK 1 -2.144 7.828 -5.676 1.00 20.00 +HETATM 28 H28 UNK 1 -1.139 9.252 -5.313 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 11 15 +CONECT 3 2 4 16 17 +CONECT 4 3 5 18 19 +CONECT 5 4 10 6 +CONECT 6 5 7 20 +CONECT 7 6 8 21 +CONECT 8 7 9 22 +CONECT 9 8 10 23 +CONECT 10 9 5 24 +CONECT 11 2 12 25 +CONECT 12 11 13 14 +CONECT 13 12 26 27 28 +CONECT 14 12 +CONECT 15 2 +CONECT 16 3 +CONECT 17 3 +CONECT 18 4 +CONECT 19 4 +CONECT 20 6 +CONECT 21 7 +CONECT 22 8 +CONECT 23 9 +CONECT 24 10 +CONECT 25 11 +CONECT 26 13 +CONECT 27 13 +CONECT 28 13 +END diff --git a/top/gaff/SM27/SM27.pdb b/top/gaff/SM27/SM27.pdb deleted file mode 120000 index fed8a0a..0000000 --- a/top/gaff/SM27/SM27.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM27/SM27.pdb \ No newline at end of file diff --git a/top/gaff/SM27/SM27.pdb b/top/gaff/SM27/SM27.pdb new file mode 100644 index 0000000..4d28d81 --- /dev/null +++ b/top/gaff/SM27/SM27.pdb @@ -0,0 +1,72 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM27 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 0.323 2.710 -4.448 1.00 20.00 +HETATM 2 S2 UNK 1 -0.793 2.520 -3.589 1.00 20.00 +HETATM 3 C3 UNK 1 -1.628 4.098 -3.273 1.00 20.00 +HETATM 4 C4 UNK 1 -2.295 4.590 -4.559 1.00 20.00 +HETATM 5 C5 UNK 1 -2.989 5.901 -4.296 1.00 20.00 +HETATM 6 C6 UNK 1 -4.310 5.915 -3.887 1.00 20.00 +HETATM 7 C7 UNK 1 -4.945 7.117 -3.641 1.00 20.00 +HETATM 8 C8 UNK 1 -4.263 8.307 -3.814 1.00 20.00 +HETATM 9 C9 UNK 1 -2.944 8.294 -4.228 1.00 20.00 +HETATM 10 C10 UNK 1 -2.307 7.091 -4.469 1.00 20.00 +HETATM 11 N11 UNK 1 -0.122 2.108 -2.132 1.00 20.00 +HETATM 12 C12 UNK 1 -0.982 1.880 -0.968 1.00 20.00 +HETATM 13 C13 UNK 1 -2.240 1.074 -1.300 1.00 20.00 +HETATM 14 C14 UNK 1 -0.227 1.370 0.273 1.00 20.00 +HETATM 15 O15 UNK 1 -1.030 2.311 1.013 1.00 20.00 +HETATM 16 C16 UNK 1 -1.258 3.149 -0.140 1.00 20.00 +HETATM 17 O17 UNK 1 -1.744 1.494 -3.840 1.00 20.00 +HETATM 18 H18 UNK 1 -2.386 3.960 -2.501 1.00 20.00 +HETATM 19 H19 UNK 1 -0.898 4.835 -2.938 1.00 20.00 +HETATM 20 H20 UNK 1 -1.538 4.728 -5.331 1.00 20.00 +HETATM 21 H21 UNK 1 -3.025 3.853 -4.894 1.00 20.00 +HETATM 22 H22 UNK 1 -4.844 4.985 -3.756 1.00 20.00 +HETATM 23 H23 UNK 1 -5.975 7.128 -3.317 1.00 20.00 +HETATM 24 H24 UNK 1 -4.760 9.247 -3.625 1.00 20.00 +HETATM 25 H25 UNK 1 -2.411 9.224 -4.364 1.00 20.00 +HETATM 26 H26 UNK 1 -1.277 7.081 -4.793 1.00 20.00 +HETATM 27 H27 UNK 1 0.840 2.017 -2.049 1.00 20.00 +HETATM 28 H28 UNK 1 -2.870 1.003 -0.414 1.00 20.00 +HETATM 29 H29 UNK 1 -2.791 1.572 -2.098 1.00 20.00 +HETATM 30 H30 UNK 1 -1.955 0.074 -1.625 1.00 20.00 +HETATM 31 H31 UNK 1 -0.431 0.328 0.517 1.00 20.00 +HETATM 32 H32 UNK 1 0.837 1.606 0.270 1.00 20.00 +HETATM 33 H33 UNK 1 -0.509 3.931 -0.269 1.00 20.00 +HETATM 34 H34 UNK 1 -2.279 3.519 -0.227 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 11 17 +CONECT 3 2 4 18 19 +CONECT 4 3 5 20 21 +CONECT 5 4 10 6 +CONECT 6 5 7 22 +CONECT 7 6 8 23 +CONECT 8 7 9 24 +CONECT 9 8 10 25 +CONECT 10 9 5 26 +CONECT 11 2 12 27 +CONECT 12 11 16 13 14 +CONECT 13 12 28 29 30 +CONECT 14 12 15 31 32 +CONECT 15 14 16 +CONECT 16 15 12 33 34 +CONECT 17 2 +CONECT 18 3 +CONECT 19 3 +CONECT 20 4 +CONECT 21 4 +CONECT 22 6 +CONECT 23 7 +CONECT 24 8 +CONECT 25 9 +CONECT 26 10 +CONECT 27 11 +CONECT 28 13 +CONECT 29 13 +CONECT 30 13 +CONECT 31 14 +CONECT 32 14 +CONECT 33 16 +CONECT 34 16 +END diff --git a/top/gaff/SM28/SM28.pdb b/top/gaff/SM28/SM28.pdb deleted file mode 120000 index 8cf1b01..0000000 --- a/top/gaff/SM28/SM28.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM28/SM28.pdb \ No newline at end of file diff --git a/top/gaff/SM28/SM28.pdb b/top/gaff/SM28/SM28.pdb new file mode 100644 index 0000000..775cb83 --- /dev/null +++ b/top/gaff/SM28/SM28.pdb @@ -0,0 +1,74 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM28 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -0.501 6.510 0.434 1.00 20.00 +HETATM 2 S2 UNK 1 -1.279 5.630 1.234 1.00 20.00 +HETATM 3 C3 UNK 1 -2.325 4.524 0.247 1.00 20.00 +HETATM 4 C4 UNK 1 -1.116 3.626 -0.023 1.00 20.00 +HETATM 5 N5 UNK 1 -1.469 2.211 -0.165 1.00 20.00 +HETATM 6 C6 UNK 1 -2.244 1.809 -1.192 1.00 20.00 +HETATM 7 C7 UNK 1 -2.515 0.342 -1.403 1.00 20.00 +HETATM 8 O8 UNK 1 -2.726 2.629 -1.944 1.00 20.00 +HETATM 9 C9 UNK 1 -0.238 4.127 -1.172 1.00 20.00 +HETATM 10 C10 UNK 1 1.000 3.236 -1.295 1.00 20.00 +HETATM 11 C11 UNK 1 1.804 3.657 -2.498 1.00 20.00 +HETATM 12 C12 UNK 1 1.557 3.080 -3.730 1.00 20.00 +HETATM 13 C13 UNK 1 2.291 3.469 -4.835 1.00 20.00 +HETATM 14 C14 UNK 1 3.279 4.427 -4.706 1.00 20.00 +HETATM 15 C15 UNK 1 3.529 5.000 -3.473 1.00 20.00 +HETATM 16 C16 UNK 1 2.791 4.615 -2.369 1.00 20.00 +HETATM 17 C17 UNK 1 -0.555 3.970 1.358 1.00 20.00 +HETATM 18 O18 UNK 1 -1.905 6.048 2.439 1.00 20.00 +HETATM 19 H19 UNK 1 -2.717 4.996 -0.654 1.00 20.00 +HETATM 20 H20 UNK 1 -3.101 4.032 0.833 1.00 20.00 +HETATM 21 H21 UNK 1 -1.146 1.563 0.481 1.00 20.00 +HETATM 22 H22 UNK 1 -1.751 -0.078 -2.058 1.00 20.00 +HETATM 23 H23 UNK 1 -2.493 -0.173 -0.442 1.00 20.00 +HETATM 24 H24 UNK 1 -3.496 0.216 -1.860 1.00 20.00 +HETATM 25 H25 UNK 1 -0.804 4.094 -2.103 1.00 20.00 +HETATM 26 H26 UNK 1 0.072 5.153 -0.971 1.00 20.00 +HETATM 27 H27 UNK 1 1.610 3.336 -0.397 1.00 20.00 +HETATM 28 H28 UNK 1 0.689 2.198 -1.410 1.00 20.00 +HETATM 29 H29 UNK 1 0.788 2.328 -3.830 1.00 20.00 +HETATM 30 H30 UNK 1 2.096 3.021 -5.798 1.00 20.00 +HETATM 31 H31 UNK 1 3.856 4.728 -5.568 1.00 20.00 +HETATM 32 H32 UNK 1 4.301 5.749 -3.372 1.00 20.00 +HETATM 33 H33 UNK 1 2.987 5.062 -1.406 1.00 20.00 +HETATM 34 H34 UNK 1 -0.991 3.372 2.159 1.00 20.00 +HETATM 35 H35 UNK 1 0.534 3.979 1.389 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 17 18 +CONECT 3 2 4 19 20 +CONECT 4 3 17 5 9 +CONECT 5 4 6 21 +CONECT 6 5 7 8 +CONECT 7 6 22 23 24 +CONECT 8 6 +CONECT 9 4 10 25 26 +CONECT 10 9 11 27 28 +CONECT 11 10 16 12 +CONECT 12 11 13 29 +CONECT 13 12 14 30 +CONECT 14 13 15 31 +CONECT 15 14 16 32 +CONECT 16 15 11 33 +CONECT 17 2 4 34 35 +CONECT 18 2 +CONECT 19 3 +CONECT 20 3 +CONECT 21 5 +CONECT 22 7 +CONECT 23 7 +CONECT 24 7 +CONECT 25 9 +CONECT 26 9 +CONECT 27 10 +CONECT 28 10 +CONECT 29 12 +CONECT 30 13 +CONECT 31 14 +CONECT 32 15 +CONECT 33 16 +CONECT 34 17 +CONECT 35 17 +END diff --git a/top/gaff/SM29/SM29.pdb b/top/gaff/SM29/SM29.pdb deleted file mode 120000 index b808e75..0000000 --- a/top/gaff/SM29/SM29.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM29/SM29.pdb \ No newline at end of file diff --git a/top/gaff/SM29/SM29.pdb b/top/gaff/SM29/SM29.pdb new file mode 100644 index 0000000..f50780d --- /dev/null +++ b/top/gaff/SM29/SM29.pdb @@ -0,0 +1,72 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM29 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 0.736 1.532 2.891 1.00 20.00 +HETATM 2 S2 UNK 1 1.137 -0.182 2.450 1.00 20.00 +HETATM 3 N3 UNK 1 -0.204 -0.726 1.645 1.00 20.00 +HETATM 4 C4 UNK 1 -0.559 -0.154 0.344 1.00 20.00 +HETATM 5 C5 UNK 1 -0.688 1.381 0.354 1.00 20.00 +HETATM 6 O6 UNK 1 0.705 1.388 -0.015 1.00 20.00 +HETATM 7 C7 UNK 1 0.646 0.066 -0.589 1.00 20.00 +HETATM 8 C8 UNK 1 -1.736 -0.868 -0.324 1.00 20.00 +HETATM 9 C9 UNK 1 -1.568 -2.381 -0.169 1.00 20.00 +HETATM 10 C10 UNK 1 -2.727 -3.084 -0.827 1.00 20.00 +HETATM 11 C11 UNK 1 -3.865 -3.374 -0.097 1.00 20.00 +HETATM 12 C12 UNK 1 -4.930 -4.015 -0.702 1.00 20.00 +HETATM 13 C13 UNK 1 -4.853 -4.376 -2.034 1.00 20.00 +HETATM 14 C14 UNK 1 -3.713 -4.091 -2.763 1.00 20.00 +HETATM 15 C15 UNK 1 -2.651 -3.445 -2.160 1.00 20.00 +HETATM 16 O16 UNK 1 1.201 -0.994 3.615 1.00 20.00 +HETATM 17 O17 UNK 1 2.170 -0.217 1.475 1.00 20.00 +HETATM 18 H18 UNK 1 -0.232 1.561 3.392 1.00 20.00 +HETATM 19 H19 UNK 1 1.503 1.924 3.559 1.00 20.00 +HETATM 20 H20 UNK 1 0.696 2.139 1.987 1.00 20.00 +HETATM 21 H21 UNK 1 -0.753 -1.424 2.035 1.00 20.00 +HETATM 22 H22 UNK 1 -1.351 1.773 -0.417 1.00 20.00 +HETATM 23 H23 UNK 1 -0.885 1.801 1.341 1.00 20.00 +HETATM 24 H24 UNK 1 1.508 -0.557 -0.351 1.00 20.00 +HETATM 25 H25 UNK 1 0.391 0.055 -1.649 1.00 20.00 +HETATM 26 H26 UNK 1 -2.667 -0.555 0.149 1.00 20.00 +HETATM 27 H27 UNK 1 -1.763 -0.612 -1.383 1.00 20.00 +HETATM 28 H28 UNK 1 -0.637 -2.694 -0.642 1.00 20.00 +HETATM 29 H29 UNK 1 -1.542 -2.637 0.890 1.00 20.00 +HETATM 30 H30 UNK 1 -3.923 -3.096 0.945 1.00 20.00 +HETATM 31 H31 UNK 1 -5.820 -4.238 -0.133 1.00 20.00 +HETATM 32 H32 UNK 1 -5.683 -4.881 -2.506 1.00 20.00 +HETATM 33 H33 UNK 1 -3.653 -4.373 -3.804 1.00 20.00 +HETATM 34 H34 UNK 1 -1.760 -3.223 -2.729 1.00 20.00 +CONECT 1 2 18 19 20 +CONECT 2 1 3 16 17 +CONECT 3 2 4 21 +CONECT 4 3 7 5 8 +CONECT 5 4 6 22 23 +CONECT 6 5 7 +CONECT 7 6 4 24 25 +CONECT 8 4 9 26 27 +CONECT 9 8 10 28 29 +CONECT 10 9 15 11 +CONECT 11 10 12 30 +CONECT 12 11 13 31 +CONECT 13 12 14 32 +CONECT 14 13 15 33 +CONECT 15 14 10 34 +CONECT 16 2 +CONECT 17 2 +CONECT 18 1 +CONECT 19 1 +CONECT 20 1 +CONECT 21 3 +CONECT 22 5 +CONECT 23 5 +CONECT 24 7 +CONECT 25 7 +CONECT 26 8 +CONECT 27 8 +CONECT 28 9 +CONECT 29 9 +CONECT 30 11 +CONECT 31 12 +CONECT 32 13 +CONECT 33 14 +CONECT 34 15 +END diff --git a/top/gaff/SM30/SM30.pdb b/top/gaff/SM30/SM30.pdb deleted file mode 120000 index a1fc3b4..0000000 --- a/top/gaff/SM30/SM30.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM30/SM30.pdb \ No newline at end of file diff --git a/top/gaff/SM30/SM30.pdb b/top/gaff/SM30/SM30.pdb new file mode 100644 index 0000000..f21c886 --- /dev/null +++ b/top/gaff/SM30/SM30.pdb @@ -0,0 +1,86 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM30 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 1.173 6.124 0.486 1.00 20.00 +HETATM 2 S2 UNK 1 -0.134 5.758 0.065 1.00 20.00 +HETATM 3 N3 UNK 1 -0.181 5.995 -1.574 1.00 20.00 +HETATM 4 C4 UNK 1 -1.400 5.686 -2.324 1.00 20.00 +HETATM 5 C5 UNK 1 -2.692 6.178 -1.643 1.00 20.00 +HETATM 6 O6 UNK 1 -2.730 4.874 -1.028 1.00 20.00 +HETATM 7 C7 UNK 1 -1.942 4.266 -2.072 1.00 20.00 +HETATM 8 C8 UNK 1 -1.300 6.054 -3.806 1.00 20.00 +HETATM 9 C9 UNK 1 -0.688 7.450 -3.944 1.00 20.00 +HETATM 10 C10 UNK 1 -0.590 7.813 -5.403 1.00 20.00 +HETATM 11 C11 UNK 1 0.551 7.500 -6.118 1.00 20.00 +HETATM 12 C12 UNK 1 0.640 7.829 -7.457 1.00 20.00 +HETATM 13 C13 UNK 1 -0.409 8.480 -8.080 1.00 20.00 +HETATM 14 C14 UNK 1 -1.548 8.798 -7.363 1.00 20.00 +HETATM 15 C15 UNK 1 -1.638 8.464 -6.025 1.00 20.00 +HETATM 16 C16 UNK 1 -1.236 6.924 0.793 1.00 20.00 +HETATM 17 C17 UNK 1 -2.513 6.536 1.153 1.00 20.00 +HETATM 18 C18 UNK 1 -3.378 7.451 1.724 1.00 20.00 +HETATM 19 C19 UNK 1 -2.966 8.754 1.935 1.00 20.00 +HETATM 20 C20 UNK 1 -1.690 9.143 1.570 1.00 20.00 +HETATM 21 C21 UNK 1 -0.824 8.227 1.003 1.00 20.00 +HETATM 22 O22 UNK 1 -0.695 4.474 0.300 1.00 20.00 +HETATM 23 H23 UNK 1 0.599 6.340 -2.036 1.00 20.00 +HETATM 24 H24 UNK 1 -2.535 6.994 -0.938 1.00 20.00 +HETATM 25 H25 UNK 1 -3.512 6.362 -2.336 1.00 20.00 +HETATM 26 H26 UNK 1 -2.534 3.867 -2.895 1.00 20.00 +HETATM 27 H27 UNK 1 -1.190 3.565 -1.708 1.00 20.00 +HETATM 28 H28 UNK 1 -0.670 5.329 -4.319 1.00 20.00 +HETATM 29 H29 UNK 1 -2.296 6.049 -4.249 1.00 20.00 +HETATM 30 H30 UNK 1 -1.319 8.176 -3.430 1.00 20.00 +HETATM 31 H31 UNK 1 0.308 7.455 -3.500 1.00 20.00 +HETATM 32 H32 UNK 1 1.372 6.995 -5.630 1.00 20.00 +HETATM 33 H33 UNK 1 1.530 7.581 -8.017 1.00 20.00 +HETATM 34 H34 UNK 1 -0.338 8.741 -9.125 1.00 20.00 +HETATM 35 H35 UNK 1 -2.367 9.307 -7.850 1.00 20.00 +HETATM 36 H36 UNK 1 -2.528 8.713 -5.465 1.00 20.00 +HETATM 37 H37 UNK 1 -2.835 5.519 0.989 1.00 20.00 +HETATM 38 H38 UNK 1 -4.376 7.149 2.005 1.00 20.00 +HETATM 39 H39 UNK 1 -3.642 9.469 2.380 1.00 20.00 +HETATM 40 H40 UNK 1 -1.370 10.161 1.730 1.00 20.00 +HETATM 41 H41 UNK 1 0.173 8.530 0.721 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 16 22 +CONECT 3 2 4 23 +CONECT 4 3 7 5 8 +CONECT 5 4 6 24 25 +CONECT 6 5 7 +CONECT 7 6 4 26 27 +CONECT 8 4 9 28 29 +CONECT 9 8 10 30 31 +CONECT 10 9 15 11 +CONECT 11 10 12 32 +CONECT 12 11 13 33 +CONECT 13 12 14 34 +CONECT 14 13 15 35 +CONECT 15 14 10 36 +CONECT 16 2 21 17 +CONECT 17 16 18 37 +CONECT 18 17 19 38 +CONECT 19 18 20 39 +CONECT 20 19 21 40 +CONECT 21 20 16 41 +CONECT 22 2 +CONECT 23 3 +CONECT 24 5 +CONECT 25 5 +CONECT 26 7 +CONECT 27 7 +CONECT 28 8 +CONECT 29 8 +CONECT 30 9 +CONECT 31 9 +CONECT 32 11 +CONECT 33 12 +CONECT 34 13 +CONECT 35 14 +CONECT 36 15 +CONECT 37 17 +CONECT 38 18 +CONECT 39 19 +CONECT 40 20 +CONECT 41 21 +END diff --git a/top/gaff/SM31/SM31.pdb b/top/gaff/SM31/SM31.pdb deleted file mode 120000 index 7e40e39..0000000 --- a/top/gaff/SM31/SM31.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM31/SM31.pdb \ No newline at end of file diff --git a/top/gaff/SM31/SM31.pdb b/top/gaff/SM31/SM31.pdb new file mode 100644 index 0000000..37a46d5 --- /dev/null +++ b/top/gaff/SM31/SM31.pdb @@ -0,0 +1,82 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM31 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 0.151 6.505 2.626 1.00 20.00 +HETATM 2 S2 UNK 1 0.479 6.009 1.335 1.00 20.00 +HETATM 3 N3 UNK 1 0.581 4.363 1.479 1.00 20.00 +HETATM 4 C4 UNK 1 1.206 3.572 0.416 1.00 20.00 +HETATM 5 C5 UNK 1 0.480 3.664 -0.939 1.00 20.00 +HETATM 6 O6 UNK 1 1.376 4.758 -1.217 1.00 20.00 +HETATM 7 C7 UNK 1 2.373 4.288 -0.288 1.00 20.00 +HETATM 8 C8 UNK 1 1.529 2.140 0.848 1.00 20.00 +HETATM 9 C9 UNK 1 0.307 1.525 1.533 1.00 20.00 +HETATM 10 C10 UNK 1 0.626 0.115 1.958 1.00 20.00 +HETATM 11 C11 UNK 1 0.379 -0.939 1.098 1.00 20.00 +HETATM 12 C12 UNK 1 0.676 -2.232 1.486 1.00 20.00 +HETATM 13 C13 UNK 1 1.210 -2.472 2.738 1.00 20.00 +HETATM 14 C14 UNK 1 1.452 -1.419 3.600 1.00 20.00 +HETATM 15 C15 UNK 1 1.160 -0.126 3.210 1.00 20.00 +HETATM 16 N16 UNK 1 -0.823 6.336 0.365 1.00 20.00 +HETATM 17 C17 UNK 1 -2.179 6.294 0.919 1.00 20.00 +HETATM 18 C18 UNK 1 -0.619 6.668 -1.047 1.00 20.00 +HETATM 19 O19 UNK 1 1.631 6.421 0.613 1.00 20.00 +HETATM 20 H20 UNK 1 0.227 3.922 2.268 1.00 20.00 +HETATM 21 H21 UNK 1 0.632 2.796 -1.581 1.00 20.00 +HETATM 22 H22 UNK 1 -0.566 3.959 -0.861 1.00 20.00 +HETATM 23 H23 UNK 1 2.829 5.079 0.308 1.00 20.00 +HETATM 24 H24 UNK 1 3.105 3.611 -0.728 1.00 20.00 +HETATM 25 H25 UNK 1 2.368 2.151 1.543 1.00 20.00 +HETATM 26 H26 UNK 1 1.792 1.547 -0.028 1.00 20.00 +HETATM 27 H27 UNK 1 -0.532 1.514 0.837 1.00 20.00 +HETATM 28 H28 UNK 1 0.045 2.118 2.409 1.00 20.00 +HETATM 29 H29 UNK 1 -0.042 -0.752 0.121 1.00 20.00 +HETATM 30 H30 UNK 1 0.487 -3.055 0.812 1.00 20.00 +HETATM 31 H31 UNK 1 1.438 -3.483 3.043 1.00 20.00 +HETATM 32 H32 UNK 1 1.869 -1.607 4.578 1.00 20.00 +HETATM 33 H33 UNK 1 1.349 0.697 3.883 1.00 20.00 +HETATM 34 H34 UNK 1 -2.263 7.021 1.727 1.00 20.00 +HETATM 35 H35 UNK 1 -2.898 6.535 0.137 1.00 20.00 +HETATM 36 H36 UNK 1 -2.382 5.296 1.305 1.00 20.00 +HETATM 37 H37 UNK 1 -0.737 5.769 -1.652 1.00 20.00 +HETATM 38 H38 UNK 1 -1.352 7.413 -1.356 1.00 20.00 +HETATM 39 H39 UNK 1 0.386 7.069 -1.185 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 16 19 +CONECT 3 2 4 20 +CONECT 4 3 7 5 8 +CONECT 5 4 6 21 22 +CONECT 6 5 7 +CONECT 7 6 4 23 24 +CONECT 8 4 9 25 26 +CONECT 9 8 10 27 28 +CONECT 10 9 15 11 +CONECT 11 10 12 29 +CONECT 12 11 13 30 +CONECT 13 12 14 31 +CONECT 14 13 15 32 +CONECT 15 14 10 33 +CONECT 16 2 17 18 +CONECT 17 16 34 35 36 +CONECT 18 16 37 38 39 +CONECT 19 2 +CONECT 20 3 +CONECT 21 5 +CONECT 22 5 +CONECT 23 7 +CONECT 24 7 +CONECT 25 8 +CONECT 26 8 +CONECT 27 9 +CONECT 28 9 +CONECT 29 11 +CONECT 30 12 +CONECT 31 13 +CONECT 32 14 +CONECT 33 15 +CONECT 34 17 +CONECT 35 17 +CONECT 36 17 +CONECT 37 18 +CONECT 38 18 +CONECT 39 18 +END diff --git a/top/gaff/SM32/SM32.pdb b/top/gaff/SM32/SM32.pdb deleted file mode 120000 index 83bdf1d..0000000 --- a/top/gaff/SM32/SM32.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM32/SM32.pdb \ No newline at end of file diff --git a/top/gaff/SM32/SM32.pdb b/top/gaff/SM32/SM32.pdb new file mode 100644 index 0000000..886e147 --- /dev/null +++ b/top/gaff/SM32/SM32.pdb @@ -0,0 +1,72 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM32 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 0.690 -0.371 0.486 1.00 20.00 +HETATM 2 S2 UNK 1 0.078 1.288 0.080 1.00 20.00 +HETATM 3 N3 UNK 1 -0.196 1.998 1.551 1.00 20.00 +HETATM 4 C4 UNK 1 -1.243 1.477 2.432 1.00 20.00 +HETATM 5 C5 UNK 1 -1.188 -0.043 2.599 1.00 20.00 +HETATM 6 S6 UNK 1 -2.089 -0.244 1.038 1.00 20.00 +HETATM 7 C7 UNK 1 -2.602 1.348 1.741 1.00 20.00 +HETATM 8 C8 UNK 1 -1.315 2.228 3.764 1.00 20.00 +HETATM 9 C9 UNK 1 0.098 2.415 4.320 1.00 20.00 +HETATM 10 C10 UNK 1 0.028 3.154 5.632 1.00 20.00 +HETATM 11 C11 UNK 1 0.093 4.534 5.651 1.00 20.00 +HETATM 12 C12 UNK 1 0.023 5.213 6.854 1.00 20.00 +HETATM 13 C13 UNK 1 -0.100 4.510 8.038 1.00 20.00 +HETATM 14 C14 UNK 1 -0.160 3.129 8.018 1.00 20.00 +HETATM 15 C15 UNK 1 -0.096 2.451 6.815 1.00 20.00 +HETATM 16 O16 UNK 1 1.111 2.072 -0.501 1.00 20.00 +HETATM 17 O17 UNK 1 -1.209 1.212 -0.518 1.00 20.00 +HETATM 18 H18 UNK 1 1.422 -0.301 1.291 1.00 20.00 +HETATM 19 H19 UNK 1 -0.143 -0.997 0.805 1.00 20.00 +HETATM 20 H20 UNK 1 1.159 -0.811 -0.394 1.00 20.00 +HETATM 21 H21 UNK 1 0.338 2.760 1.828 1.00 20.00 +HETATM 22 H22 UNK 1 -0.174 -0.441 2.563 1.00 20.00 +HETATM 23 H23 UNK 1 -1.745 -0.399 3.465 1.00 20.00 +HETATM 24 H24 UNK 1 -3.433 1.260 2.441 1.00 20.00 +HETATM 25 H25 UNK 1 -2.773 2.115 0.985 1.00 20.00 +HETATM 26 H26 UNK 1 -1.775 3.203 3.607 1.00 20.00 +HETATM 27 H27 UNK 1 -1.911 1.654 4.473 1.00 20.00 +HETATM 28 H28 UNK 1 0.559 1.439 4.477 1.00 20.00 +HETATM 29 H29 UNK 1 0.695 2.988 3.611 1.00 20.00 +HETATM 30 H30 UNK 1 0.194 5.083 4.727 1.00 20.00 +HETATM 31 H31 UNK 1 0.071 6.291 6.869 1.00 20.00 +HETATM 32 H32 UNK 1 -0.150 5.039 8.977 1.00 20.00 +HETATM 33 H33 UNK 1 -0.257 2.579 8.943 1.00 20.00 +HETATM 34 H34 UNK 1 -0.142 1.372 6.801 1.00 20.00 +CONECT 1 2 18 19 20 +CONECT 2 1 3 16 17 +CONECT 3 2 4 21 +CONECT 4 3 7 5 8 +CONECT 5 4 6 22 23 +CONECT 6 5 7 +CONECT 7 6 4 24 25 +CONECT 8 4 9 26 27 +CONECT 9 8 10 28 29 +CONECT 10 9 15 11 +CONECT 11 10 12 30 +CONECT 12 11 13 31 +CONECT 13 12 14 32 +CONECT 14 13 15 33 +CONECT 15 14 10 34 +CONECT 16 2 +CONECT 17 2 +CONECT 18 1 +CONECT 19 1 +CONECT 20 1 +CONECT 21 3 +CONECT 22 5 +CONECT 23 5 +CONECT 24 7 +CONECT 25 7 +CONECT 26 8 +CONECT 27 8 +CONECT 28 9 +CONECT 29 9 +CONECT 30 11 +CONECT 31 12 +CONECT 32 13 +CONECT 33 14 +CONECT 34 15 +END diff --git a/top/gaff/SM33/SM33.pdb b/top/gaff/SM33/SM33.pdb deleted file mode 120000 index d26e3c6..0000000 --- a/top/gaff/SM33/SM33.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM33/SM33.pdb \ No newline at end of file diff --git a/top/gaff/SM33/SM33.pdb b/top/gaff/SM33/SM33.pdb new file mode 100644 index 0000000..307d504 --- /dev/null +++ b/top/gaff/SM33/SM33.pdb @@ -0,0 +1,86 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM33 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -1.394 6.419 0.477 1.00 20.00 +HETATM 2 S2 UNK 1 -0.157 5.835 0.091 1.00 20.00 +HETATM 3 N3 UNK 1 0.029 6.159 -1.522 1.00 20.00 +HETATM 4 C4 UNK 1 -1.098 5.980 -2.441 1.00 20.00 +HETATM 5 C5 UNK 1 -2.411 6.551 -1.900 1.00 20.00 +HETATM 6 S6 UNK 1 -2.668 5.038 -0.933 1.00 20.00 +HETATM 7 C7 UNK 1 -1.696 4.572 -2.393 1.00 20.00 +HETATM 8 C8 UNK 1 -0.777 6.449 -3.861 1.00 20.00 +HETATM 9 C9 UNK 1 -0.076 7.807 -3.803 1.00 20.00 +HETATM 10 C10 UNK 1 0.241 8.269 -5.202 1.00 20.00 +HETATM 11 C11 UNK 1 1.450 7.935 -5.783 1.00 20.00 +HETATM 12 C12 UNK 1 1.739 8.355 -7.068 1.00 20.00 +HETATM 13 C13 UNK 1 0.823 9.117 -7.769 1.00 20.00 +HETATM 14 C14 UNK 1 -0.384 9.455 -7.186 1.00 20.00 +HETATM 15 C15 UNK 1 -0.675 9.031 -5.903 1.00 20.00 +HETATM 16 C16 UNK 1 -0.359 4.092 0.253 1.00 20.00 +HETATM 17 C17 UNK 1 0.614 3.236 -0.228 1.00 20.00 +HETATM 18 C18 UNK 1 0.457 1.869 -0.100 1.00 20.00 +HETATM 19 C19 UNK 1 -0.673 1.357 0.510 1.00 20.00 +HETATM 20 C20 UNK 1 -1.649 2.213 0.986 1.00 20.00 +HETATM 21 C21 UNK 1 -1.489 3.581 0.862 1.00 20.00 +HETATM 22 O22 UNK 1 1.081 6.155 0.710 1.00 20.00 +HETATM 23 H23 UNK 1 0.885 6.467 -1.860 1.00 20.00 +HETATM 24 H24 UNK 1 -2.270 7.437 -1.280 1.00 20.00 +HETATM 25 H25 UNK 1 -3.165 6.699 -2.674 1.00 20.00 +HETATM 26 H26 UNK 1 -2.312 4.338 -3.261 1.00 20.00 +HETATM 27 H27 UNK 1 -0.956 3.799 -2.185 1.00 20.00 +HETATM 28 H28 UNK 1 -0.123 5.723 -4.344 1.00 20.00 +HETATM 29 H29 UNK 1 -1.701 6.541 -4.431 1.00 20.00 +HETATM 30 H30 UNK 1 -0.730 8.533 -3.320 1.00 20.00 +HETATM 31 H31 UNK 1 0.849 7.715 -3.233 1.00 20.00 +HETATM 32 H32 UNK 1 2.168 7.344 -5.234 1.00 20.00 +HETATM 33 H33 UNK 1 2.682 8.091 -7.523 1.00 20.00 +HETATM 34 H34 UNK 1 1.050 9.448 -8.771 1.00 20.00 +HETATM 35 H35 UNK 1 -1.100 10.050 -7.733 1.00 20.00 +HETATM 36 H36 UNK 1 -1.618 9.295 -5.448 1.00 20.00 +HETATM 37 H37 UNK 1 1.498 3.636 -0.704 1.00 20.00 +HETATM 38 H38 UNK 1 1.217 1.200 -0.476 1.00 20.00 +HETATM 39 H39 UNK 1 -0.796 0.289 0.610 1.00 20.00 +HETATM 40 H40 UNK 1 -2.534 1.814 1.459 1.00 20.00 +HETATM 41 H41 UNK 1 -2.250 4.249 1.238 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 16 22 +CONECT 3 2 4 23 +CONECT 4 3 7 5 8 +CONECT 5 4 6 24 25 +CONECT 6 5 7 +CONECT 7 6 4 26 27 +CONECT 8 4 9 28 29 +CONECT 9 8 10 30 31 +CONECT 10 9 15 11 +CONECT 11 10 12 32 +CONECT 12 11 13 33 +CONECT 13 12 14 34 +CONECT 14 13 15 35 +CONECT 15 14 10 36 +CONECT 16 2 21 17 +CONECT 17 16 18 37 +CONECT 18 17 19 38 +CONECT 19 18 20 39 +CONECT 20 19 21 40 +CONECT 21 20 16 41 +CONECT 22 2 +CONECT 23 3 +CONECT 24 5 +CONECT 25 5 +CONECT 26 7 +CONECT 27 7 +CONECT 28 8 +CONECT 29 8 +CONECT 30 9 +CONECT 31 9 +CONECT 32 11 +CONECT 33 12 +CONECT 34 13 +CONECT 35 14 +CONECT 36 15 +CONECT 37 17 +CONECT 38 18 +CONECT 39 19 +CONECT 40 20 +CONECT 41 21 +END diff --git a/top/gaff/SM34/SM34.pdb b/top/gaff/SM34/SM34.pdb deleted file mode 120000 index dff5ac3..0000000 --- a/top/gaff/SM34/SM34.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM34/SM34.pdb \ No newline at end of file diff --git a/top/gaff/SM34/SM34.pdb b/top/gaff/SM34/SM34.pdb new file mode 100644 index 0000000..f1b5d5c --- /dev/null +++ b/top/gaff/SM34/SM34.pdb @@ -0,0 +1,82 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM34 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -0.439 0.604 -3.982 1.00 20.00 +HETATM 2 S2 UNK 1 0.321 1.022 -2.856 1.00 20.00 +HETATM 3 N3 UNK 1 1.589 -0.034 -2.729 1.00 20.00 +HETATM 4 C4 UNK 1 2.489 0.038 -1.575 1.00 20.00 +HETATM 5 C5 UNK 1 1.694 -0.098 -0.242 1.00 20.00 +HETATM 6 S6 UNK 1 1.719 1.731 -0.322 1.00 20.00 +HETATM 7 C7 UNK 1 3.128 1.455 -1.458 1.00 20.00 +HETATM 8 C8 UNK 1 3.571 -1.039 -1.675 1.00 20.00 +HETATM 9 C9 UNK 1 4.332 -0.877 -2.993 1.00 20.00 +HETATM 10 C10 UNK 1 5.398 -1.938 -3.091 1.00 20.00 +HETATM 11 C11 UNK 1 6.667 -1.691 -2.602 1.00 20.00 +HETATM 12 C12 UNK 1 7.643 -2.665 -2.688 1.00 20.00 +HETATM 13 C13 UNK 1 7.353 -3.884 -3.273 1.00 20.00 +HETATM 14 C14 UNK 1 6.086 -4.130 -3.766 1.00 20.00 +HETATM 15 C15 UNK 1 5.108 -3.157 -3.676 1.00 20.00 +HETATM 16 N16 UNK 1 0.953 2.503 -3.243 1.00 20.00 +HETATM 17 C17 UNK 1 1.593 2.709 -4.545 1.00 20.00 +HETATM 18 C18 UNK 1 0.874 3.607 -2.284 1.00 20.00 +HETATM 19 O19 UNK 1 -0.229 1.149 -1.552 1.00 20.00 +HETATM 20 H20 UNK 1 1.736 -0.701 -3.417 1.00 20.00 +HETATM 21 H21 UNK 1 2.267 -0.520 0.584 1.00 20.00 +HETATM 22 H22 UNK 1 0.703 -0.540 -0.352 1.00 20.00 +HETATM 23 H23 UNK 1 3.088 2.044 -2.375 1.00 20.00 +HETATM 24 H24 UNK 1 4.105 1.470 -0.975 1.00 20.00 +HETATM 25 H25 UNK 1 4.265 -0.936 -0.840 1.00 20.00 +HETATM 26 H26 UNK 1 3.107 -2.025 -1.642 1.00 20.00 +HETATM 27 H27 UNK 1 3.639 -0.980 -3.827 1.00 20.00 +HETATM 28 H28 UNK 1 4.796 0.108 -3.026 1.00 20.00 +HETATM 29 H29 UNK 1 6.894 -0.737 -2.149 1.00 20.00 +HETATM 30 H30 UNK 1 8.634 -2.473 -2.303 1.00 20.00 +HETATM 31 H31 UNK 1 8.117 -4.644 -3.344 1.00 20.00 +HETATM 32 H32 UNK 1 5.860 -5.082 -4.223 1.00 20.00 +HETATM 33 H33 UNK 1 4.118 -3.349 -4.062 1.00 20.00 +HETATM 34 H34 UNK 1 0.847 3.041 -5.268 1.00 20.00 +HETATM 35 H35 UNK 1 2.372 3.465 -4.452 1.00 20.00 +HETATM 36 H36 UNK 1 2.035 1.772 -4.885 1.00 20.00 +HETATM 37 H37 UNK 1 0.285 3.297 -1.421 1.00 20.00 +HETATM 38 H38 UNK 1 1.878 3.880 -1.960 1.00 20.00 +HETATM 39 H39 UNK 1 0.399 4.466 -2.757 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 16 19 +CONECT 3 2 4 20 +CONECT 4 3 7 5 8 +CONECT 5 4 6 21 22 +CONECT 6 5 7 +CONECT 7 6 4 23 24 +CONECT 8 4 9 25 26 +CONECT 9 8 10 27 28 +CONECT 10 9 15 11 +CONECT 11 10 12 29 +CONECT 12 11 13 30 +CONECT 13 12 14 31 +CONECT 14 13 15 32 +CONECT 15 14 10 33 +CONECT 16 2 17 18 +CONECT 17 16 34 35 36 +CONECT 18 16 37 38 39 +CONECT 19 2 +CONECT 20 3 +CONECT 21 5 +CONECT 22 5 +CONECT 23 7 +CONECT 24 7 +CONECT 25 8 +CONECT 26 8 +CONECT 27 9 +CONECT 28 9 +CONECT 29 11 +CONECT 30 12 +CONECT 31 13 +CONECT 32 14 +CONECT 33 15 +CONECT 34 17 +CONECT 35 17 +CONECT 36 17 +CONECT 37 18 +CONECT 38 18 +CONECT 39 18 +END diff --git a/top/gaff/SM35/SM35.pdb b/top/gaff/SM35/SM35.pdb deleted file mode 120000 index 5100c72..0000000 --- a/top/gaff/SM35/SM35.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM35/SM35.pdb \ No newline at end of file diff --git a/top/gaff/SM35/SM35.pdb b/top/gaff/SM35/SM35.pdb new file mode 100644 index 0000000..30b5e08 --- /dev/null +++ b/top/gaff/SM35/SM35.pdb @@ -0,0 +1,74 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM35 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 -1.467 -1.558 -1.545 1.00 20.00 +HETATM 2 S2 UNK 1 -2.556 -0.193 -2.035 1.00 20.00 +HETATM 3 N3 UNK 1 -2.318 0.963 -0.873 1.00 20.00 +HETATM 4 C4 UNK 1 -0.996 1.572 -0.706 1.00 20.00 +HETATM 5 C5 UNK 1 0.011 0.644 -0.023 1.00 20.00 +HETATM 6 S6 UNK 1 -0.657 1.116 1.597 1.00 20.00 +HETATM 7 O7 UNK 1 -2.019 0.437 1.616 1.00 20.00 +HETATM 8 C8 UNK 1 -0.920 2.527 0.487 1.00 20.00 +HETATM 9 C9 UNK 1 -0.465 2.185 -2.004 1.00 20.00 +HETATM 10 C10 UNK 1 -1.519 3.125 -2.592 1.00 20.00 +HETATM 11 C11 UNK 1 -0.950 3.825 -3.799 1.00 20.00 +HETATM 12 C12 UNK 1 -0.295 5.033 -3.653 1.00 20.00 +HETATM 13 C13 UNK 1 0.231 5.673 -4.760 1.00 20.00 +HETATM 14 C14 UNK 1 0.093 5.109 -6.015 1.00 20.00 +HETATM 15 C15 UNK 1 -0.566 3.903 -6.161 1.00 20.00 +HETATM 16 C16 UNK 1 -1.088 3.261 -5.054 1.00 20.00 +HETATM 17 O17 UNK 1 -3.920 -0.565 -1.885 1.00 20.00 +HETATM 18 O18 UNK 1 -2.089 0.412 -3.233 1.00 20.00 +HETATM 19 H19 UNK 1 -1.649 -1.811 -0.500 1.00 20.00 +HETATM 20 H20 UNK 1 -1.670 -2.428 -2.170 1.00 20.00 +HETATM 21 H21 UNK 1 -0.427 -1.256 -1.670 1.00 20.00 +HETATM 22 H22 UNK 1 -3.054 1.237 -0.304 1.00 20.00 +HETATM 23 H23 UNK 1 -0.145 -0.408 -0.261 1.00 20.00 +HETATM 24 H24 UNK 1 1.046 0.955 -0.166 1.00 20.00 +HETATM 25 H25 UNK 1 -0.065 3.202 0.442 1.00 20.00 +HETATM 26 H26 UNK 1 -1.856 3.053 0.675 1.00 20.00 +HETATM 27 H27 UNK 1 0.446 2.745 -1.795 1.00 20.00 +HETATM 28 H28 UNK 1 -0.247 1.391 -2.718 1.00 20.00 +HETATM 29 H29 UNK 1 -2.397 2.549 -2.885 1.00 20.00 +HETATM 30 H30 UNK 1 -1.804 3.865 -1.844 1.00 20.00 +HETATM 31 H31 UNK 1 -0.191 5.476 -2.674 1.00 20.00 +HETATM 32 H32 UNK 1 0.746 6.615 -4.645 1.00 20.00 +HETATM 33 H33 UNK 1 0.500 5.610 -6.880 1.00 20.00 +HETATM 34 H34 UNK 1 -0.674 3.462 -7.141 1.00 20.00 +HETATM 35 H35 UNK 1 -1.603 2.319 -5.168 1.00 20.00 +CONECT 1 2 19 20 21 +CONECT 2 1 3 17 18 +CONECT 3 2 4 22 +CONECT 4 3 8 5 9 +CONECT 5 4 6 23 24 +CONECT 6 5 7 8 +CONECT 7 6 +CONECT 8 6 4 25 26 +CONECT 9 4 10 27 28 +CONECT 10 9 11 29 30 +CONECT 11 10 16 12 +CONECT 12 11 13 31 +CONECT 13 12 14 32 +CONECT 14 13 15 33 +CONECT 15 14 16 34 +CONECT 16 15 11 35 +CONECT 17 2 +CONECT 18 2 +CONECT 19 1 +CONECT 20 1 +CONECT 21 1 +CONECT 22 3 +CONECT 23 5 +CONECT 24 5 +CONECT 25 8 +CONECT 26 8 +CONECT 27 9 +CONECT 28 9 +CONECT 29 10 +CONECT 30 10 +CONECT 31 12 +CONECT 32 13 +CONECT 33 14 +CONECT 34 15 +CONECT 35 16 +END diff --git a/top/gaff/SM36/SM36.pdb b/top/gaff/SM36/SM36.pdb deleted file mode 120000 index c020172..0000000 --- a/top/gaff/SM36/SM36.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM36/SM36.pdb \ No newline at end of file diff --git a/top/gaff/SM36/SM36.pdb b/top/gaff/SM36/SM36.pdb new file mode 100644 index 0000000..c68065a --- /dev/null +++ b/top/gaff/SM36/SM36.pdb @@ -0,0 +1,88 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM36 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 0.605 1.800 1.245 1.00 20.00 +HETATM 2 S2 UNK 1 1.279 0.576 1.501 1.00 20.00 +HETATM 3 N3 UNK 1 0.114 -0.600 1.542 1.00 20.00 +HETATM 4 C4 UNK 1 -1.099 -0.402 2.340 1.00 20.00 +HETATM 5 C5 UNK 1 -2.339 -1.049 1.721 1.00 20.00 +HETATM 6 S6 UNK 1 -3.372 0.267 2.424 1.00 20.00 +HETATM 7 O7 UNK 1 -4.165 0.760 1.221 1.00 20.00 +HETATM 8 C8 UNK 1 -1.727 0.980 2.148 1.00 20.00 +HETATM 9 C9 UNK 1 -0.898 -0.772 3.811 1.00 20.00 +HETATM 10 C10 UNK 1 -0.158 -2.108 3.905 1.00 20.00 +HETATM 11 C11 UNK 1 0.039 -2.472 5.354 1.00 20.00 +HETATM 12 C12 UNK 1 1.180 -2.064 6.020 1.00 20.00 +HETATM 13 C13 UNK 1 1.359 -2.394 7.350 1.00 20.00 +HETATM 14 C14 UNK 1 0.402 -3.141 8.012 1.00 20.00 +HETATM 15 C15 UNK 1 -0.736 -3.554 7.344 1.00 20.00 +HETATM 16 C16 UNK 1 -0.917 -3.219 6.015 1.00 20.00 +HETATM 17 C17 UNK 1 1.947 0.705 3.126 1.00 20.00 +HETATM 18 C18 UNK 1 1.385 1.580 4.037 1.00 20.00 +HETATM 19 C19 UNK 1 1.906 1.678 5.313 1.00 20.00 +HETATM 20 C20 UNK 1 2.996 0.909 5.676 1.00 20.00 +HETATM 21 C21 UNK 1 3.562 0.038 4.763 1.00 20.00 +HETATM 22 C22 UNK 1 3.037 -0.064 3.488 1.00 20.00 +HETATM 23 O23 UNK 1 2.323 0.077 0.676 1.00 20.00 +HETATM 24 H24 UNK 1 0.234 -1.420 1.038 1.00 20.00 +HETATM 25 H25 UNK 1 -2.325 -1.047 0.631 1.00 20.00 +HETATM 26 H26 UNK 1 -2.560 -2.034 2.133 1.00 20.00 +HETATM 27 H27 UNK 1 -1.435 1.695 2.917 1.00 20.00 +HETATM 28 H28 UNK 1 -1.594 1.375 1.140 1.00 20.00 +HETATM 29 H29 UNK 1 -0.312 0.004 4.304 1.00 20.00 +HETATM 30 H30 UNK 1 -1.869 -0.859 4.300 1.00 20.00 +HETATM 31 H31 UNK 1 -0.745 -2.883 3.412 1.00 20.00 +HETATM 32 H32 UNK 1 0.812 -2.021 3.416 1.00 20.00 +HETATM 33 H33 UNK 1 1.929 -1.484 5.502 1.00 20.00 +HETATM 34 H34 UNK 1 2.248 -2.072 7.871 1.00 20.00 +HETATM 35 H35 UNK 1 0.544 -3.403 9.050 1.00 20.00 +HETATM 36 H36 UNK 1 -1.483 -4.138 7.861 1.00 20.00 +HETATM 37 H37 UNK 1 -1.806 -3.542 5.494 1.00 20.00 +HETATM 38 H38 UNK 1 0.536 2.184 3.752 1.00 20.00 +HETATM 39 H39 UNK 1 1.465 2.359 6.026 1.00 20.00 +HETATM 40 H40 UNK 1 3.406 0.989 6.672 1.00 20.00 +HETATM 41 H41 UNK 1 4.413 -0.563 5.046 1.00 20.00 +HETATM 42 H42 UNK 1 3.479 -0.744 2.775 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 17 23 +CONECT 3 2 4 24 +CONECT 4 3 8 5 9 +CONECT 5 4 6 25 26 +CONECT 6 5 7 8 +CONECT 7 6 +CONECT 8 6 4 27 28 +CONECT 9 4 10 29 30 +CONECT 10 9 11 31 32 +CONECT 11 10 16 12 +CONECT 12 11 13 33 +CONECT 13 12 14 34 +CONECT 14 13 15 35 +CONECT 15 14 16 36 +CONECT 16 15 11 37 +CONECT 17 2 22 18 +CONECT 18 17 19 38 +CONECT 19 18 20 39 +CONECT 20 19 21 40 +CONECT 21 20 22 41 +CONECT 22 21 17 42 +CONECT 23 2 +CONECT 24 3 +CONECT 25 5 +CONECT 26 5 +CONECT 27 8 +CONECT 28 8 +CONECT 29 9 +CONECT 30 9 +CONECT 31 10 +CONECT 32 10 +CONECT 33 12 +CONECT 34 13 +CONECT 35 14 +CONECT 36 15 +CONECT 37 16 +CONECT 38 18 +CONECT 39 19 +CONECT 40 20 +CONECT 41 21 +CONECT 42 22 +END diff --git a/top/gaff/SM37/SM37.pdb b/top/gaff/SM37/SM37.pdb deleted file mode 120000 index 2f5c362..0000000 --- a/top/gaff/SM37/SM37.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM37/SM37.pdb \ No newline at end of file diff --git a/top/gaff/SM37/SM37.pdb b/top/gaff/SM37/SM37.pdb new file mode 100644 index 0000000..3265a77 --- /dev/null +++ b/top/gaff/SM37/SM37.pdb @@ -0,0 +1,84 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM37 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -3.068 -1.610 -2.498 1.00 20.00 +HETATM 2 S2 UNK 1 -1.908 -0.863 -2.156 1.00 20.00 +HETATM 3 N3 UNK 1 -2.441 0.620 -1.647 1.00 20.00 +HETATM 4 C4 UNK 1 -1.482 1.616 -1.162 1.00 20.00 +HETATM 5 C5 UNK 1 -0.818 1.218 0.158 1.00 20.00 +HETATM 6 S6 UNK 1 -2.260 1.839 1.068 1.00 20.00 +HETATM 7 O7 UNK 1 -3.335 0.810 0.747 1.00 20.00 +HETATM 8 C8 UNK 1 -2.149 2.804 -0.465 1.00 20.00 +HETATM 9 C9 UNK 1 -0.479 2.035 -2.238 1.00 20.00 +HETATM 10 C10 UNK 1 -1.230 2.413 -3.517 1.00 20.00 +HETATM 11 C11 UNK 1 -0.241 2.826 -4.577 1.00 20.00 +HETATM 12 C12 UNK 1 0.138 4.150 -4.690 1.00 20.00 +HETATM 13 C13 UNK 1 1.048 4.528 -5.659 1.00 20.00 +HETATM 14 C14 UNK 1 1.571 3.583 -6.522 1.00 20.00 +HETATM 15 C15 UNK 1 1.188 2.260 -6.412 1.00 20.00 +HETATM 16 C16 UNK 1 0.282 1.881 -5.439 1.00 20.00 +HETATM 17 N17 UNK 1 -1.236 -1.618 -0.844 1.00 20.00 +HETATM 18 C18 UNK 1 -2.096 -2.268 0.148 1.00 20.00 +HETATM 19 C19 UNK 1 0.220 -1.637 -0.676 1.00 20.00 +HETATM 20 O20 UNK 1 -0.846 -0.618 -3.066 1.00 20.00 +HETATM 21 H21 UNK 1 -3.388 0.829 -1.671 1.00 20.00 +HETATM 22 H22 UNK 1 -0.677 0.142 0.260 1.00 20.00 +HETATM 23 H23 UNK 1 0.093 1.780 0.365 1.00 20.00 +HETATM 24 H24 UNK 1 -1.494 3.672 -0.378 1.00 20.00 +HETATM 25 H25 UNK 1 -3.122 3.057 -0.885 1.00 20.00 +HETATM 26 H26 UNK 1 0.094 2.893 -1.886 1.00 20.00 +HETATM 27 H27 UNK 1 0.198 1.206 -2.446 1.00 20.00 +HETATM 28 H28 UNK 1 -1.803 1.555 -3.868 1.00 20.00 +HETATM 29 H29 UNK 1 -1.907 3.242 -3.309 1.00 20.00 +HETATM 30 H30 UNK 1 -0.275 4.889 -4.019 1.00 20.00 +HETATM 31 H31 UNK 1 1.347 5.563 -5.745 1.00 20.00 +HETATM 32 H32 UNK 1 2.279 3.879 -7.282 1.00 20.00 +HETATM 33 H33 UNK 1 1.597 1.522 -7.086 1.00 20.00 +HETATM 34 H34 UNK 1 -0.018 0.847 -5.354 1.00 20.00 +HETATM 35 H35 UNK 1 -2.259 -3.307 -0.137 1.00 20.00 +HETATM 36 H36 UNK 1 -1.615 -2.231 1.126 1.00 20.00 +HETATM 37 H37 UNK 1 -3.053 -1.750 0.194 1.00 20.00 +HETATM 38 H38 UNK 1 0.683 -1.026 -1.452 1.00 20.00 +HETATM 39 H39 UNK 1 0.477 -1.236 0.304 1.00 20.00 +HETATM 40 H40 UNK 1 0.582 -2.662 -0.756 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 17 20 +CONECT 3 2 4 21 +CONECT 4 3 8 5 9 +CONECT 5 4 6 22 23 +CONECT 6 5 7 8 +CONECT 7 6 +CONECT 8 6 4 24 25 +CONECT 9 4 10 26 27 +CONECT 10 9 11 28 29 +CONECT 11 10 16 12 +CONECT 12 11 13 30 +CONECT 13 12 14 31 +CONECT 14 13 15 32 +CONECT 15 14 16 33 +CONECT 16 15 11 34 +CONECT 17 2 18 19 +CONECT 18 17 35 36 37 +CONECT 19 17 38 39 40 +CONECT 20 2 +CONECT 21 3 +CONECT 22 5 +CONECT 23 5 +CONECT 24 8 +CONECT 25 8 +CONECT 26 9 +CONECT 27 9 +CONECT 28 10 +CONECT 29 10 +CONECT 30 12 +CONECT 31 13 +CONECT 32 14 +CONECT 33 15 +CONECT 34 16 +CONECT 35 18 +CONECT 36 18 +CONECT 37 18 +CONECT 38 19 +CONECT 39 19 +CONECT 40 19 +END diff --git a/top/gaff/SM38/SM38.pdb b/top/gaff/SM38/SM38.pdb deleted file mode 120000 index ae03c48..0000000 --- a/top/gaff/SM38/SM38.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM38/SM38.pdb \ No newline at end of file diff --git a/top/gaff/SM38/SM38.pdb b/top/gaff/SM38/SM38.pdb new file mode 100644 index 0000000..bc57bbf --- /dev/null +++ b/top/gaff/SM38/SM38.pdb @@ -0,0 +1,76 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM38 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 1.166 0.087 -2.790 1.00 20.00 +HETATM 2 S2 UNK 1 -0.334 -0.411 -1.900 1.00 20.00 +HETATM 3 N3 UNK 1 -0.057 0.047 -0.334 1.00 20.00 +HETATM 4 C4 UNK 1 0.135 1.463 -0.007 1.00 20.00 +HETATM 5 C5 UNK 1 -0.370 1.832 1.389 1.00 20.00 +HETATM 6 S6 UNK 1 -0.794 3.493 0.791 1.00 20.00 +HETATM 7 C7 UNK 1 -0.926 2.373 -0.630 1.00 20.00 +HETATM 8 O8 UNK 1 0.335 4.352 0.711 1.00 20.00 +HETATM 9 O9 UNK 1 -2.060 3.941 1.257 1.00 20.00 +HETATM 10 C10 UNK 1 1.565 1.936 -0.274 1.00 20.00 +HETATM 11 C11 UNK 1 2.549 1.034 0.473 1.00 20.00 +HETATM 12 C12 UNK 1 3.960 1.427 0.118 1.00 20.00 +HETATM 13 C13 UNK 1 4.595 0.830 -0.955 1.00 20.00 +HETATM 14 C14 UNK 1 5.887 1.194 -1.283 1.00 20.00 +HETATM 15 C15 UNK 1 6.549 2.147 -0.532 1.00 20.00 +HETATM 16 C16 UNK 1 5.916 2.741 0.544 1.00 20.00 +HETATM 17 C17 UNK 1 4.622 2.381 0.869 1.00 20.00 +HETATM 18 O18 UNK 1 -0.430 -1.827 -1.839 1.00 20.00 +HETATM 19 O19 UNK 1 -1.441 0.382 -2.307 1.00 20.00 +HETATM 20 H20 UNK 1 2.029 -0.425 -2.363 1.00 20.00 +HETATM 21 H21 UNK 1 1.070 -0.180 -3.843 1.00 20.00 +HETATM 22 H22 UNK 1 1.302 1.165 -2.699 1.00 20.00 +HETATM 23 H23 UNK 1 -0.021 -0.621 0.368 1.00 20.00 +HETATM 24 H24 UNK 1 -1.240 1.253 1.697 1.00 20.00 +HETATM 25 H25 UNK 1 0.417 1.836 2.143 1.00 20.00 +HETATM 26 H26 UNK 1 -0.604 2.829 -1.566 1.00 20.00 +HETATM 27 H27 UNK 1 -1.904 1.898 -0.712 1.00 20.00 +HETATM 28 H28 UNK 1 1.770 1.889 -1.344 1.00 20.00 +HETATM 29 H29 UNK 1 1.679 2.964 0.072 1.00 20.00 +HETATM 30 H30 UNK 1 2.400 1.146 1.547 1.00 20.00 +HETATM 31 H31 UNK 1 2.379 -0.004 0.188 1.00 20.00 +HETATM 32 H32 UNK 1 4.079 0.082 -1.539 1.00 20.00 +HETATM 33 H33 UNK 1 6.382 0.730 -2.124 1.00 20.00 +HETATM 34 H34 UNK 1 7.560 2.428 -0.786 1.00 20.00 +HETATM 35 H35 UNK 1 6.433 3.485 1.131 1.00 20.00 +HETATM 36 H36 UNK 1 4.128 2.844 1.711 1.00 20.00 +CONECT 1 2 20 21 22 +CONECT 2 1 3 18 19 +CONECT 3 2 4 23 +CONECT 4 3 7 5 10 +CONECT 5 4 6 24 25 +CONECT 6 5 7 8 9 +CONECT 7 6 4 26 27 +CONECT 8 6 +CONECT 9 6 +CONECT 10 4 11 28 29 +CONECT 11 10 12 30 31 +CONECT 12 11 17 13 +CONECT 13 12 14 32 +CONECT 14 13 15 33 +CONECT 15 14 16 34 +CONECT 16 15 17 35 +CONECT 17 16 12 36 +CONECT 18 2 +CONECT 19 2 +CONECT 20 1 +CONECT 21 1 +CONECT 22 1 +CONECT 23 3 +CONECT 24 5 +CONECT 25 5 +CONECT 26 7 +CONECT 27 7 +CONECT 28 10 +CONECT 29 10 +CONECT 30 11 +CONECT 31 11 +CONECT 32 13 +CONECT 33 14 +CONECT 34 15 +CONECT 35 16 +CONECT 36 17 +END diff --git a/top/gaff/SM39/SM39.pdb b/top/gaff/SM39/SM39.pdb deleted file mode 120000 index fef13ed..0000000 --- a/top/gaff/SM39/SM39.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM39/SM39.pdb \ No newline at end of file diff --git a/top/gaff/SM39/SM39.pdb b/top/gaff/SM39/SM39.pdb new file mode 100644 index 0000000..5e5d97d --- /dev/null +++ b/top/gaff/SM39/SM39.pdb @@ -0,0 +1,90 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM39 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 0.537 7.798 -3.461 1.00 20.00 +HETATM 2 S2 UNK 1 0.448 7.809 -2.043 1.00 20.00 +HETATM 3 N3 UNK 1 -0.032 6.290 -1.593 1.00 20.00 +HETATM 4 C4 UNK 1 -1.175 5.656 -2.256 1.00 20.00 +HETATM 5 C5 UNK 1 -1.083 4.129 -2.285 1.00 20.00 +HETATM 6 S6 UNK 1 -1.968 4.110 -3.869 1.00 20.00 +HETATM 7 C7 UNK 1 -1.078 5.688 -3.783 1.00 20.00 +HETATM 8 O8 UNK 1 -3.372 4.262 -3.716 1.00 20.00 +HETATM 9 O9 UNK 1 -1.398 3.208 -4.809 1.00 20.00 +HETATM 10 C10 UNK 1 -2.516 6.169 -1.728 1.00 20.00 +HETATM 11 C11 UNK 1 -2.639 5.835 -0.240 1.00 20.00 +HETATM 12 C12 UNK 1 -4.011 6.222 0.250 1.00 20.00 +HETATM 13 C13 UNK 1 -4.231 7.488 0.758 1.00 20.00 +HETATM 14 C14 UNK 1 -5.491 7.845 1.203 1.00 20.00 +HETATM 15 C15 UNK 1 -6.527 6.932 1.150 1.00 20.00 +HETATM 16 C16 UNK 1 -6.305 5.663 0.646 1.00 20.00 +HETATM 17 C17 UNK 1 -5.047 5.309 0.197 1.00 20.00 +HETATM 18 C18 UNK 1 -0.862 8.913 -1.635 1.00 20.00 +HETATM 19 C19 UNK 1 -0.968 9.416 -0.352 1.00 20.00 +HETATM 20 C20 UNK 1 -1.997 10.282 -0.031 1.00 20.00 +HETATM 21 C21 UNK 1 -2.920 10.645 -0.994 1.00 20.00 +HETATM 22 C22 UNK 1 -2.817 10.138 -2.276 1.00 20.00 +HETATM 23 C23 UNK 1 -1.786 9.276 -2.598 1.00 20.00 +HETATM 24 O24 UNK 1 1.539 8.151 -1.199 1.00 20.00 +HETATM 25 H25 UNK 1 0.442 5.819 -0.890 1.00 20.00 +HETATM 26 H26 UNK 1 -0.059 3.763 -2.361 1.00 20.00 +HETATM 27 H27 UNK 1 -1.638 3.651 -1.478 1.00 20.00 +HETATM 28 H28 UNK 1 -1.629 6.516 -4.230 1.00 20.00 +HETATM 29 H29 UNK 1 -0.053 5.623 -4.149 1.00 20.00 +HETATM 30 H30 UNK 1 -2.572 7.249 -1.864 1.00 20.00 +HETATM 31 H31 UNK 1 -3.329 5.691 -2.276 1.00 20.00 +HETATM 32 H32 UNK 1 -2.490 4.765 -0.094 1.00 20.00 +HETATM 33 H33 UNK 1 -1.884 6.387 0.320 1.00 20.00 +HETATM 34 H34 UNK 1 -3.421 8.201 0.804 1.00 20.00 +HETATM 35 H35 UNK 1 -5.664 8.836 1.597 1.00 20.00 +HETATM 36 H36 UNK 1 -7.510 7.209 1.501 1.00 20.00 +HETATM 37 H37 UNK 1 -7.115 4.950 0.605 1.00 20.00 +HETATM 38 H38 UNK 1 -4.874 4.318 -0.196 1.00 20.00 +HETATM 39 H39 UNK 1 -0.247 9.133 0.401 1.00 20.00 +HETATM 40 H40 UNK 1 -2.079 10.675 0.971 1.00 20.00 +HETATM 41 H41 UNK 1 -3.724 11.322 -0.744 1.00 20.00 +HETATM 42 H42 UNK 1 -3.541 10.418 -3.027 1.00 20.00 +HETATM 43 H43 UNK 1 -1.703 8.883 -3.600 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 18 24 +CONECT 3 2 4 25 +CONECT 4 3 7 5 10 +CONECT 5 4 6 26 27 +CONECT 6 5 7 8 9 +CONECT 7 6 4 28 29 +CONECT 8 6 +CONECT 9 6 +CONECT 10 4 11 30 31 +CONECT 11 10 12 32 33 +CONECT 12 11 17 13 +CONECT 13 12 14 34 +CONECT 14 13 15 35 +CONECT 15 14 16 36 +CONECT 16 15 17 37 +CONECT 17 16 12 38 +CONECT 18 2 23 19 +CONECT 19 18 20 39 +CONECT 20 19 21 40 +CONECT 21 20 22 41 +CONECT 22 21 23 42 +CONECT 23 22 18 43 +CONECT 24 2 +CONECT 25 3 +CONECT 26 5 +CONECT 27 5 +CONECT 28 7 +CONECT 29 7 +CONECT 30 10 +CONECT 31 10 +CONECT 32 11 +CONECT 33 11 +CONECT 34 13 +CONECT 35 14 +CONECT 36 15 +CONECT 37 16 +CONECT 38 17 +CONECT 39 19 +CONECT 40 20 +CONECT 41 21 +CONECT 42 22 +CONECT 43 23 +END diff --git a/top/gaff/SM40/SM40.pdb b/top/gaff/SM40/SM40.pdb deleted file mode 120000 index 897712f..0000000 --- a/top/gaff/SM40/SM40.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM40/SM40.pdb \ No newline at end of file diff --git a/top/gaff/SM40/SM40.pdb b/top/gaff/SM40/SM40.pdb new file mode 100644 index 0000000..99daa83 --- /dev/null +++ b/top/gaff/SM40/SM40.pdb @@ -0,0 +1,86 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM40 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -0.974 -1.888 -1.900 1.00 20.00 +HETATM 2 S2 UNK 1 -0.678 -0.498 -1.895 1.00 20.00 +HETATM 3 N3 UNK 1 -0.169 -0.134 -0.362 1.00 20.00 +HETATM 4 C4 UNK 1 0.332 1.209 -0.056 1.00 20.00 +HETATM 5 C5 UNK 1 0.030 1.652 1.377 1.00 20.00 +HETATM 6 S6 UNK 1 -0.097 3.373 0.814 1.00 20.00 +HETATM 7 C7 UNK 1 -0.570 2.324 -0.589 1.00 20.00 +HETATM 8 O8 UNK 1 1.172 3.987 0.637 1.00 20.00 +HETATM 9 O9 UNK 1 -1.202 4.060 1.384 1.00 20.00 +HETATM 10 C10 UNK 1 1.802 1.387 -0.444 1.00 20.00 +HETATM 11 C11 UNK 1 2.643 0.304 0.234 1.00 20.00 +HETATM 12 C12 UNK 1 4.103 0.557 -0.040 1.00 20.00 +HETATM 13 C13 UNK 1 4.704 -0.005 -1.151 1.00 20.00 +HETATM 14 C14 UNK 1 6.043 0.231 -1.406 1.00 20.00 +HETATM 15 C15 UNK 1 6.782 1.019 -0.544 1.00 20.00 +HETATM 16 C16 UNK 1 6.181 1.576 0.570 1.00 20.00 +HETATM 17 C17 UNK 1 4.842 1.345 0.822 1.00 20.00 +HETATM 18 N18 UNK 1 0.620 -0.294 -2.903 1.00 20.00 +HETATM 19 C19 UNK 1 1.630 -1.348 -3.020 1.00 20.00 +HETATM 20 C20 UNK 1 0.757 0.942 -3.679 1.00 20.00 +HETATM 21 O21 UNK 1 -1.624 0.500 -2.252 1.00 20.00 +HETATM 22 H22 UNK 1 -0.203 -0.809 0.334 1.00 20.00 +HETATM 23 H23 UNK 1 -0.911 1.256 1.759 1.00 20.00 +HETATM 24 H24 UNK 1 0.861 1.485 2.062 1.00 20.00 +HETATM 25 H25 UNK 1 -0.241 2.719 -1.550 1.00 20.00 +HETATM 26 H26 UNK 1 -1.627 2.057 -0.587 1.00 20.00 +HETATM 27 H27 UNK 1 1.905 1.303 -1.525 1.00 20.00 +HETATM 28 H28 UNK 1 2.146 2.370 -0.121 1.00 20.00 +HETATM 29 H29 UNK 1 2.466 0.327 1.310 1.00 20.00 +HETATM 30 H30 UNK 1 2.363 -0.673 -0.159 1.00 20.00 +HETATM 31 H31 UNK 1 4.128 -0.624 -1.822 1.00 20.00 +HETATM 32 H32 UNK 1 6.512 -0.204 -2.276 1.00 20.00 +HETATM 33 H33 UNK 1 7.828 1.200 -0.740 1.00 20.00 +HETATM 34 H34 UNK 1 6.759 2.192 1.244 1.00 20.00 +HETATM 35 H35 UNK 1 4.373 1.780 1.692 1.00 20.00 +HETATM 36 H36 UNK 1 1.349 -2.034 -3.820 1.00 20.00 +HETATM 37 H37 UNK 1 2.597 -0.901 -3.249 1.00 20.00 +HETATM 38 H38 UNK 1 1.696 -1.894 -2.079 1.00 20.00 +HETATM 39 H39 UNK 1 1.382 1.647 -3.131 1.00 20.00 +HETATM 40 H40 UNK 1 1.220 0.718 -4.640 1.00 20.00 +HETATM 41 H41 UNK 1 -0.227 1.380 -3.842 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 18 21 +CONECT 3 2 4 22 +CONECT 4 3 7 5 10 +CONECT 5 4 6 23 24 +CONECT 6 5 7 8 9 +CONECT 7 6 4 25 26 +CONECT 8 6 +CONECT 9 6 +CONECT 10 4 11 27 28 +CONECT 11 10 12 29 30 +CONECT 12 11 17 13 +CONECT 13 12 14 31 +CONECT 14 13 15 32 +CONECT 15 14 16 33 +CONECT 16 15 17 34 +CONECT 17 16 12 35 +CONECT 18 2 19 20 +CONECT 19 18 36 37 38 +CONECT 20 18 39 40 41 +CONECT 21 2 +CONECT 22 3 +CONECT 23 5 +CONECT 24 5 +CONECT 25 7 +CONECT 26 7 +CONECT 27 10 +CONECT 28 10 +CONECT 29 11 +CONECT 30 11 +CONECT 31 13 +CONECT 32 14 +CONECT 33 15 +CONECT 34 16 +CONECT 35 17 +CONECT 36 19 +CONECT 37 19 +CONECT 38 19 +CONECT 39 20 +CONECT 40 20 +CONECT 41 20 +END diff --git a/top/gaff/SM41/SM41.pdb b/top/gaff/SM41/SM41.pdb deleted file mode 120000 index 4842c9c..0000000 --- a/top/gaff/SM41/SM41.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM41/SM41.pdb \ No newline at end of file diff --git a/top/gaff/SM41/SM41.pdb b/top/gaff/SM41/SM41.pdb new file mode 100644 index 0000000..fcdf663 --- /dev/null +++ b/top/gaff/SM41/SM41.pdb @@ -0,0 +1,56 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM41 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.434 0.744 0.043 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 4 C4 UNK 1 1.184 1.678 -0.000 1.00 20.00 +HETATM 5 N5 UNK 1 1.322 2.979 0.006 1.00 20.00 +HETATM 6 O6 UNK 1 2.485 3.307 -0.003 1.00 20.00 +HETATM 7 C7 UNK 1 3.303 2.239 -0.017 1.00 20.00 +HETATM 8 C8 UNK 1 4.781 2.254 -0.031 1.00 20.00 +HETATM 9 C9 UNK 1 5.494 1.054 -0.038 1.00 20.00 +HETATM 10 C10 UNK 1 6.873 1.075 -0.055 1.00 20.00 +HETATM 11 C11 UNK 1 7.550 2.282 -0.056 1.00 20.00 +HETATM 12 C12 UNK 1 6.849 3.475 -0.043 1.00 20.00 +HETATM 13 C13 UNK 1 5.470 3.468 -0.031 1.00 20.00 +HETATM 14 C14 UNK 1 2.495 1.137 -0.010 1.00 20.00 +HETATM 15 C15 UNK 1 -1.496 2.652 -1.569 1.00 20.00 +HETATM 16 O16 UNK 1 -1.335 2.695 1.094 1.00 20.00 +HETATM 17 H17 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 18 H18 UNK 1 4.967 0.111 -0.034 1.00 20.00 +HETATM 19 H19 UNK 1 7.426 0.147 -0.065 1.00 20.00 +HETATM 20 H20 UNK 1 8.630 2.293 -0.065 1.00 20.00 +HETATM 21 H21 UNK 1 7.383 4.413 -0.044 1.00 20.00 +HETATM 22 H22 UNK 1 4.924 4.399 -0.022 1.00 20.00 +HETATM 23 H23 UNK 1 2.786 0.098 -0.013 1.00 20.00 +HETATM 24 H24 UNK 1 -1.440 1.931 -2.384 1.00 20.00 +HETATM 25 H25 UNK 1 -2.425 3.217 -1.648 1.00 20.00 +HETATM 26 H26 UNK 1 -0.649 3.334 -1.628 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 16 +CONECT 3 2 4 17 +CONECT 4 3 14 5 +CONECT 5 4 6 +CONECT 6 5 7 +CONECT 7 6 8 14 +CONECT 8 7 13 9 +CONECT 9 8 10 18 +CONECT 10 9 11 19 +CONECT 11 10 12 20 +CONECT 12 11 13 21 +CONECT 13 12 8 22 +CONECT 14 7 4 23 +CONECT 15 2 24 25 26 +CONECT 16 2 +CONECT 17 3 +CONECT 18 9 +CONECT 19 10 +CONECT 20 11 +CONECT 21 12 +CONECT 22 13 +CONECT 23 14 +CONECT 24 15 +CONECT 25 15 +CONECT 26 15 +END diff --git a/top/gaff/SM42/SM42.pdb b/top/gaff/SM42/SM42.pdb deleted file mode 120000 index 34b9acc..0000000 --- a/top/gaff/SM42/SM42.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM42/SM42.pdb \ No newline at end of file diff --git a/top/gaff/SM42/SM42.pdb b/top/gaff/SM42/SM42.pdb new file mode 100644 index 0000000..a8b42d2 --- /dev/null +++ b/top/gaff/SM42/SM42.pdb @@ -0,0 +1,70 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM42 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 1.132 -2.198 0.015 1.00 20.00 +HETATM 2 S2 UNK 1 1.447 -0.812 -0.016 1.00 20.00 +HETATM 3 N3 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 4 C4 UNK 1 -0.017 1.387 0.010 1.00 20.00 +HETATM 5 N5 UNK 1 1.020 2.186 0.004 1.00 20.00 +HETATM 6 O6 UNK 1 0.691 3.349 0.013 1.00 20.00 +HETATM 7 C7 UNK 1 -0.647 3.486 0.027 1.00 20.00 +HETATM 8 C8 UNK 1 -1.408 4.754 0.041 1.00 20.00 +HETATM 9 C9 UNK 1 -2.804 4.733 0.048 1.00 20.00 +HETATM 10 C10 UNK 1 -3.508 5.919 0.066 1.00 20.00 +HETATM 11 C11 UNK 1 -2.834 7.128 0.067 1.00 20.00 +HETATM 12 C12 UNK 1 -1.450 7.155 0.054 1.00 20.00 +HETATM 13 C13 UNK 1 -0.734 5.976 0.041 1.00 20.00 +HETATM 14 C14 UNK 1 -1.163 2.221 0.019 1.00 20.00 +HETATM 15 C15 UNK 1 2.264 -0.455 1.504 1.00 20.00 +HETATM 16 C16 UNK 1 3.113 0.632 1.593 1.00 20.00 +HETATM 17 C17 UNK 1 3.750 0.916 2.787 1.00 20.00 +HETATM 18 C18 UNK 1 3.545 0.107 3.889 1.00 20.00 +HETATM 19 C19 UNK 1 2.699 -0.983 3.799 1.00 20.00 +HETATM 20 C20 UNK 1 2.059 -1.264 2.606 1.00 20.00 +HETATM 21 O21 UNK 1 2.229 -0.215 -1.041 1.00 20.00 +HETATM 22 H22 UNK 1 -0.831 -0.500 0.007 1.00 20.00 +HETATM 23 H23 UNK 1 -3.331 3.791 0.043 1.00 20.00 +HETATM 24 H24 UNK 1 -4.588 5.905 0.076 1.00 20.00 +HETATM 25 H25 UNK 1 -3.390 8.054 0.077 1.00 20.00 +HETATM 26 H26 UNK 1 -0.930 8.101 0.054 1.00 20.00 +HETATM 27 H27 UNK 1 0.345 5.998 0.031 1.00 20.00 +HETATM 28 H28 UNK 1 -2.202 1.925 0.021 1.00 20.00 +HETATM 29 H29 UNK 1 3.277 1.262 0.731 1.00 20.00 +HETATM 30 H30 UNK 1 4.411 1.767 2.858 1.00 20.00 +HETATM 31 H31 UNK 1 4.046 0.326 4.820 1.00 20.00 +HETATM 32 H32 UNK 1 2.540 -1.616 4.659 1.00 20.00 +HETATM 33 H33 UNK 1 1.398 -2.115 2.536 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 21 +CONECT 3 2 4 22 +CONECT 4 3 14 5 +CONECT 5 4 6 +CONECT 6 5 7 +CONECT 7 6 8 14 +CONECT 8 7 13 9 +CONECT 9 8 10 23 +CONECT 10 9 11 24 +CONECT 11 10 12 25 +CONECT 12 11 13 26 +CONECT 13 12 8 27 +CONECT 14 7 4 28 +CONECT 15 2 20 16 +CONECT 16 15 17 29 +CONECT 17 16 18 30 +CONECT 18 17 19 31 +CONECT 19 18 20 32 +CONECT 20 19 15 33 +CONECT 21 2 +CONECT 22 3 +CONECT 23 9 +CONECT 24 10 +CONECT 25 11 +CONECT 26 12 +CONECT 27 13 +CONECT 28 14 +CONECT 29 16 +CONECT 30 17 +CONECT 31 18 +CONECT 32 19 +CONECT 33 20 +END diff --git a/top/gaff/SM43/SM43.pdb b/top/gaff/SM43/SM43.pdb deleted file mode 120000 index 0995fe1..0000000 --- a/top/gaff/SM43/SM43.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM43/SM43.pdb \ No newline at end of file diff --git a/top/gaff/SM43/SM43.pdb b/top/gaff/SM43/SM43.pdb new file mode 100644 index 0000000..b985f25 --- /dev/null +++ b/top/gaff/SM43/SM43.pdb @@ -0,0 +1,66 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM43 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.472 0.781 -0.017 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 4 C4 UNK 1 1.184 1.678 -0.000 1.00 20.00 +HETATM 5 N5 UNK 1 1.322 2.979 0.006 1.00 20.00 +HETATM 6 O6 UNK 1 2.485 3.307 -0.003 1.00 20.00 +HETATM 7 C7 UNK 1 3.303 2.239 -0.017 1.00 20.00 +HETATM 8 C8 UNK 1 4.781 2.254 -0.031 1.00 20.00 +HETATM 9 C9 UNK 1 5.494 1.054 -0.038 1.00 20.00 +HETATM 10 C10 UNK 1 6.873 1.075 -0.055 1.00 20.00 +HETATM 11 C11 UNK 1 7.550 2.282 -0.056 1.00 20.00 +HETATM 12 C12 UNK 1 6.849 3.475 -0.043 1.00 20.00 +HETATM 13 C13 UNK 1 5.470 3.468 -0.031 1.00 20.00 +HETATM 14 C14 UNK 1 2.495 1.137 -0.010 1.00 20.00 +HETATM 15 N15 UNK 1 -1.565 2.605 -1.410 1.00 20.00 +HETATM 16 C16 UNK 1 -2.176 1.972 -2.581 1.00 20.00 +HETATM 17 C17 UNK 1 -1.049 3.973 -1.503 1.00 20.00 +HETATM 18 O18 UNK 1 -1.361 2.752 1.045 1.00 20.00 +HETATM 19 H19 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 20 H20 UNK 1 4.967 0.111 -0.034 1.00 20.00 +HETATM 21 H21 UNK 1 7.426 0.147 -0.065 1.00 20.00 +HETATM 22 H22 UNK 1 8.630 2.293 -0.065 1.00 20.00 +HETATM 23 H23 UNK 1 7.383 4.413 -0.044 1.00 20.00 +HETATM 24 H24 UNK 1 4.924 4.399 -0.022 1.00 20.00 +HETATM 25 H25 UNK 1 2.786 0.098 -0.013 1.00 20.00 +HETATM 26 H26 UNK 1 -3.246 2.180 -2.589 1.00 20.00 +HETATM 27 H27 UNK 1 -1.722 2.369 -3.488 1.00 20.00 +HETATM 28 H28 UNK 1 -2.016 0.894 -2.536 1.00 20.00 +HETATM 29 H29 UNK 1 -0.002 3.946 -1.808 1.00 20.00 +HETATM 30 H30 UNK 1 -1.628 4.530 -2.239 1.00 20.00 +HETATM 31 H31 UNK 1 -1.131 4.459 -0.531 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 18 +CONECT 3 2 4 19 +CONECT 4 3 14 5 +CONECT 5 4 6 +CONECT 6 5 7 +CONECT 7 6 8 14 +CONECT 8 7 13 9 +CONECT 9 8 10 20 +CONECT 10 9 11 21 +CONECT 11 10 12 22 +CONECT 12 11 13 23 +CONECT 13 12 8 24 +CONECT 14 7 4 25 +CONECT 15 2 16 17 +CONECT 16 15 26 27 28 +CONECT 17 15 29 30 31 +CONECT 18 2 +CONECT 19 3 +CONECT 20 9 +CONECT 21 10 +CONECT 22 11 +CONECT 23 12 +CONECT 24 13 +CONECT 25 14 +CONECT 26 16 +CONECT 27 16 +CONECT 28 16 +CONECT 29 17 +CONECT 30 17 +CONECT 31 17 +END diff --git a/top/gaff/SM44/SM44.pdb b/top/gaff/SM44/SM44.pdb deleted file mode 120000 index f0df9cb..0000000 --- a/top/gaff/SM44/SM44.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM44/SM44.pdb \ No newline at end of file diff --git a/top/gaff/SM44/SM44.pdb b/top/gaff/SM44/SM44.pdb new file mode 100644 index 0000000..3173888 --- /dev/null +++ b/top/gaff/SM44/SM44.pdb @@ -0,0 +1,56 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM44 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.434 0.744 0.043 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 4 C4 UNK 1 1.195 1.684 -0.000 1.00 20.00 +HETATM 5 N5 UNK 1 1.335 3.017 0.006 1.00 20.00 +HETATM 6 N6 UNK 1 2.588 3.309 -0.005 1.00 20.00 +HETATM 7 C7 UNK 1 2.451 1.166 -0.010 1.00 20.00 +HETATM 8 N8 UNK 1 3.298 2.236 -0.018 1.00 20.00 +HETATM 9 C9 UNK 1 4.699 2.177 -0.032 1.00 20.00 +HETATM 10 C10 UNK 1 5.343 0.947 -0.041 1.00 20.00 +HETATM 11 C11 UNK 1 6.723 0.892 -0.061 1.00 20.00 +HETATM 12 C12 UNK 1 7.463 2.060 -0.062 1.00 20.00 +HETATM 13 C13 UNK 1 6.825 3.287 -0.048 1.00 20.00 +HETATM 14 C14 UNK 1 5.445 3.348 -0.033 1.00 20.00 +HETATM 15 C15 UNK 1 -1.496 2.652 -1.569 1.00 20.00 +HETATM 16 O16 UNK 1 -1.335 2.695 1.094 1.00 20.00 +HETATM 17 H17 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 18 H18 UNK 1 2.723 0.121 -0.012 1.00 20.00 +HETATM 19 H19 UNK 1 4.766 0.035 -0.035 1.00 20.00 +HETATM 20 H20 UNK 1 7.225 -0.064 -0.072 1.00 20.00 +HETATM 21 H21 UNK 1 8.542 2.015 -0.073 1.00 20.00 +HETATM 22 H22 UNK 1 7.405 4.197 -0.049 1.00 20.00 +HETATM 23 H23 UNK 1 4.947 4.306 -0.023 1.00 20.00 +HETATM 24 H24 UNK 1 -1.440 1.931 -2.384 1.00 20.00 +HETATM 25 H25 UNK 1 -2.425 3.217 -1.648 1.00 20.00 +HETATM 26 H26 UNK 1 -0.649 3.334 -1.628 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 16 +CONECT 3 2 4 17 +CONECT 4 3 5 7 +CONECT 5 4 6 +CONECT 6 5 8 +CONECT 7 4 8 18 +CONECT 8 7 6 9 +CONECT 9 8 14 10 +CONECT 10 9 11 19 +CONECT 11 10 12 20 +CONECT 12 11 13 21 +CONECT 13 12 14 22 +CONECT 14 13 9 23 +CONECT 15 2 24 25 26 +CONECT 16 2 +CONECT 17 3 +CONECT 18 7 +CONECT 19 10 +CONECT 20 11 +CONECT 21 12 +CONECT 22 13 +CONECT 23 14 +CONECT 24 15 +CONECT 25 15 +CONECT 26 15 +END diff --git a/top/gaff/SM45/SM45.pdb b/top/gaff/SM45/SM45.pdb deleted file mode 120000 index 7fe071d..0000000 --- a/top/gaff/SM45/SM45.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM45/SM45.pdb \ No newline at end of file diff --git a/top/gaff/SM45/SM45.pdb b/top/gaff/SM45/SM45.pdb new file mode 100644 index 0000000..c6488e8 --- /dev/null +++ b/top/gaff/SM45/SM45.pdb @@ -0,0 +1,70 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM45 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 9.431 -1.948 -0.132 1.00 20.00 +HETATM 2 S2 UNK 1 8.078 -2.379 -0.086 1.00 20.00 +HETATM 3 N3 UNK 1 7.151 -1.007 -0.070 1.00 20.00 +HETATM 4 C4 UNK 1 5.750 -1.106 -0.058 1.00 20.00 +HETATM 5 N5 UNK 1 5.025 -2.233 -0.057 1.00 20.00 +HETATM 6 N6 UNK 1 3.776 -1.930 -0.044 1.00 20.00 +HETATM 7 C7 UNK 1 4.862 -0.077 -0.050 1.00 20.00 +HETATM 8 N8 UNK 1 3.624 -0.652 -0.036 1.00 20.00 +HETATM 9 C9 UNK 1 2.399 0.031 -0.021 1.00 20.00 +HETATM 10 C10 UNK 1 1.207 -0.680 -0.013 1.00 20.00 +HETATM 11 C11 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 12 C12 UNK 1 -0.017 1.379 0.010 1.00 20.00 +HETATM 13 C13 UNK 1 1.170 2.089 0.002 1.00 20.00 +HETATM 14 C14 UNK 1 2.377 1.419 -0.013 1.00 20.00 +HETATM 15 C15 UNK 1 7.766 -3.201 -1.613 1.00 20.00 +HETATM 16 C16 UNK 1 6.753 -4.138 -1.699 1.00 20.00 +HETATM 17 C17 UNK 1 6.505 -4.780 -2.898 1.00 20.00 +HETATM 18 C18 UNK 1 7.277 -4.492 -4.008 1.00 20.00 +HETATM 19 C19 UNK 1 8.294 -3.559 -3.921 1.00 20.00 +HETATM 20 C20 UNK 1 8.538 -2.914 -2.723 1.00 20.00 +HETATM 21 O21 UNK 1 7.564 -3.222 0.936 1.00 20.00 +HETATM 22 H22 UNK 1 7.575 -0.134 -0.070 1.00 20.00 +HETATM 23 H23 UNK 1 5.089 0.979 -0.052 1.00 20.00 +HETATM 24 H24 UNK 1 1.221 -1.760 -0.019 1.00 20.00 +HETATM 25 H25 UNK 1 -0.926 -0.556 0.008 1.00 20.00 +HETATM 26 H26 UNK 1 -0.960 1.905 0.017 1.00 20.00 +HETATM 27 H27 UNK 1 1.152 3.169 0.008 1.00 20.00 +HETATM 28 H28 UNK 1 3.304 1.974 -0.019 1.00 20.00 +HETATM 29 H29 UNK 1 6.153 -4.366 -0.831 1.00 20.00 +HETATM 30 H30 UNK 1 5.712 -5.509 -2.967 1.00 20.00 +HETATM 31 H31 UNK 1 7.087 -4.997 -4.944 1.00 20.00 +HETATM 32 H32 UNK 1 8.897 -3.335 -4.788 1.00 20.00 +HETATM 33 H33 UNK 1 9.332 -2.185 -2.655 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 21 +CONECT 3 2 4 22 +CONECT 4 3 5 7 +CONECT 5 4 6 +CONECT 6 5 8 +CONECT 7 4 8 23 +CONECT 8 7 6 9 +CONECT 9 8 14 10 +CONECT 10 9 11 24 +CONECT 11 10 12 25 +CONECT 12 11 13 26 +CONECT 13 12 14 27 +CONECT 14 13 9 28 +CONECT 15 2 20 16 +CONECT 16 15 17 29 +CONECT 17 16 18 30 +CONECT 18 17 19 31 +CONECT 19 18 20 32 +CONECT 20 19 15 33 +CONECT 21 2 +CONECT 22 3 +CONECT 23 7 +CONECT 24 10 +CONECT 25 11 +CONECT 26 12 +CONECT 27 13 +CONECT 28 14 +CONECT 29 16 +CONECT 30 17 +CONECT 31 18 +CONECT 32 19 +CONECT 33 20 +END diff --git a/top/gaff/SM46/SM46.pdb b/top/gaff/SM46/SM46.pdb deleted file mode 120000 index a13f689..0000000 --- a/top/gaff/SM46/SM46.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM46/SM46.pdb \ No newline at end of file diff --git a/top/gaff/SM46/SM46.pdb b/top/gaff/SM46/SM46.pdb new file mode 100644 index 0000000..4bf16c3 --- /dev/null +++ b/top/gaff/SM46/SM46.pdb @@ -0,0 +1,66 @@ +HEADER UNK 20-07-09 1UNK +COMPND SM46 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.472 0.781 -0.017 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 4 C4 UNK 1 1.195 1.684 -0.000 1.00 20.00 +HETATM 5 N5 UNK 1 1.335 3.017 0.006 1.00 20.00 +HETATM 6 N6 UNK 1 2.588 3.309 -0.005 1.00 20.00 +HETATM 7 C7 UNK 1 2.451 1.166 -0.010 1.00 20.00 +HETATM 8 N8 UNK 1 3.298 2.236 -0.018 1.00 20.00 +HETATM 9 C9 UNK 1 4.699 2.177 -0.032 1.00 20.00 +HETATM 10 C10 UNK 1 5.343 0.947 -0.041 1.00 20.00 +HETATM 11 C11 UNK 1 6.723 0.892 -0.061 1.00 20.00 +HETATM 12 C12 UNK 1 7.463 2.060 -0.062 1.00 20.00 +HETATM 13 C13 UNK 1 6.825 3.287 -0.048 1.00 20.00 +HETATM 14 C14 UNK 1 5.445 3.348 -0.033 1.00 20.00 +HETATM 15 N15 UNK 1 -1.565 2.605 -1.410 1.00 20.00 +HETATM 16 C16 UNK 1 -2.176 1.972 -2.581 1.00 20.00 +HETATM 17 C17 UNK 1 -1.049 3.973 -1.503 1.00 20.00 +HETATM 18 O18 UNK 1 -1.361 2.752 1.045 1.00 20.00 +HETATM 19 H19 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 20 H20 UNK 1 2.723 0.121 -0.012 1.00 20.00 +HETATM 21 H21 UNK 1 4.766 0.035 -0.035 1.00 20.00 +HETATM 22 H22 UNK 1 7.225 -0.064 -0.072 1.00 20.00 +HETATM 23 H23 UNK 1 8.542 2.015 -0.073 1.00 20.00 +HETATM 24 H24 UNK 1 7.405 4.197 -0.049 1.00 20.00 +HETATM 25 H25 UNK 1 4.947 4.306 -0.023 1.00 20.00 +HETATM 26 H26 UNK 1 -3.246 2.180 -2.589 1.00 20.00 +HETATM 27 H27 UNK 1 -1.722 2.369 -3.488 1.00 20.00 +HETATM 28 H28 UNK 1 -2.016 0.894 -2.536 1.00 20.00 +HETATM 29 H29 UNK 1 -0.002 3.946 -1.808 1.00 20.00 +HETATM 30 H30 UNK 1 -1.628 4.530 -2.239 1.00 20.00 +HETATM 31 H31 UNK 1 -1.131 4.459 -0.531 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 15 18 +CONECT 3 2 4 19 +CONECT 4 3 5 7 +CONECT 5 4 6 +CONECT 6 5 8 +CONECT 7 4 8 20 +CONECT 8 7 6 9 +CONECT 9 8 14 10 +CONECT 10 9 11 21 +CONECT 11 10 12 22 +CONECT 12 11 13 23 +CONECT 13 12 14 24 +CONECT 14 13 9 25 +CONECT 15 2 16 17 +CONECT 16 15 26 27 28 +CONECT 17 15 29 30 31 +CONECT 18 2 +CONECT 19 3 +CONECT 20 7 +CONECT 21 10 +CONECT 22 11 +CONECT 23 12 +CONECT 24 13 +CONECT 25 14 +CONECT 26 16 +CONECT 27 16 +CONECT 28 16 +CONECT 29 17 +CONECT 30 17 +CONECT 31 17 +END diff --git a/top/gaff/refCMC26/refCMC26.pdb b/top/gaff/refCMC26/refCMC26.pdb deleted file mode 120000 index e65bf4d..0000000 --- a/top/gaff/refCMC26/refCMC26.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/refCMC26/refCMC26.pdb \ No newline at end of file diff --git a/top/gaff/refCMC26/refCMC26.pdb b/top/gaff/refCMC26/refCMC26.pdb new file mode 100644 index 0000000..aec9e69 --- /dev/null +++ b/top/gaff/refCMC26/refCMC26.pdb @@ -0,0 +1,62 @@ +HEADER UNK 20-07-10 1UNK +COMPND refCMC26 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 O1 UNK 1 -2.328 -0.173 0.024 1.00 20.00 +HETATM 2 C2 UNK 1 -1.266 -0.764 0.011 1.00 20.00 +HETATM 3 C3 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 4 C4 UNK 1 -0.017 1.392 0.010 1.00 20.00 +HETATM 5 C5 UNK 1 1.170 2.094 0.002 1.00 20.00 +HETATM 6 C6 UNK 1 2.378 1.419 -0.013 1.00 20.00 +HETATM 7 C7 UNK 1 2.403 0.036 -0.021 1.00 20.00 +HETATM 8 C8 UNK 1 1.224 -0.679 -0.013 1.00 20.00 +HETATM 9 N9 UNK 1 -1.245 -2.111 0.003 1.00 20.00 +HETATM 10 S10 UNK 1 -2.665 -2.962 0.013 1.00 20.00 +HETATM 11 C11 UNK 1 -3.493 -2.612 -1.503 1.00 20.00 +HETATM 12 C12 UNK 1 -4.375 -1.550 -1.579 1.00 20.00 +HETATM 13 C13 UNK 1 -5.021 -1.272 -2.769 1.00 20.00 +HETATM 14 C14 UNK 1 -4.793 -2.063 -3.880 1.00 20.00 +HETATM 15 C15 UNK 1 -3.915 -3.128 -3.802 1.00 20.00 +HETATM 16 C16 UNK 1 -3.265 -3.403 -2.614 1.00 20.00 +HETATM 17 O17 UNK 1 -2.309 -4.337 -0.033 1.00 20.00 +HETATM 18 O18 UNK 1 -3.463 -2.400 1.045 1.00 20.00 +HETATM 19 H19 UNK 1 -0.959 1.920 0.017 1.00 20.00 +HETATM 20 H20 UNK 1 1.157 3.174 0.008 1.00 20.00 +HETATM 21 H21 UNK 1 3.304 1.974 -0.019 1.00 20.00 +HETATM 22 H22 UNK 1 3.349 -0.486 -0.033 1.00 20.00 +HETATM 23 H23 UNK 1 1.245 -1.759 -0.020 1.00 20.00 +HETATM 24 H24 UNK 1 -0.397 -2.583 -0.008 1.00 20.00 +HETATM 25 H25 UNK 1 -4.556 -0.935 -0.710 1.00 20.00 +HETATM 26 H26 UNK 1 -5.707 -0.440 -2.830 1.00 20.00 +HETATM 27 H27 UNK 1 -5.301 -1.849 -4.809 1.00 20.00 +HETATM 28 H28 UNK 1 -3.738 -3.746 -4.670 1.00 20.00 +HETATM 29 H29 UNK 1 -2.580 -4.235 -2.553 1.00 20.00 +CONECT 1 2 +CONECT 2 1 3 9 +CONECT 3 2 8 4 +CONECT 4 3 5 19 +CONECT 5 4 6 20 +CONECT 6 5 7 21 +CONECT 7 6 8 22 +CONECT 8 7 3 23 +CONECT 9 2 10 24 +CONECT 10 9 11 17 18 +CONECT 11 10 16 12 +CONECT 12 11 13 25 +CONECT 13 12 14 26 +CONECT 14 13 15 27 +CONECT 15 14 16 28 +CONECT 16 15 11 29 +CONECT 17 10 +CONECT 18 10 +CONECT 19 4 +CONECT 20 5 +CONECT 21 6 +CONECT 22 7 +CONECT 23 8 +CONECT 24 9 +CONECT 25 12 +CONECT 26 13 +CONECT 27 14 +CONECT 28 15 +CONECT 29 16 +END diff --git a/top/gaff/refJMC11/refJMC11.pdb b/top/gaff/refJMC11/refJMC11.pdb deleted file mode 120000 index aed7b6d..0000000 --- a/top/gaff/refJMC11/refJMC11.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/refJMC11/refJMC11.pdb \ No newline at end of file diff --git a/top/gaff/refJMC11/refJMC11.pdb b/top/gaff/refJMC11/refJMC11.pdb new file mode 100644 index 0000000..1615dd4 --- /dev/null +++ b/top/gaff/refJMC11/refJMC11.pdb @@ -0,0 +1,62 @@ +HEADER UNK 20-07-10 1UNK +COMPND refJMC11 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 0.809 10.429 -2.312 1.00 20.00 +HETATM 2 S2 UNK 1 -0.525 9.471 -3.082 1.00 20.00 +HETATM 3 O3 UNK 1 -0.464 9.580 -4.497 1.00 20.00 +HETATM 4 O4 UNK 1 -1.747 9.668 -2.384 1.00 20.00 +HETATM 5 N5 UNK 1 -0.130 7.892 -2.776 1.00 20.00 +HETATM 6 C6 UNK 1 -0.111 7.396 -1.398 1.00 20.00 +HETATM 7 C7 UNK 1 -0.090 5.866 -1.407 1.00 20.00 +HETATM 8 C8 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 9 C9 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 10 C10 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 11 C11 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 12 C12 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 13 C13 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 14 C14 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 15 H15 UNK 1 1.762 10.153 -2.763 1.00 20.00 +HETATM 16 H16 UNK 1 0.628 11.493 -2.466 1.00 20.00 +HETATM 17 H17 UNK 1 0.839 10.217 -1.243 1.00 20.00 +HETATM 18 H18 UNK 1 0.090 7.296 -3.509 1.00 20.00 +HETATM 19 H19 UNK 1 -1.001 7.744 -0.874 1.00 20.00 +HETATM 20 H20 UNK 1 0.779 7.768 -0.889 1.00 20.00 +HETATM 21 H21 UNK 1 0.800 5.518 -1.931 1.00 20.00 +HETATM 22 H22 UNK 1 -0.980 5.493 -1.915 1.00 20.00 +HETATM 23 H23 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 24 H24 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 25 H25 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 26 H26 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 27 H27 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 28 H28 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 29 H29 UNK 1 -2.180 3.660 0.041 1.00 20.00 +CONECT 1 2 15 16 17 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 18 +CONECT 6 5 7 19 20 +CONECT 7 6 8 21 22 +CONECT 8 7 9 23 24 +CONECT 9 8 14 10 +CONECT 10 9 11 25 +CONECT 11 10 12 26 +CONECT 12 11 13 27 +CONECT 13 12 14 28 +CONECT 14 13 9 29 +CONECT 15 1 +CONECT 16 1 +CONECT 17 1 +CONECT 18 5 +CONECT 19 6 +CONECT 20 6 +CONECT 21 7 +CONECT 22 7 +CONECT 23 8 +CONECT 24 8 +CONECT 25 10 +CONECT 26 11 +CONECT 27 12 +CONECT 28 13 +CONECT 29 14 +END diff --git a/top/gaff/refJMC12/refJMC12.pdb b/top/gaff/refJMC12/refJMC12.pdb deleted file mode 120000 index 73e0090..0000000 --- a/top/gaff/refJMC12/refJMC12.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/refJMC12/refJMC12.pdb \ No newline at end of file diff --git a/top/gaff/refJMC12/refJMC12.pdb b/top/gaff/refJMC12/refJMC12.pdb new file mode 100644 index 0000000..beddbac --- /dev/null +++ b/top/gaff/refJMC12/refJMC12.pdb @@ -0,0 +1,60 @@ +HEADER UNK 20-07-10 1UNK +COMPND refJMC12 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 1.440 10.179 -1.819 1.00 20.00 +HETATM 2 S2 UNK 1 -0.152 9.709 -2.550 1.00 20.00 +HETATM 3 O3 UNK 1 -0.195 10.068 -3.925 1.00 20.00 +HETATM 4 O4 UNK 1 -1.221 10.040 -1.674 1.00 20.00 +HETATM 5 N5 UNK 1 -0.130 8.053 -2.561 1.00 20.00 +HETATM 6 C6 UNK 1 -0.111 7.373 -1.398 1.00 20.00 +HETATM 7 O7 UNK 1 -0.110 7.973 -0.344 1.00 20.00 +HETATM 8 C8 UNK 1 -0.090 5.866 -1.407 1.00 20.00 +HETATM 9 C9 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 10 C10 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 11 C11 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 12 C12 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 13 C13 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 14 C14 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 15 C15 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 16 H16 UNK 1 2.251 9.787 -2.433 1.00 20.00 +HETATM 17 H17 UNK 1 1.512 11.266 -1.773 1.00 20.00 +HETATM 18 H18 UNK 1 1.513 9.767 -0.813 1.00 20.00 +HETATM 19 H19 UNK 1 -0.131 7.574 -3.404 1.00 20.00 +HETATM 20 H20 UNK 1 0.800 5.518 -1.931 1.00 20.00 +HETATM 21 H21 UNK 1 -0.980 5.493 -1.915 1.00 20.00 +HETATM 22 H22 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 23 H23 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 24 H24 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 25 H25 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 26 H26 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 27 H27 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 28 H28 UNK 1 -2.180 3.660 0.041 1.00 20.00 +CONECT 1 2 16 17 18 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 19 +CONECT 6 5 7 8 +CONECT 7 6 +CONECT 8 6 9 20 21 +CONECT 9 8 10 22 23 +CONECT 10 9 15 11 +CONECT 11 10 12 24 +CONECT 12 11 13 25 +CONECT 13 12 14 26 +CONECT 14 13 15 27 +CONECT 15 14 10 28 +CONECT 16 1 +CONECT 17 1 +CONECT 18 1 +CONECT 19 5 +CONECT 20 8 +CONECT 21 8 +CONECT 22 9 +CONECT 23 9 +CONECT 24 11 +CONECT 25 12 +CONECT 26 13 +CONECT 27 14 +CONECT 28 15 +END diff --git a/top/gaff/refJMC13/refJMC13.pdb b/top/gaff/refJMC13/refJMC13.pdb deleted file mode 120000 index 2b64a2b..0000000 --- a/top/gaff/refJMC13/refJMC13.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/refJMC13/refJMC13.pdb \ No newline at end of file diff --git a/top/gaff/refJMC13/refJMC13.pdb b/top/gaff/refJMC13/refJMC13.pdb new file mode 100644 index 0000000..27d2939 --- /dev/null +++ b/top/gaff/refJMC13/refJMC13.pdb @@ -0,0 +1,70 @@ +HEADER UNK 20-07-10 1UNK +COMPND refJMC13 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 2.440 10.453 -2.754 1.00 20.00 +HETATM 2 N2 UNK 1 1.280 10.215 -1.891 1.00 20.00 +HETATM 3 C3 UNK 1 1.388 10.424 -0.446 1.00 20.00 +HETATM 4 S4 UNK 1 -0.152 9.709 -2.550 1.00 20.00 +HETATM 5 O5 UNK 1 -0.135 10.119 -3.911 1.00 20.00 +HETATM 6 O6 UNK 1 -1.171 10.091 -1.637 1.00 20.00 +HETATM 7 N7 UNK 1 -0.130 8.053 -2.561 1.00 20.00 +HETATM 8 C8 UNK 1 -0.111 7.373 -1.398 1.00 20.00 +HETATM 9 O9 UNK 1 -0.110 7.973 -0.344 1.00 20.00 +HETATM 10 C10 UNK 1 -0.090 5.866 -1.407 1.00 20.00 +HETATM 11 C11 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 12 C12 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 13 C13 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 14 C14 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 15 C15 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 16 C16 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 17 C17 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 18 H18 UNK 1 2.437 11.490 -3.089 1.00 20.00 +HETATM 19 H19 UNK 1 3.355 10.253 -2.197 1.00 20.00 +HETATM 20 H20 UNK 1 2.390 9.792 -3.620 1.00 20.00 +HETATM 21 H21 UNK 1 0.432 10.199 0.026 1.00 20.00 +HETATM 22 H22 UNK 1 2.157 9.767 -0.040 1.00 20.00 +HETATM 23 H23 UNK 1 1.655 11.462 -0.248 1.00 20.00 +HETATM 24 H24 UNK 1 -0.131 7.574 -3.404 1.00 20.00 +HETATM 25 H25 UNK 1 0.800 5.518 -1.931 1.00 20.00 +HETATM 26 H26 UNK 1 -0.980 5.493 -1.915 1.00 20.00 +HETATM 27 H27 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 28 H28 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 29 H29 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 30 H30 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 31 H31 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 32 H32 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 33 H33 UNK 1 -2.180 3.660 0.041 1.00 20.00 +CONECT 1 2 18 19 20 +CONECT 2 1 3 4 +CONECT 3 2 21 22 23 +CONECT 4 2 5 6 7 +CONECT 5 4 +CONECT 6 4 +CONECT 7 4 8 24 +CONECT 8 7 9 10 +CONECT 9 8 +CONECT 10 8 11 25 26 +CONECT 11 10 12 27 28 +CONECT 12 11 17 13 +CONECT 13 12 14 29 +CONECT 14 13 15 30 +CONECT 15 14 16 31 +CONECT 16 15 17 32 +CONECT 17 16 12 33 +CONECT 18 1 +CONECT 19 1 +CONECT 20 1 +CONECT 21 3 +CONECT 22 3 +CONECT 23 3 +CONECT 24 7 +CONECT 25 10 +CONECT 26 10 +CONECT 27 11 +CONECT 28 11 +CONECT 29 13 +CONECT 30 14 +CONECT 31 15 +CONECT 32 16 +CONECT 33 17 +END diff --git a/top/gaff/refJMC14/refJMC14.pdb b/top/gaff/refJMC14/refJMC14.pdb deleted file mode 120000 index 51db612..0000000 --- a/top/gaff/refJMC14/refJMC14.pdb +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/refJMC14/refJMC14.pdb \ No newline at end of file diff --git a/top/gaff/refJMC14/refJMC14.pdb b/top/gaff/refJMC14/refJMC14.pdb new file mode 100644 index 0000000..e80353d --- /dev/null +++ b/top/gaff/refJMC14/refJMC14.pdb @@ -0,0 +1,58 @@ +HEADER UNK 20-07-10 1UNK +COMPND refJMC14 +REMARK 1 corina 4.2.0 0026 27.09.2018 +HETATM 1 C1 UNK 1 1.438 9.855 -2.508 1.00 20.00 +HETATM 2 S2 UNK 1 -0.151 9.257 -3.144 1.00 20.00 +HETATM 3 O3 UNK 1 -0.191 9.358 -4.561 1.00 20.00 +HETATM 4 O4 UNK 1 -1.222 9.740 -2.345 1.00 20.00 +HETATM 5 N5 UNK 1 -0.127 7.627 -2.852 1.00 20.00 +HETATM 6 C6 UNK 1 -0.109 7.170 -1.584 1.00 20.00 +HETATM 7 O7 UNK 1 -0.112 7.955 -0.655 1.00 20.00 +HETATM 8 N8 UNK 1 -0.089 5.844 -1.346 1.00 20.00 +HETATM 9 C9 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 10 C10 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 11 C11 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 12 C12 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 13 C13 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 14 C14 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 15 C15 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 16 H16 UNK 1 2.252 9.359 -3.037 1.00 20.00 +HETATM 17 H17 UNK 1 1.509 10.932 -2.660 1.00 20.00 +HETATM 18 H18 UNK 1 1.510 9.634 -1.443 1.00 20.00 +HETATM 19 H19 UNK 1 -0.125 7.001 -3.593 1.00 20.00 +HETATM 20 H20 UNK 1 -0.087 5.218 -2.087 1.00 20.00 +HETATM 21 H21 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 22 H22 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 23 H23 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 24 H24 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 25 H25 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 26 H26 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 27 H27 UNK 1 -2.180 3.660 0.041 1.00 20.00 +CONECT 1 2 16 17 18 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 19 +CONECT 6 5 7 8 +CONECT 7 6 +CONECT 8 6 9 20 +CONECT 9 8 10 21 22 +CONECT 10 9 15 11 +CONECT 11 10 12 23 +CONECT 12 11 13 24 +CONECT 13 12 14 25 +CONECT 14 13 15 26 +CONECT 15 14 10 27 +CONECT 16 1 +CONECT 17 1 +CONECT 18 1 +CONECT 19 5 +CONECT 20 8 +CONECT 21 9 +CONECT 22 9 +CONECT 23 11 +CONECT 24 12 +CONECT 25 13 +CONECT 26 14 +CONECT 27 15 +END diff --git a/top/oplsaa/SM25/SM25.itp b/top/oplsaa/SM25/SM25.itp new file mode 120000 index 0000000..35225b6 --- /dev/null +++ b/top/oplsaa/SM25/SM25.itp @@ -0,0 +1 @@ +SM25.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM25/SM25.mol2 b/top/oplsaa/SM25/SM25.mol2 new file mode 100644 index 0000000..a0302ac --- /dev/null +++ b/top/oplsaa/SM25/SM25.mol2 @@ -0,0 +1,92 @@ +# Name: SM25 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 35 36 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -2.0952 5.2001 -1.8761 O.2 + 2 C2 -1.1555 5.8189 -2.3288 C.2 + 3 N3 -0.0945 6.1007 -1.5469 N.am + 4 S4 -0.0740 5.6020 0.0321 S.o2 + 5 C5 -0.0501 3.8402 0.0223 C.ar + 6 C6 1.1563 3.1654 0.0081 C.ar + 7 C7 1.1750 1.7832 0.0004 C.ar + 8 C8 -0.0126 1.0758 0.0080 C.ar + 9 C9 -1.2190 1.7506 0.0173 C.ar + 10 C10 -1.2377 3.1328 0.0294 C.ar + 11 O11 -1.3242 5.9833 0.5896 O.2 + 12 O12 1.1750 6.0173 0.5678 O.2 + 13 C13 -1.1742 6.2728 -3.7657 C.3 + 14 C14 -2.4814 5.8273 -4.4243 C.3 + 15 C15 -2.5001 6.2811 -5.8612 C.ar + 16 C16 -3.0310 7.5145 -6.1896 C.ar + 17 C17 -3.0437 7.9329 -7.5071 C.ar + 18 C18 -2.5352 7.1134 -8.4974 C.ar + 19 C19 -2.0092 5.8778 -8.1696 C.ar + 20 C20 -1.9916 5.4617 -6.8515 C.ar + 21 H21 0.6570 6.5957 -1.9090 H + 22 H22 2.0842 3.7181 0.0025 H + 23 H23 2.1175 1.2560 -0.0111 H + 24 H24 0.0021 -0.0041 0.0020 H + 25 H25 -2.1469 1.1980 0.0187 H + 26 H26 -2.1802 3.6600 0.0409 H + 27 H27 -1.0998 7.3595 -3.8045 H + 28 H28 -0.3309 5.8316 -4.2971 H + 29 H29 -2.5559 4.7405 -4.3855 H + 30 H30 -3.3247 6.2685 -3.8929 H + 31 H31 -3.4323 8.1529 -5.4164 H + 32 H32 -3.4551 8.8981 -7.7632 H + 33 H33 -2.5493 7.4383 -9.5273 H + 34 H34 -1.6122 5.2374 -8.9434 H + 35 H35 -1.5810 4.4962 -6.5955 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 13 1 + 4 3 4 am + 5 3 21 1 + 6 4 5 1 + 7 4 11 2 + 8 4 12 2 + 9 5 10 ar + 10 5 6 ar + 11 6 7 ar + 12 6 22 1 + 13 7 8 ar + 14 7 23 1 + 15 8 9 ar + 16 8 24 1 + 17 9 10 ar + 18 9 25 1 + 19 10 26 1 + 20 13 14 1 + 21 13 27 1 + 22 13 28 1 + 23 14 15 1 + 24 14 29 1 + 25 14 30 1 + 26 15 20 ar + 27 15 16 ar + 28 16 17 ar + 29 16 31 1 + 30 17 18 ar + 31 17 32 1 + 32 18 19 ar + 33 18 33 1 + 34 19 20 ar + 35 19 34 1 + 36 20 35 1 + +# End of record + diff --git a/top/oplsaa/SM25/SM25.mol2.1.itp b/top/oplsaa/SM25/SM25.mol2.1.itp new file mode 100644 index 0000000..1924cee --- /dev/null +++ b/top/oplsaa/SM25/SM25.mol2.1.itp @@ -0,0 +1,361 @@ +; input pdb SMILES : O=C(N[S](C1=CC=CC=C1)(=O)=O)CCC2=CC=CC=C2 +; Script arguments : SM25.mol2 "3 opls_251" "21 opls_254" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_474 1 UNK S4 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 2 opls_488 1 UNK C5 1 0.000 12.01100 ; CA # The charge for this atom has been adjusted to take into account contributions from:`CA (opls_488)' AND `CA (opls_488)' + 3 opls_475 1 UNK O11 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 4 opls_475 1 UNK O12 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 5 opls_236 1 UNK O1 3 -0.500 15.99940 ; O # O: C=O in amide. Acyl R on C in amide is neutral - + 6 opls_235 1 UNK C2 3 0.500 12.01100 ; C # C=O in amide, dmf, peptide bond + 7 opls_149 1 UNK C14 4 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 8 opls_145 1 UNK C15 4 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 9 opls_140 1 UNK H29 4 0.060 1.00800 ; HC # alkane H. + 10 opls_140 1 UNK H30 4 0.060 1.00800 ; HC # alkane H. + 11 opls_136 1 UNK C13 8 -0.120 12.01100 ; CT # alkane CH2 + 12 opls_140 1 UNK H27 8 0.060 1.00800 ; HC # alkane H. + 13 opls_140 1 UNK H28 8 0.060 1.00800 ; HC # alkane H. + 14 opls_145 1 UNK C6 12 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 15 opls_146 1 UNK H22 12 0.115 1.00800 ; HA # Benzene H - 12 site. + 16 opls_145 1 UNK C7 14 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 17 opls_146 1 UNK H23 14 0.115 1.00800 ; HA # Benzene H - 12 site. + 18 opls_145 1 UNK C8 16 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 19 opls_146 1 UNK H24 16 0.115 1.00800 ; HA # Benzene H - 12 site. + 20 opls_145 1 UNK C9 18 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 21 opls_146 1 UNK H25 18 0.115 1.00800 ; HA # Benzene H - 12 site. + 22 opls_145 1 UNK C10 20 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 23 opls_146 1 UNK H26 20 0.115 1.00800 ; HA # Benzene H - 12 site. + 24 opls_145 1 UNK C16 22 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 25 opls_146 1 UNK H31 22 0.115 1.00800 ; HA # Benzene H - 12 site. + 26 opls_145 1 UNK C17 24 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 27 opls_146 1 UNK H32 24 0.115 1.00800 ; HA # Benzene H - 12 site. + 28 opls_145 1 UNK C18 26 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 29 opls_146 1 UNK H33 26 0.115 1.00800 ; HA # Benzene H - 12 site. + 30 opls_145 1 UNK C19 28 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 31 opls_146 1 UNK H34 28 0.115 1.00800 ; HA # Benzene H - 12 site. + 32 opls_145 1 UNK C20 30 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 33 opls_146 1 UNK H35 30 0.115 1.00800 ; HA # Benzene H - 12 site. + 34 opls_251 1 UNK N3 32 -0.490 14.00670 ; N # N in imide ### user-defined OPLS atom type (opls_251) + 35 opls_254 1 UNK H21 32 0.370 1.00800 ; H # H(N) in imide ### user-defined OPLS atom type (opls_254) +; Total charge : 0.000 ### Number of unassigned atoms : 0/35 + +[ bonds ] +; ai aj funct r k + 5 6 1 ; O-C # (C-O) URAGUA,CYT,AA + 6 34 1 ; C-N # AA + 6 11 1 ; C-CT # + 34 1 1 ; N-SY # (SY-N) + 34 35 1 ; N-H # (H-N) + 1 2 1 ; SY-CA # + 1 3 1 ; SY-OY # + 1 4 1 ; SY-OY # + 2 22 1 ; CA-CA # TRP,TYR,PHE + 2 14 1 ; CA-CA # TRP,TYR,PHE + 14 16 1 ; CA-CA # TRP,TYR,PHE + 14 15 1 ; CA-HA # PHE, etc. + 16 18 1 ; CA-CA # TRP,TYR,PHE + 16 17 1 ; CA-HA # PHE, etc. + 18 20 1 ; CA-CA # TRP,TYR,PHE + 18 19 1 ; CA-HA # PHE, etc. + 20 22 1 ; CA-CA # TRP,TYR,PHE + 20 21 1 ; CA-HA # PHE, etc. + 22 23 1 ; CA-HA # PHE, etc. + 11 7 1 ; CT-CT # CHARMM 22 parameter file + 11 12 1 ; CT-HC # CHARMM 22 parameter file + 11 13 1 ; CT-HC # CHARMM 22 parameter file + 7 8 1 ; CT-CA # (CA-CT) PHE,TYR + 7 9 1 ; CT-HC # CHARMM 22 parameter file + 7 10 1 ; CT-HC # CHARMM 22 parameter file + 8 32 1 ; CA-CA # TRP,TYR,PHE + 8 24 1 ; CA-CA # TRP,TYR,PHE + 24 26 1 ; CA-CA # TRP,TYR,PHE + 24 25 1 ; CA-HA # PHE, etc. + 26 28 1 ; CA-CA # TRP,TYR,PHE + 26 27 1 ; CA-HA # PHE, etc. + 28 30 1 ; CA-CA # TRP,TYR,PHE + 28 29 1 ; CA-HA # PHE, etc. + 30 32 1 ; CA-CA # TRP,TYR,PHE + 30 31 1 ; CA-HA # PHE, etc. + 32 33 1 ; CA-HA # PHE, etc. + +[ angles ] +; ai aj ak funct theta cth + 5 6 34 1 ; O-C-N # (N-C-O) AA(OL) + 5 6 11 1 ; O-C-CT # (CT-C-O) + 34 6 11 1 ; N-C-CT # (CT-C-N) + 6 34 1 1 112.000 585.760 ; C-N-SY # LigParGen + 6 34 35 1 ; C-N-H # AA(OL) + 1 34 35 1 ; SY-N-H # (H-N-SY) + 34 1 2 1 ; N-SY-CA # + 34 1 3 1 ; N-SY-OY # (OY-SY-N) + 34 1 4 1 ; N-SY-OY # (OY-SY-N) + 2 1 3 1 ; CA-SY-OY # (OY-SY-CA) + 2 1 4 1 ; CA-SY-OY # (OY-SY-CA) + 3 1 4 1 ; OY-SY-OY # + 1 2 22 1 ; SY-CA-CA # + 1 2 14 1 ; SY-CA-CA # + 14 2 22 1 ; CA-CA-CA # PHE(OL) + 2 14 16 1 ; CA-CA-CA # PHE(OL) + 2 14 15 1 ; CA-CA-HA # + 16 14 15 1 ; CA-CA-HA # + 14 16 18 1 ; CA-CA-CA # PHE(OL) + 14 16 17 1 ; CA-CA-HA # + 18 16 17 1 ; CA-CA-HA # + 16 18 20 1 ; CA-CA-CA # PHE(OL) + 16 18 19 1 ; CA-CA-HA # + 20 18 19 1 ; CA-CA-HA # + 18 20 22 1 ; CA-CA-CA # PHE(OL) + 18 20 21 1 ; CA-CA-HA # + 22 20 21 1 ; CA-CA-HA # + 2 22 20 1 ; CA-CA-CA # PHE(OL) + 2 22 23 1 ; CA-CA-HA # + 20 22 23 1 ; CA-CA-HA # + 6 11 7 1 ; C-CT-CT # AA + 6 11 12 1 ; C-CT-HC # + 6 11 13 1 ; C-CT-HC # + 7 11 12 1 ; CT-CT-HC # CHARMM 22 parameter file + 7 11 13 1 ; CT-CT-HC # CHARMM 22 parameter file + 12 11 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 11 7 8 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 11 7 9 1 ; CT-CT-HC # CHARMM 22 parameter file + 11 7 10 1 ; CT-CT-HC # CHARMM 22 parameter file + 8 7 9 1 ; CA-CT-HC # + 8 7 10 1 ; CA-CT-HC # + 9 7 10 1 ; HC-CT-HC # CHARMM 22 parameter file + 7 8 32 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 7 8 24 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 24 8 32 1 ; CA-CA-CA # PHE(OL) + 8 24 26 1 ; CA-CA-CA # PHE(OL) + 8 24 25 1 ; CA-CA-HA # + 26 24 25 1 ; CA-CA-HA # + 24 26 28 1 ; CA-CA-CA # PHE(OL) + 24 26 27 1 ; CA-CA-HA # + 28 26 27 1 ; CA-CA-HA # + 26 28 30 1 ; CA-CA-CA # PHE(OL) + 26 28 29 1 ; CA-CA-HA # + 30 28 29 1 ; CA-CA-HA # + 28 30 32 1 ; CA-CA-CA # PHE(OL) + 28 30 31 1 ; CA-CA-HA # + 32 30 31 1 ; CA-CA-HA # + 8 32 30 1 ; CA-CA-CA # PHE(OL) + 8 32 33 1 ; CA-CA-HA # + 30 32 33 1 ; CA-CA-HA # + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 5 6 34 1 3 25.476 0.000 -25.476 -0.000 -0.000 0.000 ; O-C-N-SY # LigParGen + 5 6 34 35 3 ; O-C-N-H # (H-N-C-O) amides wlj 6/20/97 + 11 6 34 1 3 -3.431 -3.008 10.598 -4.159 -0.000 0.000 ; CT-C-N-SY # LigParGen + 11 6 34 35 3 ; CT-C-N-H # amides C-C(O)-N-H + 5 6 11 7 3 ; O-C-CT-CT # (CT-CT-C-O) propanamide + 5 6 11 12 3 ; O-C-CT-HC # (HC-CT-C-O) all carbonyls + 5 6 11 13 3 ; O-C-CT-HC # (HC-CT-C-O) all carbonyls + 34 6 11 7 3 ; N-C-CT-CT # (CT-CT-C-N) propanamide + 34 6 11 12 3 ; N-C-CT-HC # (HC-CT-C-N) acetamide + 34 6 11 13 3 ; N-C-CT-HC # (HC-CT-C-N) acetamide + 6 34 1 2 3 -2.897 11.182 12.410 -20.694 -0.000 0.000 ; C-N-SY-CA # LigParGen + 6 34 1 3 3 ; C-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 6 34 1 4 3 ; C-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 35 34 1 2 3 ; H-N-SY-CA # (CA-SY-N-H) sulfonamide + 35 34 1 3 3 ; H-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 35 34 1 4 3 ; H-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 34 1 2 22 3 ; N-SY-CA-CA # (CA-CA-SY-N) sulfonamide + 34 1 2 14 3 ; N-SY-CA-CA # (CA-CA-SY-N) sulfonamide + 3 1 2 22 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 3 1 2 14 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 4 1 2 22 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 4 1 2 14 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 1 2 22 20 3 ; SY-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 1 2 22 23 3 ; SY-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 2 22 20 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 2 22 23 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 1 2 14 16 3 ; SY-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 1 2 14 15 3 ; SY-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 2 14 16 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 2 14 15 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 14 16 18 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 14 16 17 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 14 16 18 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 14 16 17 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 16 18 20 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 16 18 19 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 16 18 20 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 16 18 19 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 18 20 22 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 18 20 21 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 18 20 22 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 18 20 21 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 20 22 2 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 20 22 23 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 20 22 2 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 20 22 23 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 6 11 7 8 3 ; C-CT-CT-CA # aldehyde & ketone & acyl halide + 6 11 7 9 3 ; C-CT-CT-HC # + 6 11 7 10 3 ; C-CT-CT-HC # + 12 11 7 8 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 12 11 7 9 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 12 11 7 10 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 13 11 7 8 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 13 11 7 9 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 13 11 7 10 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 11 7 8 32 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 11 7 8 24 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 9 7 8 32 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 9 7 8 24 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 10 7 8 32 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 10 7 8 24 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 7 8 32 30 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 7 8 32 33 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 8 32 30 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 8 32 33 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 7 8 24 26 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 7 8 24 25 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 8 24 26 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 8 24 25 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 8 24 26 28 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 8 24 26 27 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 24 26 28 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 24 26 27 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 26 28 30 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 26 28 29 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 26 28 30 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 26 28 29 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 28 30 32 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 28 30 31 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 28 30 32 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 28 30 31 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 30 32 8 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 30 32 33 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 30 32 8 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 30 32 33 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 34 11 6 5 1 improper_O_C_X_Y ; N-CT-C-O + 1 35 34 6 1 improper_Z_N_X_Y ; SY-H-N-C + 22 14 2 1 1 improper_Z_CA_X_Y ; CA-CA-CA-SY + 16 15 14 2 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 18 17 16 14 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 20 19 18 16 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 22 21 20 18 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 20 23 22 2 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 32 24 8 7 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 26 25 24 8 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 28 27 26 24 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 30 29 28 26 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 32 31 30 28 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 30 33 32 8 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + +[ pairs ] +; ai aj funct + 5 1 1 + 5 35 1 + 5 7 1 + 5 12 1 + 5 13 1 + 6 2 1 + 6 3 1 + 6 4 1 + 6 8 1 + 6 9 1 + 6 10 1 + 34 7 1 + 34 12 1 + 34 13 1 + 34 22 1 + 34 14 1 + 1 11 1 + 1 20 1 + 1 23 1 + 1 16 1 + 1 15 1 + 2 35 1 + 2 18 1 + 2 21 1 + 2 17 1 + 14 3 1 + 14 4 1 + 14 20 1 + 14 23 1 + 14 19 1 + 16 22 1 + 16 21 1 + 18 15 1 + 18 23 1 + 20 17 1 + 22 3 1 + 22 4 1 + 22 15 1 + 22 19 1 + 3 35 1 + 4 35 1 + 11 35 1 + 11 32 1 + 11 24 1 + 7 30 1 + 7 33 1 + 7 26 1 + 7 25 1 + 8 12 1 + 8 13 1 + 8 28 1 + 8 31 1 + 8 27 1 + 24 9 1 + 24 10 1 + 24 30 1 + 24 33 1 + 24 29 1 + 26 32 1 + 26 31 1 + 28 25 1 + 28 33 1 + 30 27 1 + 32 9 1 + 32 10 1 + 32 25 1 + 32 29 1 + 15 17 1 + 17 19 1 + 19 21 1 + 21 23 1 + 12 9 1 + 12 10 1 + 13 9 1 + 13 10 1 + 25 27 1 + 27 29 1 + 29 31 1 + 31 33 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 5 1 1000 1000 1000 + 6 1 1000 1000 1000 + 34 1 1000 1000 1000 + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 14 1 1000 1000 1000 + 16 1 1000 1000 1000 + 18 1 1000 1000 1000 + 20 1 1000 1000 1000 + 22 1 1000 1000 1000 + 3 1 1000 1000 1000 + 4 1 1000 1000 1000 + 11 1 1000 1000 1000 + 7 1 1000 1000 1000 + 8 1 1000 1000 1000 + 24 1 1000 1000 1000 + 26 1 1000 1000 1000 + 28 1 1000 1000 1000 + 30 1 1000 1000 1000 + 32 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM25/SM25.mol2.1.pdb b/top/oplsaa/SM25/SM25.mol2.1.pdb new file mode 100644 index 0000000..cd4943f --- /dev/null +++ b/top/oplsaa/SM25/SM25.mol2.1.pdb @@ -0,0 +1,36 @@ +HETATM 1 S4 UNK 1 -0.074 5.602 0.032 1.00 20.00 +HETATM 2 C5 UNK 1 -0.050 3.840 0.022 1.00 20.00 +HETATM 3 O11 UNK 1 -1.324 5.983 0.590 1.00 20.00 +HETATM 4 O12 UNK 1 1.175 6.017 0.568 1.00 20.00 +HETATM 5 O1 UNK 1 -2.095 5.200 -1.876 1.00 20.00 +HETATM 6 C2 UNK 1 -1.155 5.819 -2.329 1.00 20.00 +HETATM 7 C14 UNK 1 -2.481 5.827 -4.424 1.00 20.00 +HETATM 8 C15 UNK 1 -2.500 6.281 -5.861 1.00 20.00 +HETATM 9 H29 UNK 1 -2.556 4.740 -4.386 1.00 20.00 +HETATM 10 H30 UNK 1 -3.325 6.269 -3.893 1.00 20.00 +HETATM 11 C13 UNK 1 -1.174 6.273 -3.766 1.00 20.00 +HETATM 12 H27 UNK 1 -1.100 7.359 -3.804 1.00 20.00 +HETATM 13 H28 UNK 1 -0.331 5.832 -4.297 1.00 20.00 +HETATM 14 C6 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 15 H22 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 16 C7 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 17 H23 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 18 C8 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 19 H24 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 20 C9 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 21 H25 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 22 C10 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 23 H26 UNK 1 -2.180 3.660 0.041 1.00 20.00 +HETATM 24 C16 UNK 1 -3.031 7.514 -6.190 1.00 20.00 +HETATM 25 H31 UNK 1 -3.432 8.153 -5.416 1.00 20.00 +HETATM 26 C17 UNK 1 -3.044 7.933 -7.507 1.00 20.00 +HETATM 27 H32 UNK 1 -3.455 8.898 -7.763 1.00 20.00 +HETATM 28 C18 UNK 1 -2.535 7.113 -8.497 1.00 20.00 +HETATM 29 H33 UNK 1 -2.549 7.438 -9.527 1.00 20.00 +HETATM 30 C19 UNK 1 -2.009 5.878 -8.170 1.00 20.00 +HETATM 31 H34 UNK 1 -1.612 5.237 -8.943 1.00 20.00 +HETATM 32 C20 UNK 1 -1.992 5.462 -6.851 1.00 20.00 +HETATM 33 H35 UNK 1 -1.581 4.496 -6.596 1.00 20.00 +HETATM 34 N3 UNK 1 -0.095 6.101 -1.547 1.00 20.00 +HETATM 35 H21 UNK 1 0.657 6.596 -1.909 1.00 20.00 +END diff --git a/top/oplsaa/SM25/SM25.pdb b/top/oplsaa/SM25/SM25.pdb new file mode 120000 index 0000000..a267ac9 --- /dev/null +++ b/top/oplsaa/SM25/SM25.pdb @@ -0,0 +1 @@ +SM25.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM26/SM26.itp b/top/oplsaa/SM26/SM26.itp new file mode 120000 index 0000000..a163d03 --- /dev/null +++ b/top/oplsaa/SM26/SM26.itp @@ -0,0 +1 @@ +SM26.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM26/SM26.mol2 b/top/oplsaa/SM26/SM26.mol2 new file mode 100644 index 0000000..463b3e1 --- /dev/null +++ b/top/oplsaa/SM26/SM26.mol2 @@ -0,0 +1,77 @@ +# Name: SM26 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 28 28 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -1.3540 8.1583 -0.8917 O.2 + 2 S2 -0.1147 7.6796 -1.3959 S.o2 + 3 C3 -0.0901 5.8658 -1.4071 C.3 + 4 C4 -0.0705 5.3471 0.0321 C.3 + 5 C5 -0.0501 3.8402 0.0228 C.ar + 6 C6 1.1563 3.1654 0.0081 C.ar + 7 C7 1.1750 1.7832 0.0004 C.ar + 8 C8 -0.0126 1.0758 0.0080 C.ar + 9 C9 -1.2190 1.7506 0.0173 C.ar + 10 C10 -1.2377 3.1328 0.0294 C.ar + 11 N11 -0.1344 8.1025 -2.9968 N.am + 12 C12 -1.1948 7.7833 -3.7651 C.2 + 13 C13 -1.2127 8.1682 -5.2221 C.3 + 14 O14 -2.1345 7.1864 -3.2840 O.2 + 15 O15 1.1197 8.1920 -0.9132 O.2 + 16 H16 0.8001 5.5177 -1.9309 H + 17 H17 -0.9796 5.4935 -1.9154 H + 18 H18 -0.9608 5.6951 0.5560 H + 19 H19 0.8190 5.7193 0.5404 H + 20 H20 2.0842 3.7181 0.0029 H + 21 H21 2.1175 1.2560 -0.0111 H + 22 H22 0.0021 -0.0041 0.0020 H + 23 H23 -2.1469 1.1980 0.0187 H + 24 H24 -2.1802 3.6600 0.0413 H + 25 H25 0.6172 8.5799 -3.3817 H + 26 H26 -0.3689 7.7026 -5.7313 H + 27 H27 -2.1436 7.8284 -5.6762 H + 28 H28 -1.1387 9.2519 -5.3125 H +@BOND + 1 1 2 2 + 2 2 3 1 + 3 2 11 am + 4 2 15 2 + 5 3 4 1 + 6 3 16 1 + 7 3 17 1 + 8 4 5 1 + 9 4 18 1 + 10 4 19 1 + 11 5 10 ar + 12 5 6 ar + 13 6 7 ar + 14 6 20 1 + 15 7 8 ar + 16 7 21 1 + 17 8 9 ar + 18 8 22 1 + 19 9 10 ar + 20 9 23 1 + 21 10 24 1 + 22 11 12 am + 23 11 25 1 + 24 12 13 1 + 25 12 14 2 + 26 13 26 1 + 27 13 27 1 + 28 13 28 1 + +# End of record + diff --git a/top/oplsaa/SM26/SM26.mol2.1.itp b/top/oplsaa/SM26/SM26.mol2.1.itp new file mode 100644 index 0000000..aa6cd4f --- /dev/null +++ b/top/oplsaa/SM26/SM26.mol2.1.itp @@ -0,0 +1,284 @@ +; input pdb SMILES : O=[S](CCC1=CC=CC=C1)(NC(C)=O)=O +; Script arguments : SM26.mol2 "11 opls_251" "25 opls_254" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 2 opls_474 1 UNK S2 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 3 opls_475 1 UNK O15 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 4 opls_139 1 UNK C3 3 -0.360 12.01100 ; CT # adapted CH2 attached to S of sulfonamide + 5 opls_477 1 UNK H16 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 6 opls_477 1 UNK H17 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 7 opls_235 1 UNK C12 7 0.500 12.01100 ; C # C=O in amide, dmf, peptide bond + 8 opls_236 1 UNK O14 7 -0.500 15.99940 ; O # O: C=O in amide. Acyl R on C in amide is neutral - + 9 opls_149 1 UNK C4 8 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 10 opls_145 1 UNK C5 8 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 11 opls_140 1 UNK H18 8 0.060 1.00800 ; HC # alkane H. + 12 opls_140 1 UNK H19 8 0.060 1.00800 ; HC # alkane H. + 13 opls_135 1 UNK C13 12 -0.180 12.01100 ; CT # alkane CH3 + 14 opls_140 1 UNK H26 12 0.060 1.00800 ; HC # alkane H. + 15 opls_140 1 UNK H27 12 0.060 1.00800 ; HC # alkane H. + 16 opls_140 1 UNK H28 12 0.060 1.00800 ; HC # alkane H. + 17 opls_145 1 UNK C6 22 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 18 opls_146 1 UNK H20 22 0.115 1.00800 ; HA # Benzene H - 12 site. + 19 opls_145 1 UNK C7 24 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 20 opls_146 1 UNK H21 24 0.115 1.00800 ; HA # Benzene H - 12 site. + 21 opls_145 1 UNK C8 26 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 22 opls_146 1 UNK H22 26 0.115 1.00800 ; HA # Benzene H - 12 site. + 23 opls_145 1 UNK C9 28 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 24 opls_146 1 UNK H23 28 0.115 1.00800 ; HA # Benzene H - 12 site. + 25 opls_145 1 UNK C10 30 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 26 opls_146 1 UNK H24 30 0.115 1.00800 ; HA # Benzene H - 12 site. + 27 opls_251 1 UNK N11 32 -0.490 14.00670 ; N # N in imide ### user-defined OPLS atom type (opls_251) + 28 opls_254 1 UNK H25 32 0.370 1.00800 ; H # H(N) in imide ### user-defined OPLS atom type (opls_254) +; Total charge : -0.000 ### Number of unassigned atoms : 0/28 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 4 1 ; SY-CT # + 2 27 1 ; SY-N # + 2 3 1 ; SY-OY # + 4 9 1 ; CT-CT # CHARMM 22 parameter file + 4 5 1 ; CT-HC # CHARMM 22 parameter file + 4 6 1 ; CT-HC # CHARMM 22 parameter file + 9 10 1 ; CT-CA # (CA-CT) PHE,TYR + 9 11 1 ; CT-HC # CHARMM 22 parameter file + 9 12 1 ; CT-HC # CHARMM 22 parameter file + 10 25 1 ; CA-CA # TRP,TYR,PHE + 10 17 1 ; CA-CA # TRP,TYR,PHE + 17 19 1 ; CA-CA # TRP,TYR,PHE + 17 18 1 ; CA-HA # PHE, etc. + 19 21 1 ; CA-CA # TRP,TYR,PHE + 19 20 1 ; CA-HA # PHE, etc. + 21 23 1 ; CA-CA # TRP,TYR,PHE + 21 22 1 ; CA-HA # PHE, etc. + 23 25 1 ; CA-CA # TRP,TYR,PHE + 23 24 1 ; CA-HA # PHE, etc. + 25 26 1 ; CA-HA # PHE, etc. + 27 7 1 ; N-C # (C-N) AA + 27 28 1 ; N-H # (H-N) + 7 13 1 ; C-CT # + 7 8 1 ; C-O # URAGUA,CYT,AA + 13 14 1 ; CT-HC # CHARMM 22 parameter file + 13 15 1 ; CT-HC # CHARMM 22 parameter file + 13 16 1 ; CT-HC # CHARMM 22 parameter file + +[ angles ] +; ai aj ak funct theta cth + 1 2 4 1 ; OY-SY-CT # + 1 2 27 1 ; OY-SY-N # + 1 2 3 1 ; OY-SY-OY # + 4 2 27 1 ; CT-SY-N # (N-SY-CT) + 4 2 3 1 ; CT-SY-OY # (OY-SY-CT) + 27 2 3 1 ; N-SY-OY # (OY-SY-N) + 2 4 9 1 ; SY-CT-CT # (CT-CT-SY) + 2 4 5 1 ; SY-CT-HC # + 2 4 6 1 ; SY-CT-HC # + 9 4 5 1 ; CT-CT-HC # CHARMM 22 parameter file + 9 4 6 1 ; CT-CT-HC # CHARMM 22 parameter file + 5 4 6 1 ; HC-CT-HC # CHARMM 22 parameter file + 4 9 10 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 4 9 11 1 ; CT-CT-HC # CHARMM 22 parameter file + 4 9 12 1 ; CT-CT-HC # CHARMM 22 parameter file + 10 9 11 1 ; CA-CT-HC # + 10 9 12 1 ; CA-CT-HC # + 11 9 12 1 ; HC-CT-HC # CHARMM 22 parameter file + 9 10 25 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 9 10 17 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 17 10 25 1 ; CA-CA-CA # PHE(OL) + 10 17 19 1 ; CA-CA-CA # PHE(OL) + 10 17 18 1 ; CA-CA-HA # + 19 17 18 1 ; CA-CA-HA # + 17 19 21 1 ; CA-CA-CA # PHE(OL) + 17 19 20 1 ; CA-CA-HA # + 21 19 20 1 ; CA-CA-HA # + 19 21 23 1 ; CA-CA-CA # PHE(OL) + 19 21 22 1 ; CA-CA-HA # + 23 21 22 1 ; CA-CA-HA # + 21 23 25 1 ; CA-CA-CA # PHE(OL) + 21 23 24 1 ; CA-CA-HA # + 25 23 24 1 ; CA-CA-HA # + 10 25 23 1 ; CA-CA-CA # PHE(OL) + 10 25 26 1 ; CA-CA-HA # + 23 25 26 1 ; CA-CA-HA # + 2 27 7 1 112.000 585.760 ; SY-N-C # LigParGen + 2 27 28 1 ; SY-N-H # (H-N-SY) + 7 27 28 1 ; C-N-H # AA(OL) + 27 7 13 1 ; N-C-CT # (CT-C-N) + 27 7 8 1 ; N-C-O # AA(OL) + 13 7 8 1 ; CT-C-O # + 7 13 14 1 ; C-CT-HC # + 7 13 15 1 ; C-CT-HC # + 7 13 16 1 ; C-CT-HC # + 14 13 15 1 ; HC-CT-HC # CHARMM 22 parameter file + 14 13 16 1 ; HC-CT-HC # CHARMM 22 parameter file + 15 13 16 1 ; HC-CT-HC # CHARMM 22 parameter file + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 4 9 3 ; OY-SY-CT-CT # (OY-SY-CT-X generic proper dihedral) sulfonamide + 1 2 4 5 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 1 2 4 6 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 27 2 4 9 3 ; N-SY-CT-CT # (CT-CT-SY-N) sulfonamide + 27 2 4 5 3 ; N-SY-CT-HC # (HC-CT-SY-N) sulfonamide + 27 2 4 6 3 ; N-SY-CT-HC # (HC-CT-SY-N) sulfonamide + 3 2 4 9 3 ; OY-SY-CT-CT # (OY-SY-CT-X generic proper dihedral) sulfonamide + 3 2 4 5 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 3 2 4 6 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 1 2 27 7 3 ; OY-SY-N-C # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 27 28 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 27 7 3 -2.897 11.182 12.410 -20.694 -0.000 0.000 ; CT-SY-N-C # LigParGen + 4 2 27 28 3 ; CT-SY-N-H # sulfonamide + 3 2 27 7 3 ; OY-SY-N-C # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 27 28 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 4 9 10 3 2.784 0.278 0.828 -3.891 -0.000 0.000 ; SY-CT-CT-CA # LigParGen + 2 4 9 11 3 ; SY-CT-CT-HC # (HC-CT-CT-SY) sulfide all-atom + 2 4 9 12 3 ; SY-CT-CT-HC # (HC-CT-CT-SY) sulfide all-atom + 5 4 9 10 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 5 4 9 11 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 5 4 9 12 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 6 4 9 10 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 6 4 9 11 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 6 4 9 12 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 4 9 10 25 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 4 9 10 17 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 11 9 10 25 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 11 9 10 17 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 12 9 10 25 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 12 9 10 17 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 9 10 25 23 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 9 10 25 26 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 10 25 23 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 10 25 26 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 9 10 17 19 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 9 10 17 18 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 10 17 19 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 10 17 18 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 17 19 21 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 17 19 20 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 17 19 21 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 17 19 20 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 19 21 23 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 19 21 22 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 20 19 21 23 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 20 19 21 22 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 21 23 25 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 21 23 24 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 21 23 25 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 21 23 24 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 23 25 10 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 23 25 26 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 10 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 26 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 27 7 13 3 -3.431 -3.008 10.598 -4.159 -0.000 0.000 ; SY-N-C-CT # LigParGen + 2 27 7 8 3 25.476 0.000 -25.476 -0.000 -0.000 0.000 ; SY-N-C-O # LigParGen + 28 27 7 13 3 ; H-N-C-CT # (CT-C-N-H) amides C-C(O)-N-H + 28 27 7 8 3 ; H-N-C-O # amides wlj 6/20/97 + 27 7 13 14 3 ; N-C-CT-HC # (HC-CT-C-N) acetamide + 27 7 13 15 3 ; N-C-CT-HC # (HC-CT-C-N) acetamide + 27 7 13 16 3 ; N-C-CT-HC # (HC-CT-C-N) acetamide + 8 7 13 14 3 ; O-C-CT-HC # (HC-CT-C-O) all carbonyls + 8 7 13 15 3 ; O-C-CT-HC # (HC-CT-C-O) all carbonyls + 8 7 13 16 3 ; O-C-CT-HC # (HC-CT-C-O) all carbonyls + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 25 17 10 9 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 19 18 17 10 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 21 20 19 17 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 23 22 21 19 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 25 24 23 21 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 23 26 25 10 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 7 28 27 2 1 improper_Z_N_X_Y ; C-H-N-SY + 27 13 7 8 1 improper_O_C_X_Y ; N-CT-C-O + +[ pairs ] +; ai aj funct + 1 9 1 + 1 5 1 + 1 6 1 + 1 7 1 + 1 28 1 + 2 10 1 + 2 11 1 + 2 12 1 + 2 13 1 + 2 8 1 + 4 7 1 + 4 28 1 + 4 25 1 + 4 17 1 + 9 27 1 + 9 3 1 + 9 23 1 + 9 26 1 + 9 19 1 + 9 18 1 + 10 5 1 + 10 6 1 + 10 21 1 + 10 24 1 + 10 20 1 + 17 11 1 + 17 12 1 + 17 23 1 + 17 26 1 + 17 22 1 + 19 25 1 + 19 24 1 + 21 18 1 + 21 26 1 + 23 20 1 + 25 11 1 + 25 12 1 + 25 18 1 + 25 22 1 + 27 5 1 + 27 6 1 + 27 14 1 + 27 15 1 + 27 16 1 + 7 3 1 + 13 28 1 + 8 28 1 + 8 14 1 + 8 15 1 + 8 16 1 + 3 5 1 + 3 6 1 + 3 28 1 + 5 11 1 + 5 12 1 + 6 11 1 + 6 12 1 + 18 20 1 + 20 22 1 + 22 24 1 + 24 26 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 4 1 1000 1000 1000 + 9 1 1000 1000 1000 + 10 1 1000 1000 1000 + 17 1 1000 1000 1000 + 19 1 1000 1000 1000 + 21 1 1000 1000 1000 + 23 1 1000 1000 1000 + 25 1 1000 1000 1000 + 27 1 1000 1000 1000 + 7 1 1000 1000 1000 + 13 1 1000 1000 1000 + 8 1 1000 1000 1000 + 3 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM26/SM26.mol2.1.pdb b/top/oplsaa/SM26/SM26.mol2.1.pdb new file mode 100644 index 0000000..510dbe9 --- /dev/null +++ b/top/oplsaa/SM26/SM26.mol2.1.pdb @@ -0,0 +1,29 @@ +HETATM 1 O1 UNK 1 -1.354 8.158 -0.892 1.00 20.00 +HETATM 2 S2 UNK 1 -0.115 7.680 -1.396 1.00 20.00 +HETATM 3 O15 UNK 1 1.120 8.192 -0.913 1.00 20.00 +HETATM 4 C3 UNK 1 -0.090 5.866 -1.407 1.00 20.00 +HETATM 5 H16 UNK 1 0.800 5.518 -1.931 1.00 20.00 +HETATM 6 H17 UNK 1 -0.980 5.494 -1.915 1.00 20.00 +HETATM 7 C12 UNK 1 -1.195 7.783 -3.765 1.00 20.00 +HETATM 8 O14 UNK 1 -2.135 7.186 -3.284 1.00 20.00 +HETATM 9 C4 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 10 C5 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 11 H18 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 12 H19 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 13 C13 UNK 1 -1.213 8.168 -5.222 1.00 20.00 +HETATM 14 H26 UNK 1 -0.369 7.703 -5.731 1.00 20.00 +HETATM 15 H27 UNK 1 -2.144 7.828 -5.676 1.00 20.00 +HETATM 16 H28 UNK 1 -1.139 9.252 -5.312 1.00 20.00 +HETATM 17 C6 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 18 H20 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 19 C7 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 20 H21 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 21 C8 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 22 H22 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 23 C9 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 24 H23 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 25 C10 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 26 H24 UNK 1 -2.180 3.660 0.041 1.00 20.00 +HETATM 27 N11 UNK 1 -0.134 8.102 -2.997 1.00 20.00 +HETATM 28 H25 UNK 1 0.617 8.580 -3.382 1.00 20.00 +END diff --git a/top/oplsaa/SM26/SM26.pdb b/top/oplsaa/SM26/SM26.pdb new file mode 120000 index 0000000..a0713d5 --- /dev/null +++ b/top/oplsaa/SM26/SM26.pdb @@ -0,0 +1 @@ +SM26.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM27/SM27.mol2 b/top/oplsaa/SM27/SM27.mol2 deleted file mode 120000 index 158d642..0000000 --- a/top/oplsaa/SM27/SM27.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM27/SM27.mol2 \ No newline at end of file diff --git a/top/oplsaa/SM27/SM27.mol2 b/top/oplsaa/SM27/SM27.mol2 new file mode 100644 index 0000000..9be2629 --- /dev/null +++ b/top/oplsaa/SM27/SM27.mol2 @@ -0,0 +1,90 @@ +# Name: SM27 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 34 35 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 0.3235 2.7098 -4.4476 O.2 + 2 S2 -0.7929 2.5197 -3.5892 S.o2 + 3 C3 -1.6284 4.0985 -3.2726 C.3 + 4 C4 -2.2952 4.5896 -4.5591 C.3 + 5 C5 -2.9893 5.9011 -4.2960 C.ar + 6 C6 -4.3097 5.9145 -3.8869 C.ar + 7 C7 -4.9449 7.1174 -3.6410 C.ar + 8 C8 -4.2628 8.3072 -3.8138 C.ar + 9 C9 -2.9441 8.2940 -4.2284 C.ar + 10 C10 -2.3073 7.0910 -4.4693 C.ar + 11 N11 -0.1225 2.1075 -2.1322 N.am + 12 C12 -0.9825 1.8800 -0.9683 C.3 + 13 C13 -2.2401 1.0742 -1.3001 C.3 + 14 C14 -0.2268 1.3701 0.2733 C.3 + 15 O15 -1.0305 2.3108 1.0135 O.3 + 16 C16 -1.2575 3.1495 -0.1404 C.3 + 17 O17 -1.7437 1.4940 -3.8402 O.2 + 18 H18 -2.3856 3.9604 -2.5007 H + 19 H19 -0.8982 4.8352 -2.9377 H + 20 H20 -1.5381 4.7276 -5.3310 H + 21 H21 -3.0254 3.8529 -4.8940 H + 22 H22 -4.8438 4.9850 -3.7558 H + 23 H23 -5.9752 7.1277 -3.3174 H + 24 H24 -4.7602 9.2471 -3.6252 H + 25 H25 -2.4113 9.2236 -4.3637 H + 26 H26 -1.2771 7.0807 -4.7932 H + 27 H27 0.8397 2.0168 -2.0495 H + 28 H28 -2.8702 1.0026 -0.4136 H + 29 H29 -2.7908 1.5725 -2.0980 H + 30 H30 -1.9553 0.0736 -1.6252 H + 31 H31 -0.4315 0.3276 0.5169 H + 32 H32 0.8373 1.6063 0.2697 H + 33 H33 -0.5086 3.9309 -0.2693 H + 34 H34 -2.2792 3.5194 -0.2267 H +@BOND + 1 1 2 2 + 2 2 3 1 + 3 2 11 am + 4 2 17 2 + 5 3 4 1 + 6 3 18 1 + 7 3 19 1 + 8 4 5 1 + 9 4 20 1 + 10 4 21 1 + 11 5 10 ar + 12 5 6 ar + 13 6 7 ar + 14 6 22 1 + 15 7 8 ar + 16 7 23 1 + 17 8 9 ar + 18 8 24 1 + 19 9 10 ar + 20 9 25 1 + 21 10 26 1 + 22 11 12 1 + 23 11 27 1 + 24 12 16 1 + 25 12 13 1 + 26 12 14 1 + 27 13 28 1 + 28 13 29 1 + 29 13 30 1 + 30 14 15 1 + 31 14 31 1 + 32 14 32 1 + 33 15 16 1 + 34 16 33 1 + 35 16 34 1 + +# End of record + diff --git a/top/oplsaa/SM28/SM28.mol2 b/top/oplsaa/SM28/SM28.mol2 deleted file mode 120000 index 30917fb..0000000 --- a/top/oplsaa/SM28/SM28.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM28/SM28.mol2 \ No newline at end of file diff --git a/top/oplsaa/SM28/SM28.mol2 b/top/oplsaa/SM28/SM28.mol2 new file mode 100644 index 0000000..04681e2 --- /dev/null +++ b/top/oplsaa/SM28/SM28.mol2 @@ -0,0 +1,92 @@ +# Name: SM28 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 35 36 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -0.5009 6.5095 0.4338 O.2 + 2 S2 -1.2787 5.6296 1.2338 S.o2 + 3 C3 -2.3249 4.5238 0.2467 C.3 + 4 C4 -1.1155 3.6256 -0.0234 C.3 + 5 N5 -1.4690 2.2109 -0.1650 N.am + 6 C6 -2.2435 1.8094 -1.1923 C.2 + 7 C7 -2.5146 0.3420 -1.4029 C.3 + 8 O8 -2.7264 2.6293 -1.9442 O.2 + 9 C9 -0.2379 4.1275 -1.1718 C.3 + 10 C10 0.9995 3.2362 -1.2951 C.3 + 11 C11 1.8035 3.6567 -2.4983 C.ar + 12 C12 1.5570 3.0801 -3.7302 C.ar + 13 C13 2.2912 3.4692 -4.8349 C.ar + 14 C14 3.2791 4.4275 -4.7057 C.ar + 15 C15 3.5292 5.0004 -3.4727 C.ar + 16 C16 2.7914 4.6150 -2.3691 C.ar + 17 C17 -0.5553 3.9704 1.3584 C.3 + 18 O18 -1.9048 6.0481 2.4388 O.2 + 19 H19 -2.7175 4.9961 -0.6538 H + 20 H20 -3.1013 4.0322 0.8328 H + 21 H21 -1.1456 1.5632 0.4806 H + 22 H22 -1.7515 -0.0781 -2.0580 H + 23 H23 -2.4927 -0.1730 -0.4425 H + 24 H24 -3.4958 0.2158 -1.8605 H + 25 H25 -0.8038 4.0943 -2.1028 H + 26 H26 0.0715 5.1532 -0.9710 H + 27 H27 1.6099 3.3357 -0.3975 H + 28 H28 0.6893 2.1977 -1.4102 H + 29 H29 0.7881 2.3282 -3.8304 H + 30 H30 2.0960 3.0214 -5.7981 H + 31 H31 3.8557 4.7283 -5.5679 H + 32 H32 4.3012 5.7488 -3.3716 H + 33 H33 2.9871 5.0623 -1.4057 H + 34 H34 -0.9907 3.3722 2.1588 H + 35 H35 0.5342 3.9792 1.3891 H +@BOND + 1 1 2 2 + 2 2 3 1 + 3 2 17 1 + 4 2 18 2 + 5 3 4 1 + 6 3 19 1 + 7 3 20 1 + 8 4 17 1 + 9 4 5 1 + 10 4 9 1 + 11 5 6 am + 12 5 21 1 + 13 6 7 1 + 14 6 8 2 + 15 7 22 1 + 16 7 23 1 + 17 7 24 1 + 18 9 10 1 + 19 9 25 1 + 20 9 26 1 + 21 10 11 1 + 22 10 27 1 + 23 10 28 1 + 24 11 16 ar + 25 11 12 ar + 26 12 13 ar + 27 12 29 1 + 28 13 14 ar + 29 13 30 1 + 30 14 15 ar + 31 14 31 1 + 32 15 16 ar + 33 15 32 1 + 34 16 33 1 + 35 17 34 1 + 36 17 35 1 + +# End of record + diff --git a/top/oplsaa/SM29/SM29.mol2 b/top/oplsaa/SM29/SM29.mol2 deleted file mode 120000 index d2550c0..0000000 --- a/top/oplsaa/SM29/SM29.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM29/SM29.mol2 \ No newline at end of file diff --git a/top/oplsaa/SM29/SM29.mol2 b/top/oplsaa/SM29/SM29.mol2 new file mode 100644 index 0000000..ae01644 --- /dev/null +++ b/top/oplsaa/SM29/SM29.mol2 @@ -0,0 +1,90 @@ +# Name: SM29 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 34 35 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 C1 0.7361 1.5316 2.8910 C.3 + 2 S2 1.1371 -0.1818 2.4504 S.o2 + 3 N3 -0.2036 -0.7261 1.6451 N.am + 4 C4 -0.5593 -0.1537 0.3443 C.3 + 5 C5 -0.6881 1.3813 0.3544 C.3 + 6 O6 0.7054 1.3876 -0.0153 O.3 + 7 C7 0.6460 0.0663 -0.5892 C.3 + 8 C8 -1.7359 -0.8680 -0.3238 C.3 + 9 C9 -1.5684 -2.3809 -0.1692 C.3 + 10 C10 -2.7272 -3.0845 -0.8273 C.ar + 11 C11 -3.8647 -3.3743 -0.0972 C.ar + 12 C12 -4.9296 -4.0153 -0.7021 C.ar + 13 C13 -4.8529 -4.3760 -2.0343 C.ar + 14 C14 -3.7134 -4.0909 -2.7631 C.ar + 15 C15 -2.6506 -3.4451 -2.1596 C.ar + 16 O16 1.2005 -0.9942 3.6145 O.2 + 17 O17 2.1701 -0.2172 1.4752 O.2 + 18 H18 -0.2316 1.5609 3.3918 H + 19 H19 1.5029 1.9240 3.5588 H + 20 H20 0.6959 2.1393 1.9870 H + 21 H21 -0.7533 -1.4239 2.0346 H + 22 H22 -1.3508 1.7733 -0.4171 H + 23 H23 -0.8845 1.8008 1.3411 H + 24 H24 1.5078 -0.5571 -0.3509 H + 25 H25 0.3911 0.0545 -1.6489 H + 26 H26 -2.6668 -0.5553 0.1492 H + 27 H27 -1.7625 -0.6117 -1.3829 H + 28 H28 -0.6375 -2.6936 -0.6422 H + 29 H29 -1.5417 -2.6371 0.8899 H + 30 H30 -3.9229 -3.0964 0.9449 H + 31 H31 -5.8198 -4.2384 -0.1326 H + 32 H32 -5.6832 -4.8808 -2.5058 H + 33 H33 -3.6534 -4.3729 -3.8039 H + 34 H34 -1.7601 -3.2227 -2.7288 H +@BOND + 1 1 2 1 + 2 1 18 1 + 3 1 19 1 + 4 1 20 1 + 5 2 3 am + 6 2 16 2 + 7 2 17 2 + 8 3 4 1 + 9 3 21 1 + 10 4 7 1 + 11 4 5 1 + 12 4 8 1 + 13 5 6 1 + 14 5 22 1 + 15 5 23 1 + 16 6 7 1 + 17 7 24 1 + 18 7 25 1 + 19 8 9 1 + 20 8 26 1 + 21 8 27 1 + 22 9 10 1 + 23 9 28 1 + 24 9 29 1 + 25 10 15 ar + 26 10 11 ar + 27 11 12 ar + 28 11 30 1 + 29 12 13 ar + 30 12 31 1 + 31 13 14 ar + 32 13 32 1 + 33 14 15 ar + 34 14 33 1 + 35 15 34 1 + +# End of record + diff --git a/top/oplsaa/SM30/SM30.mol2 b/top/oplsaa/SM30/SM30.mol2 deleted file mode 120000 index c3d1265..0000000 --- a/top/oplsaa/SM30/SM30.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM30/SM30.mol2 \ No newline at end of file diff --git a/top/oplsaa/SM30/SM30.mol2 b/top/oplsaa/SM30/SM30.mol2 new file mode 100644 index 0000000..965bde8 --- /dev/null +++ b/top/oplsaa/SM30/SM30.mol2 @@ -0,0 +1,105 @@ +# Name: SM30 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 41 43 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 1.1728 6.1240 0.4860 O.2 + 2 S2 -0.1340 5.7580 0.0647 S.o2 + 3 N3 -0.1809 5.9955 -1.5735 N.am + 4 C4 -1.4003 5.6856 -2.3240 C.3 + 5 C5 -2.6915 6.1776 -1.6434 C.3 + 6 O6 -2.7296 4.8742 -1.0283 O.3 + 7 C7 -1.9421 4.2659 -2.0717 C.3 + 8 C8 -1.3005 6.0545 -3.8055 C.3 + 9 C9 -0.6881 7.4498 -3.9435 C.3 + 10 C10 -0.5898 7.8131 -5.4027 C.ar + 11 C11 0.5513 7.5002 -6.1176 C.ar + 12 C12 0.6396 7.8292 -7.4573 C.ar + 13 C13 -0.4090 8.4805 -8.0796 C.ar + 14 C14 -1.5479 8.7981 -7.3635 C.ar + 15 C15 -1.6383 8.4644 -6.0250 C.ar + 16 C16 -1.2363 6.9241 0.7926 C.ar + 17 C17 -2.5132 6.5364 1.1531 C.ar + 18 C18 -3.3782 7.4514 1.7237 C.ar + 19 C19 -2.9658 8.7538 1.9346 C.ar + 20 C20 -1.6905 9.1427 1.5697 C.ar + 21 C21 -0.8243 8.2268 1.0027 C.ar + 22 O22 -0.6954 4.4740 0.3002 O.2 + 23 H23 0.5990 6.3398 -2.0362 H + 24 H24 -2.5348 6.9937 -0.9380 H + 25 H25 -3.5124 6.3624 -2.3363 H + 26 H26 -2.5341 3.8670 -2.8953 H + 27 H27 -1.1905 3.5652 -1.7081 H + 28 H28 -0.6700 5.3286 -4.3190 H + 29 H29 -2.2961 6.0491 -4.2492 H + 30 H30 -1.3186 8.1757 -3.4300 H + 31 H31 0.3075 7.4551 -3.4999 H + 32 H32 1.3723 6.9953 -5.6303 H + 33 H33 1.5295 7.5814 -8.0167 H + 34 H34 -0.3383 8.7415 -9.1252 H + 35 H35 -2.3670 9.3072 -7.8496 H + 36 H36 -2.5280 8.7129 -5.4655 H + 37 H37 -2.8353 5.5187 0.9886 H + 38 H38 -4.3759 7.1486 2.0050 H + 39 H39 -3.6416 9.4687 2.3805 H + 40 H40 -1.3699 10.1614 1.7304 H + 41 H41 0.1733 8.5298 0.7207 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 16 1 + 4 2 22 2 + 5 3 4 1 + 6 3 23 1 + 7 4 7 1 + 8 4 5 1 + 9 4 8 1 + 10 5 6 1 + 11 5 24 1 + 12 5 25 1 + 13 6 7 1 + 14 7 26 1 + 15 7 27 1 + 16 8 9 1 + 17 8 28 1 + 18 8 29 1 + 19 9 10 1 + 20 9 30 1 + 21 9 31 1 + 22 10 15 ar + 23 10 11 ar + 24 11 12 ar + 25 11 32 1 + 26 12 13 ar + 27 12 33 1 + 28 13 14 ar + 29 13 34 1 + 30 14 15 ar + 31 14 35 1 + 32 15 36 1 + 33 16 21 ar + 34 16 17 ar + 35 17 18 ar + 36 17 37 1 + 37 18 19 ar + 38 18 38 1 + 39 19 20 ar + 40 19 39 1 + 41 20 21 ar + 42 20 40 1 + 43 21 41 1 + +# End of record + diff --git a/top/oplsaa/SM31/SM31.itp b/top/oplsaa/SM31/SM31.itp new file mode 120000 index 0000000..2afa2eb --- /dev/null +++ b/top/oplsaa/SM31/SM31.itp @@ -0,0 +1 @@ +SM31.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM31/SM31.mol2 b/top/oplsaa/SM31/SM31.mol2 new file mode 100644 index 0000000..e28e7bd --- /dev/null +++ b/top/oplsaa/SM31/SM31.mol2 @@ -0,0 +1,100 @@ +# Name: SM31 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 39 40 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 0.1515 6.5053 2.6260 O.2 + 2 S2 0.4785 6.0091 1.3352 S.o2 + 3 N3 0.5808 4.3625 1.4793 N.am + 4 C4 1.2056 3.5716 0.4161 C.3 + 5 C5 0.4800 3.6636 -0.9395 C.3 + 6 O6 1.3761 4.7584 -1.2169 O.3 + 7 C7 2.3733 4.2882 -0.2878 C.3 + 8 C8 1.5294 2.1399 0.8477 C.3 + 9 C9 0.3072 1.5249 1.5326 C.3 + 10 C10 0.6261 0.1148 1.9577 C.ar + 11 C11 0.3793 -0.9390 1.0977 C.ar + 12 C12 0.6763 -2.2320 1.4858 C.ar + 13 C13 1.2105 -2.4724 2.7379 C.ar + 14 C14 1.4524 -1.4192 3.5999 C.ar + 15 C15 1.1603 -0.1256 3.2098 C.ar + 16 N16 -0.8229 6.3364 0.3649 N.am + 17 C17 -2.1785 6.2944 0.9188 C.3 + 18 C18 -0.6186 6.6679 -1.0474 C.3 + 19 O19 1.6310 6.4211 0.6133 O.2 + 20 H20 0.2270 3.9217 2.2676 H + 21 H21 0.6324 2.7956 -1.5810 H + 22 H22 -0.5662 3.9591 -0.8606 H + 23 H23 2.8288 5.0792 0.3080 H + 24 H24 3.1050 3.6110 -0.7284 H + 25 H25 2.3684 2.1511 1.5434 H + 26 H26 1.7917 1.5469 -0.0284 H + 27 H27 -0.5318 1.5137 0.8369 H + 28 H28 0.0448 2.1180 2.4087 H + 29 H29 -0.0421 -0.7516 0.1211 H + 30 H30 0.4869 -3.0549 0.8125 H + 31 H31 1.4384 -3.4831 3.0428 H + 32 H32 1.8694 -1.6070 4.5783 H + 33 H33 1.3490 0.6972 3.8834 H + 34 H34 -2.2634 7.0207 1.7271 H + 35 H35 -2.8983 6.5355 0.1366 H + 36 H36 -2.3825 5.2956 1.3049 H + 37 H37 -0.7371 5.7691 -1.6524 H + 38 H38 -1.3524 7.4127 -1.3555 H + 39 H39 0.3857 7.0687 -1.1849 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 16 am + 4 2 19 2 + 5 3 4 1 + 6 3 20 1 + 7 4 7 1 + 8 4 5 1 + 9 4 8 1 + 10 5 6 1 + 11 5 21 1 + 12 5 22 1 + 13 6 7 1 + 14 7 23 1 + 15 7 24 1 + 16 8 9 1 + 17 8 25 1 + 18 8 26 1 + 19 9 10 1 + 20 9 27 1 + 21 9 28 1 + 22 10 15 ar + 23 10 11 ar + 24 11 12 ar + 25 11 29 1 + 26 12 13 ar + 27 12 30 1 + 28 13 14 ar + 29 13 31 1 + 30 14 15 ar + 31 14 32 1 + 32 15 33 1 + 33 16 17 1 + 34 16 18 1 + 35 17 34 1 + 36 17 35 1 + 37 17 36 1 + 38 18 37 1 + 39 18 38 1 + 40 18 39 1 + +# End of record + diff --git a/top/oplsaa/SM31/SM31.mol2.1.itp b/top/oplsaa/SM31/SM31.mol2.1.itp new file mode 100644 index 0000000..ed1d6da --- /dev/null +++ b/top/oplsaa/SM31/SM31.mol2.1.itp @@ -0,0 +1,402 @@ +; input pdb SMILES : O=[S](NC1(COC1)CCC2=CC=CC=C2)(N(C)C)=O +; Script arguments : SM31.mol2 "20 opls_241 0.482" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 2 opls_474 1 UNK S2 1 0.852 32.06000 ; SY # S in sulfamide, S(=O)2(NR2) + 3 opls_480 1 UNK N16 1 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 4 opls_475 1 UNK O19 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 5 opls_480 1 UNK N3 3 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 6 opls_482 1 UNK C18 5 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 7 opls_483 1 UNK H37 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 8 opls_483 1 UNK H38 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 9 opls_483 1 UNK H39 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 10 opls_482 1 UNK C17 11 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 11 opls_483 1 UNK H34 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 12 opls_483 1 UNK H35 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 13 opls_483 1 UNK H36 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 14 opls_182 1 UNK C5 29 0.140 12.01100 ; CT # C(H2OR): ethyl ether + 15 opls_180 1 UNK O6 29 -0.400 15.99940 ; OS # O: dialkyl ether + 16 opls_185 1 UNK H21 29 0.030 1.00800 ; HC # H(COR): alpha H ether + 17 opls_185 1 UNK H22 29 0.030 1.00800 ; HC # H(COR): alpha H ether + 18 opls_182 1 UNK C7 31 0.140 12.01100 ; CT # C(H2OR): ethyl ether + 19 opls_185 1 UNK H23 31 0.030 1.00800 ; HC # H(COR): alpha H ether + 20 opls_185 1 UNK H24 31 0.030 1.00800 ; HC # H(COR): alpha H ether + 21 opls_149 1 UNK C9 33 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 22 opls_145 1 UNK C10 33 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 23 opls_140 1 UNK H27 33 0.060 1.00800 ; HC # alkane H. + 24 opls_140 1 UNK H28 33 0.060 1.00800 ; HC # alkane H. + 25 opls_136 1 UNK C8 57 -0.120 12.01100 ; CT # alkane CH2 + 26 opls_140 1 UNK H25 57 0.060 1.00800 ; HC # alkane H. + 27 opls_140 1 UNK H26 57 0.060 1.00800 ; HC # alkane H. + 28 opls_139 1 UNK C4 61 0.000 12.01100 ; CT # alkane C + 29 opls_145 1 UNK C11 85 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 30 opls_146 1 UNK H29 85 0.115 1.00800 ; HA # Benzene H - 12 site. + 31 opls_145 1 UNK C12 87 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 32 opls_146 1 UNK H30 87 0.115 1.00800 ; HA # Benzene H - 12 site. + 33 opls_145 1 UNK C13 89 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 34 opls_146 1 UNK H31 89 0.115 1.00800 ; HA # Benzene H - 12 site. + 35 opls_145 1 UNK C14 91 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 36 opls_146 1 UNK H32 91 0.115 1.00800 ; HA # Benzene H - 12 site. + 37 opls_145 1 UNK C15 93 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 38 opls_146 1 UNK H33 93 0.115 1.00800 ; HA # Benzene H - 12 site. + 39 opls_241 1 UNK H20 95 0.482 1.00800 ; H # H on N: secondary amide ### user-defined OPLS atom type (opls_241) atom charge (0.482) +; Total charge : 0.000 ### Number of unassigned atoms : 0/39 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 5 1 ; SY-N # + 2 3 1 ; SY-N # + 2 4 1 ; SY-OY # + 5 28 1 ; N-CT # (CT-N) + 5 39 1 ; N-H # (H-N) + 28 18 1 ; CT-CT # CHARMM 22 parameter file + 28 14 1 ; CT-CT # CHARMM 22 parameter file + 28 25 1 ; CT-CT # CHARMM 22 parameter file + 14 15 1 ; CT-OS # + 14 16 1 ; CT-HC # CHARMM 22 parameter file + 14 17 1 ; CT-HC # CHARMM 22 parameter file + 15 18 1 ; OS-CT # (CT-OS) + 18 19 1 ; CT-HC # CHARMM 22 parameter file + 18 20 1 ; CT-HC # CHARMM 22 parameter file + 25 21 1 ; CT-CT # CHARMM 22 parameter file + 25 26 1 ; CT-HC # CHARMM 22 parameter file + 25 27 1 ; CT-HC # CHARMM 22 parameter file + 21 22 1 ; CT-CA # (CA-CT) PHE,TYR + 21 23 1 ; CT-HC # CHARMM 22 parameter file + 21 24 1 ; CT-HC # CHARMM 22 parameter file + 22 37 1 ; CA-CA # TRP,TYR,PHE + 22 29 1 ; CA-CA # TRP,TYR,PHE + 29 31 1 ; CA-CA # TRP,TYR,PHE + 29 30 1 ; CA-HA # PHE, etc. + 31 33 1 ; CA-CA # TRP,TYR,PHE + 31 32 1 ; CA-HA # PHE, etc. + 33 35 1 ; CA-CA # TRP,TYR,PHE + 33 34 1 ; CA-HA # PHE, etc. + 35 37 1 ; CA-CA # TRP,TYR,PHE + 35 36 1 ; CA-HA # PHE, etc. + 37 38 1 ; CA-HA # PHE, etc. + 3 10 1 ; N-CT # (CT-N) + 3 6 1 ; N-CT # (CT-N) + 10 11 1 ; CT-HC # CHARMM 22 parameter file + 10 12 1 ; CT-HC # CHARMM 22 parameter file + 10 13 1 ; CT-HC # CHARMM 22 parameter file + 6 7 1 ; CT-HC # CHARMM 22 parameter file + 6 8 1 ; CT-HC # CHARMM 22 parameter file + 6 9 1 ; CT-HC # CHARMM 22 parameter file + +[ angles ] +; ai aj ak funct theta cth + 1 2 5 1 ; OY-SY-N # + 1 2 3 1 ; OY-SY-N # + 1 2 4 1 ; OY-SY-OY # + 5 2 3 1 107.000 1004.160 ; N-SY-N # by analogy from OY-SY-N : + 5 2 4 1 ; N-SY-OY # (OY-SY-N) + 3 2 4 1 ; N-SY-OY # (OY-SY-N) + 2 5 28 1 ; SY-N-CT # + 2 5 39 1 ; SY-N-H # (H-N-SY) + 28 5 39 1 ; CT-N-H # + 5 28 18 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 28 14 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 28 25 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 18 28 25 1 ; CT-CT-CT # CHARMM 22 parameter file + 14 28 18 1 ; CT-CT-CT # CHARMM 22 parameter file + 14 28 25 1 ; CT-CT-CT # CHARMM 22 parameter file + 28 14 15 1 ; CT-CT-OS # + 28 14 16 1 ; CT-CT-HC # CHARMM 22 parameter file + 28 14 17 1 ; CT-CT-HC # CHARMM 22 parameter file + 15 14 16 1 ; OS-CT-HC # (HC-CT-OS) SUG + 15 14 17 1 ; OS-CT-HC # (HC-CT-OS) SUG + 16 14 17 1 ; HC-CT-HC # CHARMM 22 parameter file + 14 15 18 1 ; CT-OS-CT # + 28 18 15 1 ; CT-CT-OS # + 28 18 19 1 ; CT-CT-HC # CHARMM 22 parameter file + 28 18 20 1 ; CT-CT-HC # CHARMM 22 parameter file + 15 18 19 1 ; OS-CT-HC # (HC-CT-OS) SUG + 15 18 20 1 ; OS-CT-HC # (HC-CT-OS) SUG + 19 18 20 1 ; HC-CT-HC # CHARMM 22 parameter file + 28 25 21 1 ; CT-CT-CT # CHARMM 22 parameter file + 28 25 26 1 ; CT-CT-HC # CHARMM 22 parameter file + 28 25 27 1 ; CT-CT-HC # CHARMM 22 parameter file + 21 25 26 1 ; CT-CT-HC # CHARMM 22 parameter file + 21 25 27 1 ; CT-CT-HC # CHARMM 22 parameter file + 26 25 27 1 ; HC-CT-HC # CHARMM 22 parameter file + 25 21 22 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 25 21 23 1 ; CT-CT-HC # CHARMM 22 parameter file + 25 21 24 1 ; CT-CT-HC # CHARMM 22 parameter file + 22 21 23 1 ; CA-CT-HC # + 22 21 24 1 ; CA-CT-HC # + 23 21 24 1 ; HC-CT-HC # CHARMM 22 parameter file + 21 22 37 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 21 22 29 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 29 22 37 1 ; CA-CA-CA # PHE(OL) + 22 29 31 1 ; CA-CA-CA # PHE(OL) + 22 29 30 1 ; CA-CA-HA # + 31 29 30 1 ; CA-CA-HA # + 29 31 33 1 ; CA-CA-CA # PHE(OL) + 29 31 32 1 ; CA-CA-HA # + 33 31 32 1 ; CA-CA-HA # + 31 33 35 1 ; CA-CA-CA # PHE(OL) + 31 33 34 1 ; CA-CA-HA # + 35 33 34 1 ; CA-CA-HA # + 33 35 37 1 ; CA-CA-CA # PHE(OL) + 33 35 36 1 ; CA-CA-HA # + 37 35 36 1 ; CA-CA-HA # + 22 37 35 1 ; CA-CA-CA # PHE(OL) + 22 37 38 1 ; CA-CA-HA # + 35 37 38 1 ; CA-CA-HA # + 2 3 10 1 ; SY-N-CT # + 2 3 6 1 ; SY-N-CT # + 10 3 6 1 ; CT-N-CT # PRO(OL) DETAR JACS 99,1232 + 3 10 11 1 ; N-CT-HC # (HC-CT-N) + 3 10 12 1 ; N-CT-HC # (HC-CT-N) + 3 10 13 1 ; N-CT-HC # (HC-CT-N) + 11 10 12 1 ; HC-CT-HC # CHARMM 22 parameter file + 11 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 12 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 3 6 7 1 ; N-CT-HC # (HC-CT-N) + 3 6 8 1 ; N-CT-HC # (HC-CT-N) + 3 6 9 1 ; N-CT-HC # (HC-CT-N) + 7 6 8 1 ; HC-CT-HC # CHARMM 22 parameter file + 7 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + 8 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 5 28 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 5 39 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 5 28 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 3 2 5 39 3 -15.611 0.703 20.506 -5.598 -0.000 0.000 ; N-SY-N-H # LigParGen + 4 2 5 28 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 5 39 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 5 2 3 10 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 5 2 3 6 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 4 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 5 28 18 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 28 14 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 28 25 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 39 5 28 18 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 39 5 28 14 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 39 5 28 25 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 5 28 18 15 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-OS # (OS-CT-CT-N) by analogy with CT-CT-CT-N : N-propylformamide + 5 28 18 19 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 28 18 20 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 14 28 18 15 3 ; CT-CT-CT-OS # alcohols, ethers AA + 14 28 18 19 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 14 28 18 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 25 28 18 15 3 ; CT-CT-CT-OS # alcohols, ethers AA + 25 28 18 19 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 25 28 18 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 28 14 15 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-OS # (OS-CT-CT-N) by analogy with CT-CT-CT-N : N-propylformamide + 5 28 14 16 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 28 14 17 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 18 28 14 15 3 ; CT-CT-CT-OS # alcohols, ethers AA + 18 28 14 16 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 18 28 14 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 25 28 14 15 3 ; CT-CT-CT-OS # alcohols, ethers AA + 25 28 14 16 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 25 28 14 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 28 25 21 3 ; N-CT-CT-CT # (CT-CT-CT-N) N-propylformamide + 5 28 25 26 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 28 25 27 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 18 28 25 21 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 18 28 25 26 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 18 28 25 27 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 14 28 25 21 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 14 28 25 26 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 14 28 25 27 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 28 14 15 18 3 ; CT-CT-OS-CT # ethers AA + 16 14 15 18 3 ; HC-CT-OS-CT # (CT-OS-CT-HC) ethers AA + 17 14 15 18 3 ; HC-CT-OS-CT # (CT-OS-CT-HC) ethers AA + 14 15 18 28 3 ; CT-OS-CT-CT # (CT-CT-OS-CT) ethers AA + 14 15 18 19 3 ; CT-OS-CT-HC # ethers AA + 14 15 18 20 3 ; CT-OS-CT-HC # ethers AA + 28 25 21 22 3 ; CT-CT-CT-CA # (CA-CT-CT-CT) + 28 25 21 23 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 28 25 21 24 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 26 25 21 22 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 26 25 21 23 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 26 25 21 24 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 27 25 21 22 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 27 25 21 23 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 27 25 21 24 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 25 21 22 37 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 25 21 22 29 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 23 21 22 37 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 23 21 22 29 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 24 21 22 37 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 24 21 22 29 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 21 22 37 35 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 22 37 38 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 22 37 35 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 22 37 38 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 22 29 31 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 22 29 30 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 37 22 29 31 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 37 22 29 30 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 29 31 33 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 29 31 32 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 29 31 33 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 29 31 32 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 31 33 35 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 31 33 34 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 31 33 35 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 31 33 34 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 33 35 37 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 33 35 36 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 33 35 37 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 33 35 36 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 35 37 22 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 35 37 38 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 36 35 37 22 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 36 35 37 38 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 10 11 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 12 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 13 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 6 3 10 11 3 ; CT-N-CT-HC # tert. amide + 6 3 10 12 3 ; CT-N-CT-HC # tert. amide + 6 3 10 13 3 ; CT-N-CT-HC # tert. amide + 2 3 6 7 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 8 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 9 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 10 3 6 7 3 ; CT-N-CT-HC # tert. amide + 10 3 6 8 3 ; CT-N-CT-HC # tert. amide + 10 3 6 9 3 ; CT-N-CT-HC # tert. amide + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 2 39 5 28 1 improper_Z_N_X_Y ; SY-H-N-CT + 37 29 22 21 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 31 30 29 22 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 33 32 31 29 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 35 34 33 31 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 37 36 35 33 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 35 38 37 22 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 2 6 3 10 1 improper_Z_N_X_Y ; SY-CT-N-CT + +[ pairs ] +; ai aj funct + 1 28 1 + 1 39 1 + 1 10 1 + 1 6 1 + 2 18 1 + 2 14 1 + 2 25 1 + 2 11 1 + 2 12 1 + 2 13 1 + 2 7 1 + 2 8 1 + 2 9 1 + 5 10 1 + 5 6 1 + 5 15 1 + 5 19 1 + 5 20 1 + 5 16 1 + 5 17 1 + 5 21 1 + 5 26 1 + 5 27 1 + 28 3 1 + 28 4 1 + 28 22 1 + 28 23 1 + 28 24 1 + 14 39 1 + 14 19 1 + 14 20 1 + 14 21 1 + 14 26 1 + 14 27 1 + 15 25 1 + 18 39 1 + 18 16 1 + 18 17 1 + 18 21 1 + 18 26 1 + 18 27 1 + 25 39 1 + 25 19 1 + 25 20 1 + 25 16 1 + 25 17 1 + 25 37 1 + 25 29 1 + 21 35 1 + 21 38 1 + 21 31 1 + 21 30 1 + 22 26 1 + 22 27 1 + 22 33 1 + 22 36 1 + 22 32 1 + 29 23 1 + 29 24 1 + 29 35 1 + 29 38 1 + 29 34 1 + 31 37 1 + 31 36 1 + 33 30 1 + 33 38 1 + 35 32 1 + 37 23 1 + 37 24 1 + 37 30 1 + 37 34 1 + 3 39 1 + 10 4 1 + 10 7 1 + 10 8 1 + 10 9 1 + 6 4 1 + 6 11 1 + 6 12 1 + 6 13 1 + 4 39 1 + 26 23 1 + 26 24 1 + 27 23 1 + 27 24 1 + 30 32 1 + 32 34 1 + 34 36 1 + 36 38 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 5 1 1000 1000 1000 + 28 1 1000 1000 1000 + 14 1 1000 1000 1000 + 15 1 1000 1000 1000 + 18 1 1000 1000 1000 + 25 1 1000 1000 1000 + 21 1 1000 1000 1000 + 22 1 1000 1000 1000 + 29 1 1000 1000 1000 + 31 1 1000 1000 1000 + 33 1 1000 1000 1000 + 35 1 1000 1000 1000 + 37 1 1000 1000 1000 + 3 1 1000 1000 1000 + 10 1 1000 1000 1000 + 6 1 1000 1000 1000 + 4 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM31/SM31.mol2.1.pdb b/top/oplsaa/SM31/SM31.mol2.1.pdb new file mode 100644 index 0000000..0e682f1 --- /dev/null +++ b/top/oplsaa/SM31/SM31.mol2.1.pdb @@ -0,0 +1,40 @@ +HETATM 1 O1 UNK 1 0.151 6.505 2.626 1.00 20.00 +HETATM 2 S2 UNK 1 0.478 6.009 1.335 1.00 20.00 +HETATM 3 N16 UNK 1 -0.823 6.336 0.365 1.00 20.00 +HETATM 4 O19 UNK 1 1.631 6.421 0.613 1.00 20.00 +HETATM 5 N3 UNK 1 0.581 4.362 1.479 1.00 20.00 +HETATM 6 C18 UNK 1 -0.619 6.668 -1.047 1.00 20.00 +HETATM 7 H37 UNK 1 -0.737 5.769 -1.652 1.00 20.00 +HETATM 8 H38 UNK 1 -1.352 7.413 -1.355 1.00 20.00 +HETATM 9 H39 UNK 1 0.386 7.069 -1.185 1.00 20.00 +HETATM 10 C17 UNK 1 -2.179 6.294 0.919 1.00 20.00 +HETATM 11 H34 UNK 1 -2.263 7.021 1.727 1.00 20.00 +HETATM 12 H35 UNK 1 -2.898 6.535 0.137 1.00 20.00 +HETATM 13 H36 UNK 1 -2.382 5.296 1.305 1.00 20.00 +HETATM 14 C5 UNK 1 0.480 3.664 -0.940 1.00 20.00 +HETATM 15 O6 UNK 1 1.376 4.758 -1.217 1.00 20.00 +HETATM 16 H21 UNK 1 0.632 2.796 -1.581 1.00 20.00 +HETATM 17 H22 UNK 1 -0.566 3.959 -0.861 1.00 20.00 +HETATM 18 C7 UNK 1 2.373 4.288 -0.288 1.00 20.00 +HETATM 19 H23 UNK 1 2.829 5.079 0.308 1.00 20.00 +HETATM 20 H24 UNK 1 3.105 3.611 -0.728 1.00 20.00 +HETATM 21 C9 UNK 1 0.307 1.525 1.533 1.00 20.00 +HETATM 22 C10 UNK 1 0.626 0.115 1.958 1.00 20.00 +HETATM 23 H27 UNK 1 -0.532 1.514 0.837 1.00 20.00 +HETATM 24 H28 UNK 1 0.045 2.118 2.409 1.00 20.00 +HETATM 25 C8 UNK 1 1.529 2.140 0.848 1.00 20.00 +HETATM 26 H25 UNK 1 2.368 2.151 1.543 1.00 20.00 +HETATM 27 H26 UNK 1 1.792 1.547 -0.028 1.00 20.00 +HETATM 28 C4 UNK 1 1.206 3.572 0.416 1.00 20.00 +HETATM 29 C11 UNK 1 0.379 -0.939 1.098 1.00 20.00 +HETATM 30 H29 UNK 1 -0.042 -0.752 0.121 1.00 20.00 +HETATM 31 C12 UNK 1 0.676 -2.232 1.486 1.00 20.00 +HETATM 32 H30 UNK 1 0.487 -3.055 0.812 1.00 20.00 +HETATM 33 C13 UNK 1 1.210 -2.472 2.738 1.00 20.00 +HETATM 34 H31 UNK 1 1.438 -3.483 3.043 1.00 20.00 +HETATM 35 C14 UNK 1 1.452 -1.419 3.600 1.00 20.00 +HETATM 36 H32 UNK 1 1.869 -1.607 4.578 1.00 20.00 +HETATM 37 C15 UNK 1 1.160 -0.126 3.210 1.00 20.00 +HETATM 38 H33 UNK 1 1.349 0.697 3.883 1.00 20.00 +HETATM 39 H20 UNK 1 0.227 3.922 2.268 1.00 20.00 +END diff --git a/top/oplsaa/SM31/SM31.pdb b/top/oplsaa/SM31/SM31.pdb new file mode 120000 index 0000000..0f88c71 --- /dev/null +++ b/top/oplsaa/SM31/SM31.pdb @@ -0,0 +1 @@ +SM31.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM32/SM32.itp b/top/oplsaa/SM32/SM32.itp new file mode 120000 index 0000000..7cc2b15 --- /dev/null +++ b/top/oplsaa/SM32/SM32.itp @@ -0,0 +1 @@ +SM32.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM32/SM32.mol2 b/top/oplsaa/SM32/SM32.mol2 new file mode 100644 index 0000000..164b8d1 --- /dev/null +++ b/top/oplsaa/SM32/SM32.mol2 @@ -0,0 +1,90 @@ +# Name: SM32 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 34 35 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 C1 0.6902 -0.3709 0.4861 C.3 + 2 S2 0.0783 1.2878 0.0801 S.o2 + 3 N3 -0.1956 1.9985 1.5506 N.am + 4 C4 -1.2432 1.4773 2.4322 C.3 + 5 C5 -1.1876 -0.0429 2.5995 C.3 + 6 S6 -2.0894 -0.2441 1.0381 S.3 + 7 C7 -2.6023 1.3480 1.7407 C.3 + 8 C8 -1.3146 2.2277 3.7637 C.3 + 9 C9 0.0982 2.4146 4.3203 C.3 + 10 C10 0.0279 3.1537 5.6317 C.ar + 11 C11 0.0929 4.5344 5.6512 C.ar + 12 C12 0.0235 5.2126 6.8538 C.ar + 13 C13 -0.1005 4.5096 8.0376 C.ar + 14 C14 -0.1602 3.1287 8.0184 C.ar + 15 C15 -0.0961 2.4507 6.8155 C.ar + 16 O16 1.1112 2.0719 -0.5010 O.2 + 17 O17 -1.2086 1.2121 -0.5177 O.2 + 18 H18 1.4220 -0.3014 1.2909 H + 19 H19 -0.1427 -0.9974 0.8054 H + 20 H20 1.1590 -0.8108 -0.3942 H + 21 H21 0.3375 2.7598 1.8282 H + 22 H22 -0.1736 -0.4412 2.5631 H + 23 H23 -1.7453 -0.3994 3.4654 H + 24 H24 -3.4328 1.2596 2.4412 H + 25 H25 -2.7733 2.1147 0.9850 H + 26 H26 -1.7752 3.2031 3.6067 H + 27 H27 -1.9115 1.6539 4.4726 H + 28 H28 0.5589 1.4392 4.4772 H + 29 H29 0.6951 2.9884 3.6113 H + 30 H30 0.1941 5.0834 4.7267 H + 31 H31 0.0705 6.2915 6.8688 H + 32 H32 -0.1502 5.0393 8.9775 H + 33 H33 -0.2567 2.5795 8.9433 H + 34 H34 -0.1424 1.3718 6.8005 H +@BOND + 1 1 2 1 + 2 1 18 1 + 3 1 19 1 + 4 1 20 1 + 5 2 3 am + 6 2 16 2 + 7 2 17 2 + 8 3 4 1 + 9 3 21 1 + 10 4 7 1 + 11 4 5 1 + 12 4 8 1 + 13 5 6 1 + 14 5 22 1 + 15 5 23 1 + 16 6 7 1 + 17 7 24 1 + 18 7 25 1 + 19 8 9 1 + 20 8 26 1 + 21 8 27 1 + 22 9 10 1 + 23 9 28 1 + 24 9 29 1 + 25 10 15 ar + 26 10 11 ar + 27 11 12 ar + 28 11 30 1 + 29 12 13 ar + 30 12 31 1 + 31 13 14 ar + 32 13 32 1 + 33 14 15 ar + 34 14 33 1 + 35 15 34 1 + +# End of record + diff --git a/top/oplsaa/SM32/SM32.mol2.1.itp b/top/oplsaa/SM32/SM32.mol2.1.itp new file mode 100644 index 0000000..732f886 --- /dev/null +++ b/top/oplsaa/SM32/SM32.mol2.1.itp @@ -0,0 +1,362 @@ +; input pdb SMILES : C[S](NC1(CSC1)CCC2=CC=CC=C2)(=O)=O +; Script arguments : SM32.mol2 "4 opls_139 0.270" "5 opls_210" "7 opls_210" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_474 1 UNK S2 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 2 opls_475 1 UNK O16 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 3 opls_475 1 UNK O17 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 4 opls_476 1 UNK C1 3 -0.540 12.01100 ; CT # CH3 attached to S of sulfonamide + 5 opls_477 1 UNK H18 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 6 opls_477 1 UNK H19 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 7 opls_477 1 UNK H20 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 8 opls_480 1 UNK N3 15 -0.800 14.00670 ; N # N secondary amide of sulfonamide + 9 opls_139 1 UNK C4 15 0.270 12.01100 ; CT # alkane C ### user-defined OPLS atom type (opls_139) atom charge (0.270) + 10 opls_481 1 UNK H21 15 0.410 1.00800 ; H # H on N: secondary sulfonamide + 11 opls_202 1 UNK S6 27 -0.336 32.06000 ; S # dialkyl/diaryl sulfide, adapted from all-atom S: sulfides, S=C (opls_202) + 12 opls_210 1 UNK C5 29 0.048 12.01100 ; CT # all-atom C: CH2, sulfides ### user-defined OPLS atom type (opls_210) + 13 opls_140 1 UNK H22 29 0.060 1.00800 ; HC # alkane H. + 14 opls_140 1 UNK H23 29 0.060 1.00800 ; HC # alkane H. + 15 opls_210 1 UNK C7 31 0.048 12.01100 ; CT # all-atom C: CH2, sulfides ### user-defined OPLS atom type (opls_210) + 16 opls_140 1 UNK H24 31 0.060 1.00800 ; HC # alkane H. + 17 opls_140 1 UNK H25 31 0.060 1.00800 ; HC # alkane H. + 18 opls_149 1 UNK C9 33 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 19 opls_145 1 UNK C10 33 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 20 opls_140 1 UNK H28 33 0.060 1.00800 ; HC # alkane H. + 21 opls_140 1 UNK H29 33 0.060 1.00800 ; HC # alkane H. + 22 opls_136 1 UNK C8 51 -0.120 12.01100 ; CT # alkane CH2 + 23 opls_140 1 UNK H26 51 0.060 1.00800 ; HC # alkane H. + 24 opls_140 1 UNK H27 51 0.060 1.00800 ; HC # alkane H. + 25 opls_145 1 UNK C11 79 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 26 opls_146 1 UNK H30 79 0.115 1.00800 ; HA # Benzene H - 12 site. + 27 opls_145 1 UNK C12 81 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 28 opls_146 1 UNK H31 81 0.115 1.00800 ; HA # Benzene H - 12 site. + 29 opls_145 1 UNK C13 83 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 30 opls_146 1 UNK H32 83 0.115 1.00800 ; HA # Benzene H - 12 site. + 31 opls_145 1 UNK C14 85 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 32 opls_146 1 UNK H33 85 0.115 1.00800 ; HA # Benzene H - 12 site. + 33 opls_145 1 UNK C15 87 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 34 opls_146 1 UNK H34 87 0.115 1.00800 ; HA # Benzene H - 12 site. +; Total charge : -0.000 ### Number of unassigned atoms : 0/34 + +[ bonds ] +; ai aj funct r k + 4 1 1 ; CT-SY # (SY-CT) + 4 5 1 ; CT-HC # CHARMM 22 parameter file + 4 6 1 ; CT-HC # CHARMM 22 parameter file + 4 7 1 ; CT-HC # CHARMM 22 parameter file + 1 8 1 ; SY-N # + 1 2 1 ; SY-OY # + 1 3 1 ; SY-OY # + 8 9 1 ; N-CT # (CT-N) + 8 10 1 ; N-H # (H-N) + 9 15 1 ; CT-CT # CHARMM 22 parameter file + 9 12 1 ; CT-CT # CHARMM 22 parameter file + 9 22 1 ; CT-CT # CHARMM 22 parameter file + 12 11 1 ; CT-S # CYX(OL) + 12 13 1 ; CT-HC # CHARMM 22 parameter file + 12 14 1 ; CT-HC # CHARMM 22 parameter file + 11 15 1 ; S-CT # (CT-S) CYX(OL) + 15 16 1 ; CT-HC # CHARMM 22 parameter file + 15 17 1 ; CT-HC # CHARMM 22 parameter file + 22 18 1 ; CT-CT # CHARMM 22 parameter file + 22 23 1 ; CT-HC # CHARMM 22 parameter file + 22 24 1 ; CT-HC # CHARMM 22 parameter file + 18 19 1 ; CT-CA # (CA-CT) PHE,TYR + 18 20 1 ; CT-HC # CHARMM 22 parameter file + 18 21 1 ; CT-HC # CHARMM 22 parameter file + 19 33 1 ; CA-CA # TRP,TYR,PHE + 19 25 1 ; CA-CA # TRP,TYR,PHE + 25 27 1 ; CA-CA # TRP,TYR,PHE + 25 26 1 ; CA-HA # PHE, etc. + 27 29 1 ; CA-CA # TRP,TYR,PHE + 27 28 1 ; CA-HA # PHE, etc. + 29 31 1 ; CA-CA # TRP,TYR,PHE + 29 30 1 ; CA-HA # PHE, etc. + 31 33 1 ; CA-CA # TRP,TYR,PHE + 31 32 1 ; CA-HA # PHE, etc. + 33 34 1 ; CA-HA # PHE, etc. + +[ angles ] +; ai aj ak funct theta cth + 1 4 5 1 ; SY-CT-HC # + 1 4 6 1 ; SY-CT-HC # + 1 4 7 1 ; SY-CT-HC # + 5 4 6 1 ; HC-CT-HC # CHARMM 22 parameter file + 5 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + 6 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + 4 1 8 1 ; CT-SY-N # (N-SY-CT) + 4 1 2 1 ; CT-SY-OY # (OY-SY-CT) + 4 1 3 1 ; CT-SY-OY # (OY-SY-CT) + 8 1 2 1 ; N-SY-OY # (OY-SY-N) + 8 1 3 1 ; N-SY-OY # (OY-SY-N) + 2 1 3 1 ; OY-SY-OY # + 1 8 9 1 ; SY-N-CT # + 1 8 10 1 ; SY-N-H # (H-N-SY) + 9 8 10 1 ; CT-N-H # + 8 9 15 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 8 9 12 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 8 9 22 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 15 9 22 1 ; CT-CT-CT # CHARMM 22 parameter file + 12 9 15 1 ; CT-CT-CT # CHARMM 22 parameter file + 12 9 22 1 ; CT-CT-CT # CHARMM 22 parameter file + 9 12 11 1 ; CT-CT-S # CYX SCHERAGA JPC 79,1428 + 9 12 13 1 ; CT-CT-HC # CHARMM 22 parameter file + 9 12 14 1 ; CT-CT-HC # CHARMM 22 parameter file + 11 12 13 1 ; S-CT-HC # (HC-CT-S) + 11 12 14 1 ; S-CT-HC # (HC-CT-S) + 13 12 14 1 ; HC-CT-HC # CHARMM 22 parameter file + 12 11 15 1 ; CT-S-CT # MET(OL) + 9 15 11 1 ; CT-CT-S # CYX SCHERAGA JPC 79,1428 + 9 15 16 1 ; CT-CT-HC # CHARMM 22 parameter file + 9 15 17 1 ; CT-CT-HC # CHARMM 22 parameter file + 11 15 16 1 ; S-CT-HC # (HC-CT-S) + 11 15 17 1 ; S-CT-HC # (HC-CT-S) + 16 15 17 1 ; HC-CT-HC # CHARMM 22 parameter file + 9 22 18 1 ; CT-CT-CT # CHARMM 22 parameter file + 9 22 23 1 ; CT-CT-HC # CHARMM 22 parameter file + 9 22 24 1 ; CT-CT-HC # CHARMM 22 parameter file + 18 22 23 1 ; CT-CT-HC # CHARMM 22 parameter file + 18 22 24 1 ; CT-CT-HC # CHARMM 22 parameter file + 23 22 24 1 ; HC-CT-HC # CHARMM 22 parameter file + 22 18 19 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 22 18 20 1 ; CT-CT-HC # CHARMM 22 parameter file + 22 18 21 1 ; CT-CT-HC # CHARMM 22 parameter file + 19 18 20 1 ; CA-CT-HC # + 19 18 21 1 ; CA-CT-HC # + 20 18 21 1 ; HC-CT-HC # CHARMM 22 parameter file + 18 19 33 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 18 19 25 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 25 19 33 1 ; CA-CA-CA # PHE(OL) + 19 25 27 1 ; CA-CA-CA # PHE(OL) + 19 25 26 1 ; CA-CA-HA # + 27 25 26 1 ; CA-CA-HA # + 25 27 29 1 ; CA-CA-CA # PHE(OL) + 25 27 28 1 ; CA-CA-HA # + 29 27 28 1 ; CA-CA-HA # + 27 29 31 1 ; CA-CA-CA # PHE(OL) + 27 29 30 1 ; CA-CA-HA # + 31 29 30 1 ; CA-CA-HA # + 29 31 33 1 ; CA-CA-CA # PHE(OL) + 29 31 32 1 ; CA-CA-HA # + 33 31 32 1 ; CA-CA-HA # + 19 33 31 1 ; CA-CA-CA # PHE(OL) + 19 33 34 1 ; CA-CA-HA # + 31 33 34 1 ; CA-CA-HA # + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 5 4 1 8 3 ; HC-CT-SY-N # sulfonamide + 5 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 5 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 6 4 1 8 3 ; HC-CT-SY-N # sulfonamide + 6 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 6 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 7 4 1 8 3 ; HC-CT-SY-N # sulfonamide + 7 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 7 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 4 1 8 9 3 ; CT-SY-N-CT # (CT-N-SY-CT) sulfonamide + 4 1 8 10 3 ; CT-SY-N-H # sulfonamide + 2 1 8 9 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 1 8 10 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 1 8 9 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 1 8 10 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 8 9 15 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 1 8 9 12 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 1 8 9 22 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 10 8 9 15 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 10 8 9 12 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 10 8 9 22 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 8 9 15 11 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-S # (S-CT-CT-N) adapted from CT-CT-CT-N : N-propylformamide + 8 9 15 16 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 8 9 15 17 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 12 9 15 11 3 ; CT-CT-CT-S # sulfide all-atom + 12 9 15 16 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 12 9 15 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 22 9 15 11 3 ; CT-CT-CT-S # sulfide all-atom + 22 9 15 16 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 22 9 15 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 8 9 12 11 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-S # (S-CT-CT-N) adapted from CT-CT-CT-N : N-propylformamide + 8 9 12 13 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 8 9 12 14 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 15 9 12 11 3 ; CT-CT-CT-S # sulfide all-atom + 15 9 12 13 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 15 9 12 14 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 22 9 12 11 3 ; CT-CT-CT-S # sulfide all-atom + 22 9 12 13 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 22 9 12 14 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 8 9 22 18 3 ; N-CT-CT-CT # (CT-CT-CT-N) N-propylformamide + 8 9 22 23 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 8 9 22 24 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 15 9 22 18 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 15 9 22 23 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 15 9 22 24 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 12 9 22 18 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 12 9 22 23 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 12 9 22 24 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 9 12 11 15 3 ; CT-CT-S-CT # sulfide all-atom + 13 12 11 15 3 ; HC-CT-S-CT # (CT-S-CT-HC) sulfide all-atom + 14 12 11 15 3 ; HC-CT-S-CT # (CT-S-CT-HC) sulfide all-atom + 12 11 15 9 3 ; CT-S-CT-CT # (CT-CT-S-CT) sulfide all-atom + 12 11 15 16 3 ; CT-S-CT-HC # sulfide all-atom + 12 11 15 17 3 ; CT-S-CT-HC # sulfide all-atom + 9 22 18 19 3 ; CT-CT-CT-CA # (CA-CT-CT-CT) + 9 22 18 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 9 22 18 21 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 23 22 18 19 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 23 22 18 20 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 23 22 18 21 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 24 22 18 19 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 24 22 18 20 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 24 22 18 21 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 22 18 19 33 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 22 18 19 25 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 20 18 19 33 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 20 18 19 25 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 21 18 19 33 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 21 18 19 25 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 18 19 33 31 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 19 33 34 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 19 33 31 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 19 33 34 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 19 25 27 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 19 25 26 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 19 25 27 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 19 25 26 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 25 27 29 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 25 27 28 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 25 27 29 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 25 27 28 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 27 29 31 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 27 29 30 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 27 29 31 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 27 29 30 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 29 31 33 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 29 31 32 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 29 31 33 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 29 31 32 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 31 33 19 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 31 33 34 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 31 33 19 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 31 33 34 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 1 10 8 9 1 improper_Z_N_X_Y ; SY-H-N-CT + 33 25 19 18 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 27 26 25 19 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 29 28 27 25 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 31 30 29 27 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 33 32 31 29 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 31 34 33 19 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + +[ pairs ] +; ai aj funct + 4 9 1 + 4 10 1 + 1 15 1 + 1 12 1 + 1 22 1 + 8 5 1 + 8 6 1 + 8 7 1 + 8 11 1 + 8 16 1 + 8 17 1 + 8 13 1 + 8 14 1 + 8 18 1 + 8 23 1 + 8 24 1 + 9 2 1 + 9 3 1 + 9 19 1 + 9 20 1 + 9 21 1 + 12 10 1 + 12 16 1 + 12 17 1 + 12 18 1 + 12 23 1 + 12 24 1 + 11 22 1 + 15 10 1 + 15 13 1 + 15 14 1 + 15 18 1 + 15 23 1 + 15 24 1 + 22 10 1 + 22 16 1 + 22 17 1 + 22 13 1 + 22 14 1 + 22 33 1 + 22 25 1 + 18 31 1 + 18 34 1 + 18 27 1 + 18 26 1 + 19 23 1 + 19 24 1 + 19 29 1 + 19 32 1 + 19 28 1 + 25 20 1 + 25 21 1 + 25 31 1 + 25 34 1 + 25 30 1 + 27 33 1 + 27 32 1 + 29 26 1 + 29 34 1 + 31 28 1 + 33 20 1 + 33 21 1 + 33 26 1 + 33 30 1 + 2 5 1 + 2 6 1 + 2 7 1 + 2 10 1 + 3 5 1 + 3 6 1 + 3 7 1 + 3 10 1 + 23 20 1 + 23 21 1 + 24 20 1 + 24 21 1 + 26 28 1 + 28 30 1 + 30 32 1 + 32 34 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 4 1 1000 1000 1000 + 1 1 1000 1000 1000 + 8 1 1000 1000 1000 + 9 1 1000 1000 1000 + 12 1 1000 1000 1000 + 11 1 1000 1000 1000 + 15 1 1000 1000 1000 + 22 1 1000 1000 1000 + 18 1 1000 1000 1000 + 19 1 1000 1000 1000 + 25 1 1000 1000 1000 + 27 1 1000 1000 1000 + 29 1 1000 1000 1000 + 31 1 1000 1000 1000 + 33 1 1000 1000 1000 + 2 1 1000 1000 1000 + 3 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM32/SM32.mol2.1.pdb b/top/oplsaa/SM32/SM32.mol2.1.pdb new file mode 100644 index 0000000..d300b26 --- /dev/null +++ b/top/oplsaa/SM32/SM32.mol2.1.pdb @@ -0,0 +1,35 @@ +HETATM 1 S2 UNK 1 0.078 1.288 0.080 1.00 20.00 +HETATM 2 O16 UNK 1 1.111 2.072 -0.501 1.00 20.00 +HETATM 3 O17 UNK 1 -1.209 1.212 -0.518 1.00 20.00 +HETATM 4 C1 UNK 1 0.690 -0.371 0.486 1.00 20.00 +HETATM 5 H18 UNK 1 1.422 -0.301 1.291 1.00 20.00 +HETATM 6 H19 UNK 1 -0.143 -0.997 0.805 1.00 20.00 +HETATM 7 H20 UNK 1 1.159 -0.811 -0.394 1.00 20.00 +HETATM 8 N3 UNK 1 -0.196 1.998 1.551 1.00 20.00 +HETATM 9 C4 UNK 1 -1.243 1.477 2.432 1.00 20.00 +HETATM 10 H21 UNK 1 0.338 2.760 1.828 1.00 20.00 +HETATM 11 S6 UNK 1 -2.089 -0.244 1.038 1.00 20.00 +HETATM 12 C5 UNK 1 -1.188 -0.043 2.599 1.00 20.00 +HETATM 13 H22 UNK 1 -0.174 -0.441 2.563 1.00 20.00 +HETATM 14 H23 UNK 1 -1.745 -0.399 3.465 1.00 20.00 +HETATM 15 C7 UNK 1 -2.602 1.348 1.741 1.00 20.00 +HETATM 16 H24 UNK 1 -3.433 1.260 2.441 1.00 20.00 +HETATM 17 H25 UNK 1 -2.773 2.115 0.985 1.00 20.00 +HETATM 18 C9 UNK 1 0.098 2.415 4.320 1.00 20.00 +HETATM 19 C10 UNK 1 0.028 3.154 5.632 1.00 20.00 +HETATM 20 H28 UNK 1 0.559 1.439 4.477 1.00 20.00 +HETATM 21 H29 UNK 1 0.695 2.988 3.611 1.00 20.00 +HETATM 22 C8 UNK 1 -1.315 2.228 3.764 1.00 20.00 +HETATM 23 H26 UNK 1 -1.775 3.203 3.607 1.00 20.00 +HETATM 24 H27 UNK 1 -1.911 1.654 4.473 1.00 20.00 +HETATM 25 C11 UNK 1 0.093 4.534 5.651 1.00 20.00 +HETATM 26 H30 UNK 1 0.194 5.083 4.727 1.00 20.00 +HETATM 27 C12 UNK 1 0.024 5.213 6.854 1.00 20.00 +HETATM 28 H31 UNK 1 0.070 6.292 6.869 1.00 20.00 +HETATM 29 C13 UNK 1 -0.101 4.510 8.038 1.00 20.00 +HETATM 30 H32 UNK 1 -0.150 5.039 8.977 1.00 20.00 +HETATM 31 C14 UNK 1 -0.160 3.129 8.018 1.00 20.00 +HETATM 32 H33 UNK 1 -0.257 2.579 8.943 1.00 20.00 +HETATM 33 C15 UNK 1 -0.096 2.451 6.816 1.00 20.00 +HETATM 34 H34 UNK 1 -0.142 1.372 6.801 1.00 20.00 +END diff --git a/top/oplsaa/SM32/SM32.pdb b/top/oplsaa/SM32/SM32.pdb new file mode 120000 index 0000000..acab050 --- /dev/null +++ b/top/oplsaa/SM32/SM32.pdb @@ -0,0 +1 @@ +SM32.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM33/SM33.itp b/top/oplsaa/SM33/SM33.itp new file mode 120000 index 0000000..ed788d1 --- /dev/null +++ b/top/oplsaa/SM33/SM33.itp @@ -0,0 +1 @@ +SM33.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM33/SM33.mol2 b/top/oplsaa/SM33/SM33.mol2 new file mode 100644 index 0000000..3478f22 --- /dev/null +++ b/top/oplsaa/SM33/SM33.mol2 @@ -0,0 +1,105 @@ +# Name: SM33 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 41 43 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -1.3938 6.4195 0.4770 O.2 + 2 S2 -0.1575 5.8351 0.0908 S.o2 + 3 N3 0.0291 6.1588 -1.5225 N.am + 4 C4 -1.0983 5.9798 -2.4407 C.3 + 5 C5 -2.4111 6.5513 -1.9002 C.3 + 6 S6 -2.6681 5.0378 -0.9335 S.3 + 7 C7 -1.6958 4.5716 -2.3926 C.3 + 8 C8 -0.7766 6.4486 -3.8611 C.3 + 9 C9 -0.0756 7.8073 -3.8033 C.3 + 10 C10 0.2412 8.2690 -5.2024 C.ar + 11 C11 1.4505 7.9353 -5.7831 C.ar + 12 C12 1.7391 8.3548 -7.0683 C.ar + 13 C13 0.8229 9.1168 -7.7688 C.ar + 14 C14 -0.3842 9.4549 -7.1861 C.ar + 15 C15 -0.6750 9.0310 -5.9029 C.ar + 16 C16 -0.3587 4.0922 0.2532 C.ar + 17 C17 0.6143 3.2362 -0.2279 C.ar + 18 C18 0.4569 1.8689 -0.0997 C.ar + 19 C19 -0.6734 1.3575 0.5100 C.ar + 20 C20 -1.6490 2.2132 0.9864 C.ar + 21 C21 -1.4895 3.5807 0.8621 C.ar + 22 O22 1.0807 6.1555 0.7102 O.2 + 23 H23 0.8849 6.4670 -1.8595 H + 24 H24 -2.2700 7.4368 -1.2804 H + 25 H25 -3.1649 6.6989 -2.6736 H + 26 H26 -2.3116 4.3376 -3.2609 H + 27 H27 -0.9555 3.7989 -2.1852 H + 28 H28 -0.1225 5.7225 -4.3439 H + 29 H29 -1.7010 6.5406 -4.4314 H + 30 H30 -0.7297 8.5333 -3.3204 H + 31 H31 0.8487 7.7153 -3.2330 H + 32 H32 2.1682 7.3437 -5.2341 H + 33 H33 2.6824 8.0910 -7.5234 H + 34 H34 1.0502 9.4482 -8.7712 H + 35 H35 -1.0999 10.0505 -7.7333 H + 36 H36 -1.6180 9.2954 -5.4475 H + 37 H37 1.4977 3.6358 -0.7036 H + 38 H38 1.2171 1.2002 -0.4756 H + 39 H39 -0.7965 0.2892 0.6102 H + 40 H40 -2.5341 1.8135 1.4587 H + 41 H41 -2.2495 4.2494 1.2383 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 16 1 + 4 2 22 2 + 5 3 4 1 + 6 3 23 1 + 7 4 7 1 + 8 4 5 1 + 9 4 8 1 + 10 5 6 1 + 11 5 24 1 + 12 5 25 1 + 13 6 7 1 + 14 7 26 1 + 15 7 27 1 + 16 8 9 1 + 17 8 28 1 + 18 8 29 1 + 19 9 10 1 + 20 9 30 1 + 21 9 31 1 + 22 10 15 ar + 23 10 11 ar + 24 11 12 ar + 25 11 32 1 + 26 12 13 ar + 27 12 33 1 + 28 13 14 ar + 29 13 34 1 + 30 14 15 ar + 31 14 35 1 + 32 15 36 1 + 33 16 21 ar + 34 16 17 ar + 35 17 18 ar + 36 17 37 1 + 37 18 19 ar + 38 18 38 1 + 39 19 20 ar + 40 19 39 1 + 41 20 21 ar + 42 20 40 1 + 43 21 41 1 + +# End of record + diff --git a/top/oplsaa/SM33/SM33.mol2.1.itp b/top/oplsaa/SM33/SM33.mol2.1.itp new file mode 100644 index 0000000..d6cd7c1 --- /dev/null +++ b/top/oplsaa/SM33/SM33.mol2.1.itp @@ -0,0 +1,439 @@ +; input pdb SMILES : O=[S](NC1(CSC1)CCC2=CC=CC=C2)(C3=CC=CC=C3)=O +; Script arguments : SM33.mol2 "4 opls_139 0.270" "5 opls_210" "7 opls_210" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 2 opls_474 1 UNK S2 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 3 opls_488 1 UNK C16 1 0.000 12.01100 ; CA # The charge for this atom has been adjusted to take into account contributions from:`CA (opls_488)' AND `CA (opls_488)' + 4 opls_475 1 UNK O22 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 5 opls_480 1 UNK N3 3 -0.800 14.00670 ; N # N secondary amide of sulfonamide + 6 opls_139 1 UNK C4 3 0.270 12.01100 ; CT # alkane C ### user-defined OPLS atom type (opls_139) atom charge (0.270) + 7 opls_481 1 UNK H23 3 0.410 1.00800 ; H # H on N: secondary sulfonamide + 8 opls_202 1 UNK S6 15 -0.336 32.06000 ; S # dialkyl/diaryl sulfide, adapted from all-atom S: sulfides, S=C (opls_202) + 9 opls_210 1 UNK C5 17 0.048 12.01100 ; CT # all-atom C: CH2, sulfides ### user-defined OPLS atom type (opls_210) + 10 opls_140 1 UNK H24 17 0.060 1.00800 ; HC # alkane H. + 11 opls_140 1 UNK H25 17 0.060 1.00800 ; HC # alkane H. + 12 opls_210 1 UNK C7 19 0.048 12.01100 ; CT # all-atom C: CH2, sulfides ### user-defined OPLS atom type (opls_210) + 13 opls_140 1 UNK H26 19 0.060 1.00800 ; HC # alkane H. + 14 opls_140 1 UNK H27 19 0.060 1.00800 ; HC # alkane H. + 15 opls_149 1 UNK C9 21 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 16 opls_145 1 UNK C10 21 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 17 opls_140 1 UNK H30 21 0.060 1.00800 ; HC # alkane H. + 18 opls_140 1 UNK H31 21 0.060 1.00800 ; HC # alkane H. + 19 opls_136 1 UNK C8 33 -0.120 12.01100 ; CT # alkane CH2 + 20 opls_140 1 UNK H28 33 0.060 1.00800 ; HC # alkane H. + 21 opls_140 1 UNK H29 33 0.060 1.00800 ; HC # alkane H. + 22 opls_145 1 UNK C11 61 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 23 opls_146 1 UNK H32 61 0.115 1.00800 ; HA # Benzene H - 12 site. + 24 opls_145 1 UNK C12 63 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 25 opls_146 1 UNK H33 63 0.115 1.00800 ; HA # Benzene H - 12 site. + 26 opls_145 1 UNK C13 65 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 27 opls_146 1 UNK H34 65 0.115 1.00800 ; HA # Benzene H - 12 site. + 28 opls_145 1 UNK C14 67 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 29 opls_146 1 UNK H35 67 0.115 1.00800 ; HA # Benzene H - 12 site. + 30 opls_145 1 UNK C15 69 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 31 opls_146 1 UNK H36 69 0.115 1.00800 ; HA # Benzene H - 12 site. + 32 opls_145 1 UNK C17 71 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 33 opls_146 1 UNK H37 71 0.115 1.00800 ; HA # Benzene H - 12 site. + 34 opls_145 1 UNK C18 73 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 35 opls_146 1 UNK H38 73 0.115 1.00800 ; HA # Benzene H - 12 site. + 36 opls_145 1 UNK C19 75 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 37 opls_146 1 UNK H39 75 0.115 1.00800 ; HA # Benzene H - 12 site. + 38 opls_145 1 UNK C20 77 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 39 opls_146 1 UNK H40 77 0.115 1.00800 ; HA # Benzene H - 12 site. + 40 opls_145 1 UNK C21 79 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 41 opls_146 1 UNK H41 79 0.115 1.00800 ; HA # Benzene H - 12 site. +; Total charge : 0.000 ### Number of unassigned atoms : 0/41 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 5 1 ; SY-N # + 2 3 1 ; SY-CA # + 2 4 1 ; SY-OY # + 5 6 1 ; N-CT # (CT-N) + 5 7 1 ; N-H # (H-N) + 6 12 1 ; CT-CT # CHARMM 22 parameter file + 6 9 1 ; CT-CT # CHARMM 22 parameter file + 6 19 1 ; CT-CT # CHARMM 22 parameter file + 9 8 1 ; CT-S # CYX(OL) + 9 10 1 ; CT-HC # CHARMM 22 parameter file + 9 11 1 ; CT-HC # CHARMM 22 parameter file + 8 12 1 ; S-CT # (CT-S) CYX(OL) + 12 13 1 ; CT-HC # CHARMM 22 parameter file + 12 14 1 ; CT-HC # CHARMM 22 parameter file + 19 15 1 ; CT-CT # CHARMM 22 parameter file + 19 20 1 ; CT-HC # CHARMM 22 parameter file + 19 21 1 ; CT-HC # CHARMM 22 parameter file + 15 16 1 ; CT-CA # (CA-CT) PHE,TYR + 15 17 1 ; CT-HC # CHARMM 22 parameter file + 15 18 1 ; CT-HC # CHARMM 22 parameter file + 16 30 1 ; CA-CA # TRP,TYR,PHE + 16 22 1 ; CA-CA # TRP,TYR,PHE + 22 24 1 ; CA-CA # TRP,TYR,PHE + 22 23 1 ; CA-HA # PHE, etc. + 24 26 1 ; CA-CA # TRP,TYR,PHE + 24 25 1 ; CA-HA # PHE, etc. + 26 28 1 ; CA-CA # TRP,TYR,PHE + 26 27 1 ; CA-HA # PHE, etc. + 28 30 1 ; CA-CA # TRP,TYR,PHE + 28 29 1 ; CA-HA # PHE, etc. + 30 31 1 ; CA-HA # PHE, etc. + 3 40 1 ; CA-CA # TRP,TYR,PHE + 3 32 1 ; CA-CA # TRP,TYR,PHE + 32 34 1 ; CA-CA # TRP,TYR,PHE + 32 33 1 ; CA-HA # PHE, etc. + 34 36 1 ; CA-CA # TRP,TYR,PHE + 34 35 1 ; CA-HA # PHE, etc. + 36 38 1 ; CA-CA # TRP,TYR,PHE + 36 37 1 ; CA-HA # PHE, etc. + 38 40 1 ; CA-CA # TRP,TYR,PHE + 38 39 1 ; CA-HA # PHE, etc. + 40 41 1 ; CA-HA # PHE, etc. + +[ angles ] +; ai aj ak funct theta cth + 1 2 5 1 ; OY-SY-N # + 1 2 3 1 ; OY-SY-CA # + 1 2 4 1 ; OY-SY-OY # + 5 2 3 1 ; N-SY-CA # + 5 2 4 1 ; N-SY-OY # (OY-SY-N) + 3 2 4 1 ; CA-SY-OY # (OY-SY-CA) + 2 5 6 1 ; SY-N-CT # + 2 5 7 1 ; SY-N-H # (H-N-SY) + 6 5 7 1 ; CT-N-H # + 5 6 12 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 6 9 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 6 19 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 12 6 19 1 ; CT-CT-CT # CHARMM 22 parameter file + 9 6 12 1 ; CT-CT-CT # CHARMM 22 parameter file + 9 6 19 1 ; CT-CT-CT # CHARMM 22 parameter file + 6 9 8 1 ; CT-CT-S # CYX SCHERAGA JPC 79,1428 + 6 9 10 1 ; CT-CT-HC # CHARMM 22 parameter file + 6 9 11 1 ; CT-CT-HC # CHARMM 22 parameter file + 8 9 10 1 ; S-CT-HC # (HC-CT-S) + 8 9 11 1 ; S-CT-HC # (HC-CT-S) + 10 9 11 1 ; HC-CT-HC # CHARMM 22 parameter file + 9 8 12 1 ; CT-S-CT # MET(OL) + 6 12 8 1 ; CT-CT-S # CYX SCHERAGA JPC 79,1428 + 6 12 13 1 ; CT-CT-HC # CHARMM 22 parameter file + 6 12 14 1 ; CT-CT-HC # CHARMM 22 parameter file + 8 12 13 1 ; S-CT-HC # (HC-CT-S) + 8 12 14 1 ; S-CT-HC # (HC-CT-S) + 13 12 14 1 ; HC-CT-HC # CHARMM 22 parameter file + 6 19 15 1 ; CT-CT-CT # CHARMM 22 parameter file + 6 19 20 1 ; CT-CT-HC # CHARMM 22 parameter file + 6 19 21 1 ; CT-CT-HC # CHARMM 22 parameter file + 15 19 20 1 ; CT-CT-HC # CHARMM 22 parameter file + 15 19 21 1 ; CT-CT-HC # CHARMM 22 parameter file + 20 19 21 1 ; HC-CT-HC # CHARMM 22 parameter file + 19 15 16 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 19 15 17 1 ; CT-CT-HC # CHARMM 22 parameter file + 19 15 18 1 ; CT-CT-HC # CHARMM 22 parameter file + 16 15 17 1 ; CA-CT-HC # + 16 15 18 1 ; CA-CT-HC # + 17 15 18 1 ; HC-CT-HC # CHARMM 22 parameter file + 15 16 30 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 15 16 22 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 22 16 30 1 ; CA-CA-CA # PHE(OL) + 16 22 24 1 ; CA-CA-CA # PHE(OL) + 16 22 23 1 ; CA-CA-HA # + 24 22 23 1 ; CA-CA-HA # + 22 24 26 1 ; CA-CA-CA # PHE(OL) + 22 24 25 1 ; CA-CA-HA # + 26 24 25 1 ; CA-CA-HA # + 24 26 28 1 ; CA-CA-CA # PHE(OL) + 24 26 27 1 ; CA-CA-HA # + 28 26 27 1 ; CA-CA-HA # + 26 28 30 1 ; CA-CA-CA # PHE(OL) + 26 28 29 1 ; CA-CA-HA # + 30 28 29 1 ; CA-CA-HA # + 16 30 28 1 ; CA-CA-CA # PHE(OL) + 16 30 31 1 ; CA-CA-HA # + 28 30 31 1 ; CA-CA-HA # + 2 3 40 1 ; SY-CA-CA # + 2 3 32 1 ; SY-CA-CA # + 32 3 40 1 ; CA-CA-CA # PHE(OL) + 3 32 34 1 ; CA-CA-CA # PHE(OL) + 3 32 33 1 ; CA-CA-HA # + 34 32 33 1 ; CA-CA-HA # + 32 34 36 1 ; CA-CA-CA # PHE(OL) + 32 34 35 1 ; CA-CA-HA # + 36 34 35 1 ; CA-CA-HA # + 34 36 38 1 ; CA-CA-CA # PHE(OL) + 34 36 37 1 ; CA-CA-HA # + 38 36 37 1 ; CA-CA-HA # + 36 38 40 1 ; CA-CA-CA # PHE(OL) + 36 38 39 1 ; CA-CA-HA # + 40 38 39 1 ; CA-CA-HA # + 3 40 38 1 ; CA-CA-CA # PHE(OL) + 3 40 41 1 ; CA-CA-HA # + 38 40 41 1 ; CA-CA-HA # + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 5 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 5 7 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 5 6 3 ; CA-SY-N-CT # sulfonamide + 3 2 5 7 3 ; CA-SY-N-H # sulfonamide + 4 2 5 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 5 7 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 40 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 1 2 3 32 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 5 2 3 40 3 ; N-SY-CA-CA # (CA-CA-SY-N) sulfonamide + 5 2 3 32 3 ; N-SY-CA-CA # (CA-CA-SY-N) sulfonamide + 4 2 3 40 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 4 2 3 32 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 2 5 6 12 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 6 9 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 6 19 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 7 5 6 12 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 7 5 6 9 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 7 5 6 19 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 5 6 12 8 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-S # (S-CT-CT-N) adapted from CT-CT-CT-N : N-propylformamide + 5 6 12 13 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 6 12 14 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 9 6 12 8 3 ; CT-CT-CT-S # sulfide all-atom + 9 6 12 13 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 9 6 12 14 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 19 6 12 8 3 ; CT-CT-CT-S # sulfide all-atom + 19 6 12 13 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 19 6 12 14 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 6 9 8 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-S # (S-CT-CT-N) adapted from CT-CT-CT-N : N-propylformamide + 5 6 9 10 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 6 9 11 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 12 6 9 8 3 ; CT-CT-CT-S # sulfide all-atom + 12 6 9 10 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 12 6 9 11 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 19 6 9 8 3 ; CT-CT-CT-S # sulfide all-atom + 19 6 9 10 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 19 6 9 11 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 6 19 15 3 ; N-CT-CT-CT # (CT-CT-CT-N) N-propylformamide + 5 6 19 20 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 6 19 21 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 12 6 19 15 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 12 6 19 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 12 6 19 21 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 9 6 19 15 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 9 6 19 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 9 6 19 21 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 6 9 8 12 3 ; CT-CT-S-CT # sulfide all-atom + 10 9 8 12 3 ; HC-CT-S-CT # (CT-S-CT-HC) sulfide all-atom + 11 9 8 12 3 ; HC-CT-S-CT # (CT-S-CT-HC) sulfide all-atom + 9 8 12 6 3 ; CT-S-CT-CT # (CT-CT-S-CT) sulfide all-atom + 9 8 12 13 3 ; CT-S-CT-HC # sulfide all-atom + 9 8 12 14 3 ; CT-S-CT-HC # sulfide all-atom + 6 19 15 16 3 ; CT-CT-CT-CA # (CA-CT-CT-CT) + 6 19 15 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 6 19 15 18 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 20 19 15 16 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 20 19 15 17 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 20 19 15 18 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 21 19 15 16 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 21 19 15 17 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 21 19 15 18 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 19 15 16 30 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 19 15 16 22 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 17 15 16 30 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 17 15 16 22 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 18 15 16 30 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 18 15 16 22 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 15 16 30 28 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 16 30 31 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 16 30 28 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 16 30 31 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 16 22 24 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 16 22 23 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 16 22 24 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 16 22 23 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 22 24 26 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 22 24 25 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 22 24 26 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 22 24 25 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 24 26 28 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 24 26 27 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 24 26 28 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 24 26 27 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 26 28 30 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 26 28 29 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 26 28 30 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 26 28 29 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 28 30 16 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 28 30 31 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 28 30 16 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 28 30 31 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 40 38 3 ; SY-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 40 41 3 ; SY-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 3 40 38 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 3 40 41 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 32 34 3 ; SY-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 32 33 3 ; SY-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 40 3 32 34 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 40 3 32 33 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 3 32 34 36 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 3 32 34 35 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 32 34 36 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 32 34 35 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 34 36 38 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 34 36 37 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 35 34 36 38 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 35 34 36 37 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 36 38 40 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 36 38 39 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 37 36 38 40 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 37 36 38 39 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 36 38 40 3 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 36 38 40 41 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 39 38 40 3 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 39 38 40 41 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 2 7 5 6 1 improper_Z_N_X_Y ; SY-H-N-CT + 30 22 16 15 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 24 23 22 16 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 26 25 24 22 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 28 27 26 24 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 30 29 28 26 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 28 31 30 16 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 40 32 3 2 1 improper_Z_CA_X_Y ; CA-CA-CA-SY + 34 33 32 3 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 36 35 34 32 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 38 37 36 34 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 40 39 38 36 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 38 41 40 3 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + +[ pairs ] +; ai aj funct + 1 6 1 + 1 7 1 + 1 40 1 + 1 32 1 + 2 12 1 + 2 9 1 + 2 19 1 + 2 38 1 + 2 41 1 + 2 34 1 + 2 33 1 + 5 40 1 + 5 32 1 + 5 8 1 + 5 13 1 + 5 14 1 + 5 10 1 + 5 11 1 + 5 15 1 + 5 20 1 + 5 21 1 + 6 3 1 + 6 4 1 + 6 16 1 + 6 17 1 + 6 18 1 + 9 7 1 + 9 13 1 + 9 14 1 + 9 15 1 + 9 20 1 + 9 21 1 + 8 19 1 + 12 7 1 + 12 10 1 + 12 11 1 + 12 15 1 + 12 20 1 + 12 21 1 + 19 7 1 + 19 13 1 + 19 14 1 + 19 10 1 + 19 11 1 + 19 30 1 + 19 22 1 + 15 28 1 + 15 31 1 + 15 24 1 + 15 23 1 + 16 20 1 + 16 21 1 + 16 26 1 + 16 29 1 + 16 25 1 + 22 17 1 + 22 18 1 + 22 28 1 + 22 31 1 + 22 27 1 + 24 30 1 + 24 29 1 + 26 23 1 + 26 31 1 + 28 25 1 + 30 17 1 + 30 18 1 + 30 23 1 + 30 27 1 + 3 7 1 + 3 36 1 + 3 39 1 + 3 35 1 + 32 4 1 + 32 38 1 + 32 41 1 + 32 37 1 + 34 40 1 + 34 39 1 + 36 33 1 + 36 41 1 + 38 35 1 + 40 4 1 + 40 33 1 + 40 37 1 + 4 7 1 + 20 17 1 + 20 18 1 + 21 17 1 + 21 18 1 + 23 25 1 + 25 27 1 + 27 29 1 + 29 31 1 + 33 35 1 + 35 37 1 + 37 39 1 + 39 41 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 5 1 1000 1000 1000 + 6 1 1000 1000 1000 + 9 1 1000 1000 1000 + 8 1 1000 1000 1000 + 12 1 1000 1000 1000 + 19 1 1000 1000 1000 + 15 1 1000 1000 1000 + 16 1 1000 1000 1000 + 22 1 1000 1000 1000 + 24 1 1000 1000 1000 + 26 1 1000 1000 1000 + 28 1 1000 1000 1000 + 30 1 1000 1000 1000 + 3 1 1000 1000 1000 + 32 1 1000 1000 1000 + 34 1 1000 1000 1000 + 36 1 1000 1000 1000 + 38 1 1000 1000 1000 + 40 1 1000 1000 1000 + 4 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM33/SM33.mol2.1.pdb b/top/oplsaa/SM33/SM33.mol2.1.pdb new file mode 100644 index 0000000..2b9b746 --- /dev/null +++ b/top/oplsaa/SM33/SM33.mol2.1.pdb @@ -0,0 +1,42 @@ +HETATM 1 O1 UNK 1 -1.394 6.420 0.477 1.00 20.00 +HETATM 2 S2 UNK 1 -0.158 5.835 0.091 1.00 20.00 +HETATM 3 C16 UNK 1 -0.359 4.092 0.253 1.00 20.00 +HETATM 4 O22 UNK 1 1.081 6.155 0.710 1.00 20.00 +HETATM 5 N3 UNK 1 0.029 6.159 -1.522 1.00 20.00 +HETATM 6 C4 UNK 1 -1.098 5.980 -2.441 1.00 20.00 +HETATM 7 H23 UNK 1 0.885 6.467 -1.859 1.00 20.00 +HETATM 8 S6 UNK 1 -2.668 5.038 -0.933 1.00 20.00 +HETATM 9 C5 UNK 1 -2.411 6.551 -1.900 1.00 20.00 +HETATM 10 H24 UNK 1 -2.270 7.437 -1.280 1.00 20.00 +HETATM 11 H25 UNK 1 -3.165 6.699 -2.674 1.00 20.00 +HETATM 12 C7 UNK 1 -1.696 4.572 -2.393 1.00 20.00 +HETATM 13 H26 UNK 1 -2.312 4.338 -3.261 1.00 20.00 +HETATM 14 H27 UNK 1 -0.956 3.799 -2.185 1.00 20.00 +HETATM 15 C9 UNK 1 -0.076 7.807 -3.803 1.00 20.00 +HETATM 16 C10 UNK 1 0.241 8.269 -5.202 1.00 20.00 +HETATM 17 H30 UNK 1 -0.730 8.533 -3.320 1.00 20.00 +HETATM 18 H31 UNK 1 0.849 7.715 -3.233 1.00 20.00 +HETATM 19 C8 UNK 1 -0.777 6.449 -3.861 1.00 20.00 +HETATM 20 H28 UNK 1 -0.122 5.723 -4.344 1.00 20.00 +HETATM 21 H29 UNK 1 -1.701 6.541 -4.431 1.00 20.00 +HETATM 22 C11 UNK 1 1.450 7.935 -5.783 1.00 20.00 +HETATM 23 H32 UNK 1 2.168 7.344 -5.234 1.00 20.00 +HETATM 24 C12 UNK 1 1.739 8.355 -7.068 1.00 20.00 +HETATM 25 H33 UNK 1 2.682 8.091 -7.523 1.00 20.00 +HETATM 26 C13 UNK 1 0.823 9.117 -7.769 1.00 20.00 +HETATM 27 H34 UNK 1 1.050 9.448 -8.771 1.00 20.00 +HETATM 28 C14 UNK 1 -0.384 9.455 -7.186 1.00 20.00 +HETATM 29 H35 UNK 1 -1.100 10.050 -7.733 1.00 20.00 +HETATM 30 C15 UNK 1 -0.675 9.031 -5.903 1.00 20.00 +HETATM 31 H36 UNK 1 -1.618 9.295 -5.447 1.00 20.00 +HETATM 32 C17 UNK 1 0.614 3.236 -0.228 1.00 20.00 +HETATM 33 H37 UNK 1 1.498 3.636 -0.704 1.00 20.00 +HETATM 34 C18 UNK 1 0.457 1.869 -0.100 1.00 20.00 +HETATM 35 H38 UNK 1 1.217 1.200 -0.476 1.00 20.00 +HETATM 36 C19 UNK 1 -0.673 1.357 0.510 1.00 20.00 +HETATM 37 H39 UNK 1 -0.796 0.289 0.610 1.00 20.00 +HETATM 38 C20 UNK 1 -1.649 2.213 0.986 1.00 20.00 +HETATM 39 H40 UNK 1 -2.534 1.813 1.459 1.00 20.00 +HETATM 40 C21 UNK 1 -1.490 3.581 0.862 1.00 20.00 +HETATM 41 H41 UNK 1 -2.249 4.249 1.238 1.00 20.00 +END diff --git a/top/oplsaa/SM33/SM33.pdb b/top/oplsaa/SM33/SM33.pdb new file mode 120000 index 0000000..ab8c0cd --- /dev/null +++ b/top/oplsaa/SM33/SM33.pdb @@ -0,0 +1 @@ +SM33.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM34/SM34.itp b/top/oplsaa/SM34/SM34.itp new file mode 120000 index 0000000..71564df --- /dev/null +++ b/top/oplsaa/SM34/SM34.itp @@ -0,0 +1 @@ +SM34.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM34/SM34.mol2 b/top/oplsaa/SM34/SM34.mol2 new file mode 100644 index 0000000..665194a --- /dev/null +++ b/top/oplsaa/SM34/SM34.mol2 @@ -0,0 +1,100 @@ +# Name: SM34 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 39 40 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -0.4388 0.6038 -3.9820 O.2 + 2 S2 0.3206 1.0225 -2.8562 S.o2 + 3 N3 1.5890 -0.0345 -2.7285 N.am + 4 C4 2.4894 0.0377 -1.5751 C.3 + 5 C5 1.6936 -0.0983 -0.2416 C.3 + 6 S6 1.7187 1.7306 -0.3217 S.3 + 7 C7 3.1275 1.4551 -1.4581 C.3 + 8 C8 3.5715 -1.0393 -1.6751 C.3 + 9 C9 4.3320 -0.8775 -2.9928 C.3 + 10 C10 5.3978 -1.9383 -3.0912 C.ar + 11 C11 6.6668 -1.6906 -2.6021 C.ar + 12 C12 7.6431 -2.6654 -2.6881 C.ar + 13 C13 7.3534 -3.8842 -3.2726 C.ar + 14 C14 6.0858 -4.1300 -3.7663 C.ar + 15 C15 5.1081 -3.1571 -3.6757 C.ar + 16 N16 0.9533 2.5031 -3.2434 N.am + 17 C17 1.5928 2.7086 -4.5453 C.3 + 18 C18 0.8736 3.6073 -2.2839 C.3 + 19 O19 -0.2287 1.1495 -1.5519 O.2 + 20 H20 1.7359 -0.7014 -3.4175 H + 21 H21 2.2672 -0.5205 0.5836 H + 22 H22 0.7032 -0.5400 -0.3517 H + 23 H23 3.0878 2.0435 -2.3748 H + 24 H24 4.1047 1.4702 -0.9754 H + 25 H25 4.2649 -0.9363 -0.8404 H + 26 H26 3.1072 -2.0250 -1.6422 H + 27 H27 3.6386 -0.9805 -3.8275 H + 28 H28 4.7963 0.1082 -3.0256 H + 29 H29 6.8944 -0.7368 -2.1495 H + 30 H30 8.6335 -2.4733 -2.3026 H + 31 H31 8.1174 -4.6442 -3.3437 H + 32 H32 5.8595 -5.0820 -4.2233 H + 33 H33 4.1179 -3.3490 -4.0618 H + 34 H34 0.8474 3.0415 -5.2677 H + 35 H35 2.3717 3.4654 -4.4521 H + 36 H36 2.0350 1.7720 -4.8849 H + 37 H37 0.2851 3.2967 -1.4206 H + 38 H38 1.8779 3.8802 -1.9598 H + 39 H39 0.3986 4.4665 -2.7574 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 16 am + 4 2 19 2 + 5 3 4 1 + 6 3 20 1 + 7 4 7 1 + 8 4 5 1 + 9 4 8 1 + 10 5 6 1 + 11 5 21 1 + 12 5 22 1 + 13 6 7 1 + 14 7 23 1 + 15 7 24 1 + 16 8 9 1 + 17 8 25 1 + 18 8 26 1 + 19 9 10 1 + 20 9 27 1 + 21 9 28 1 + 22 10 15 ar + 23 10 11 ar + 24 11 12 ar + 25 11 29 1 + 26 12 13 ar + 27 12 30 1 + 28 13 14 ar + 29 13 31 1 + 30 14 15 ar + 31 14 32 1 + 32 15 33 1 + 33 16 17 1 + 34 16 18 1 + 35 17 34 1 + 36 17 35 1 + 37 17 36 1 + 38 18 37 1 + 39 18 38 1 + 40 18 39 1 + +# End of record + diff --git a/top/oplsaa/SM34/SM34.mol2.1.itp b/top/oplsaa/SM34/SM34.mol2.1.itp new file mode 100644 index 0000000..57e2de0 --- /dev/null +++ b/top/oplsaa/SM34/SM34.mol2.1.itp @@ -0,0 +1,402 @@ +; input pdb SMILES : O=[S](NC1(CSC1)CCC2=CC=CC=C2)(N(C)C)=O +; Script arguments : SM34.mol2 "4 opls_139 0.000" "5 opls_210" "7 opls_210" "20 opls_241 0.482" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 2 opls_474 1 UNK S2 1 0.852 32.06000 ; SY # S in sulfamide, S(=O)2(NR2) + 3 opls_480 1 UNK N16 1 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 4 opls_475 1 UNK O19 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 5 opls_480 1 UNK N3 3 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 6 opls_482 1 UNK C18 5 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 7 opls_483 1 UNK H37 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 8 opls_483 1 UNK H38 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 9 opls_483 1 UNK H39 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 10 opls_482 1 UNK C17 11 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 11 opls_483 1 UNK H34 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 12 opls_483 1 UNK H35 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 13 opls_483 1 UNK H36 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 14 opls_202 1 UNK S6 29 -0.336 32.06000 ; S # dialkyl/diaryl sulfide, adapted from all-atom S: sulfides, S=C (opls_202) + 15 opls_210 1 UNK C5 31 0.048 12.01100 ; CT # all-atom C: CH2, sulfides ### user-defined OPLS atom type (opls_210) + 16 opls_140 1 UNK H21 31 0.060 1.00800 ; HC # alkane H. + 17 opls_140 1 UNK H22 31 0.060 1.00800 ; HC # alkane H. + 18 opls_210 1 UNK C7 33 0.048 12.01100 ; CT # all-atom C: CH2, sulfides ### user-defined OPLS atom type (opls_210) + 19 opls_140 1 UNK H23 33 0.060 1.00800 ; HC # alkane H. + 20 opls_140 1 UNK H24 33 0.060 1.00800 ; HC # alkane H. + 21 opls_149 1 UNK C9 35 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 22 opls_145 1 UNK C10 35 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 23 opls_140 1 UNK H27 35 0.060 1.00800 ; HC # alkane H. + 24 opls_140 1 UNK H28 35 0.060 1.00800 ; HC # alkane H. + 25 opls_136 1 UNK C8 59 -0.120 12.01100 ; CT # alkane CH2 + 26 opls_140 1 UNK H25 59 0.060 1.00800 ; HC # alkane H. + 27 opls_140 1 UNK H26 59 0.060 1.00800 ; HC # alkane H. + 28 opls_139 1 UNK C4 63 0.000 12.01100 ; CT # alkane C ### user-defined OPLS atom type (opls_139) atom charge (0.000) + 29 opls_145 1 UNK C11 87 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 30 opls_146 1 UNK H29 87 0.115 1.00800 ; HA # Benzene H - 12 site. + 31 opls_145 1 UNK C12 89 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 32 opls_146 1 UNK H30 89 0.115 1.00800 ; HA # Benzene H - 12 site. + 33 opls_145 1 UNK C13 91 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 34 opls_146 1 UNK H31 91 0.115 1.00800 ; HA # Benzene H - 12 site. + 35 opls_145 1 UNK C14 93 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 36 opls_146 1 UNK H32 93 0.115 1.00800 ; HA # Benzene H - 12 site. + 37 opls_145 1 UNK C15 95 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 38 opls_146 1 UNK H33 95 0.115 1.00800 ; HA # Benzene H - 12 site. + 39 opls_241 1 UNK H20 97 0.482 1.00800 ; H # H on N: secondary amide ### user-defined OPLS atom type (opls_241) atom charge (0.482) +; Total charge : 0.000 ### Number of unassigned atoms : 0/39 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 5 1 ; SY-N # + 2 3 1 ; SY-N # + 2 4 1 ; SY-OY # + 5 28 1 ; N-CT # (CT-N) + 5 39 1 ; N-H # (H-N) + 28 18 1 ; CT-CT # CHARMM 22 parameter file + 28 15 1 ; CT-CT # CHARMM 22 parameter file + 28 25 1 ; CT-CT # CHARMM 22 parameter file + 15 14 1 ; CT-S # CYX(OL) + 15 16 1 ; CT-HC # CHARMM 22 parameter file + 15 17 1 ; CT-HC # CHARMM 22 parameter file + 14 18 1 ; S-CT # (CT-S) CYX(OL) + 18 19 1 ; CT-HC # CHARMM 22 parameter file + 18 20 1 ; CT-HC # CHARMM 22 parameter file + 25 21 1 ; CT-CT # CHARMM 22 parameter file + 25 26 1 ; CT-HC # CHARMM 22 parameter file + 25 27 1 ; CT-HC # CHARMM 22 parameter file + 21 22 1 ; CT-CA # (CA-CT) PHE,TYR + 21 23 1 ; CT-HC # CHARMM 22 parameter file + 21 24 1 ; CT-HC # CHARMM 22 parameter file + 22 37 1 ; CA-CA # TRP,TYR,PHE + 22 29 1 ; CA-CA # TRP,TYR,PHE + 29 31 1 ; CA-CA # TRP,TYR,PHE + 29 30 1 ; CA-HA # PHE, etc. + 31 33 1 ; CA-CA # TRP,TYR,PHE + 31 32 1 ; CA-HA # PHE, etc. + 33 35 1 ; CA-CA # TRP,TYR,PHE + 33 34 1 ; CA-HA # PHE, etc. + 35 37 1 ; CA-CA # TRP,TYR,PHE + 35 36 1 ; CA-HA # PHE, etc. + 37 38 1 ; CA-HA # PHE, etc. + 3 10 1 ; N-CT # (CT-N) + 3 6 1 ; N-CT # (CT-N) + 10 11 1 ; CT-HC # CHARMM 22 parameter file + 10 12 1 ; CT-HC # CHARMM 22 parameter file + 10 13 1 ; CT-HC # CHARMM 22 parameter file + 6 7 1 ; CT-HC # CHARMM 22 parameter file + 6 8 1 ; CT-HC # CHARMM 22 parameter file + 6 9 1 ; CT-HC # CHARMM 22 parameter file + +[ angles ] +; ai aj ak funct theta cth + 1 2 5 1 ; OY-SY-N # + 1 2 3 1 ; OY-SY-N # + 1 2 4 1 ; OY-SY-OY # + 5 2 3 1 107.000 1004.160 ; N-SY-N # by analogy from OY-SY-N : + 5 2 4 1 ; N-SY-OY # (OY-SY-N) + 3 2 4 1 ; N-SY-OY # (OY-SY-N) + 2 5 28 1 ; SY-N-CT # + 2 5 39 1 ; SY-N-H # (H-N-SY) + 28 5 39 1 ; CT-N-H # + 5 28 18 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 28 15 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 28 25 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 18 28 25 1 ; CT-CT-CT # CHARMM 22 parameter file + 15 28 18 1 ; CT-CT-CT # CHARMM 22 parameter file + 15 28 25 1 ; CT-CT-CT # CHARMM 22 parameter file + 28 15 14 1 ; CT-CT-S # CYX SCHERAGA JPC 79,1428 + 28 15 16 1 ; CT-CT-HC # CHARMM 22 parameter file + 28 15 17 1 ; CT-CT-HC # CHARMM 22 parameter file + 14 15 16 1 ; S-CT-HC # (HC-CT-S) + 14 15 17 1 ; S-CT-HC # (HC-CT-S) + 16 15 17 1 ; HC-CT-HC # CHARMM 22 parameter file + 15 14 18 1 ; CT-S-CT # MET(OL) + 28 18 14 1 ; CT-CT-S # CYX SCHERAGA JPC 79,1428 + 28 18 19 1 ; CT-CT-HC # CHARMM 22 parameter file + 28 18 20 1 ; CT-CT-HC # CHARMM 22 parameter file + 14 18 19 1 ; S-CT-HC # (HC-CT-S) + 14 18 20 1 ; S-CT-HC # (HC-CT-S) + 19 18 20 1 ; HC-CT-HC # CHARMM 22 parameter file + 28 25 21 1 ; CT-CT-CT # CHARMM 22 parameter file + 28 25 26 1 ; CT-CT-HC # CHARMM 22 parameter file + 28 25 27 1 ; CT-CT-HC # CHARMM 22 parameter file + 21 25 26 1 ; CT-CT-HC # CHARMM 22 parameter file + 21 25 27 1 ; CT-CT-HC # CHARMM 22 parameter file + 26 25 27 1 ; HC-CT-HC # CHARMM 22 parameter file + 25 21 22 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 25 21 23 1 ; CT-CT-HC # CHARMM 22 parameter file + 25 21 24 1 ; CT-CT-HC # CHARMM 22 parameter file + 22 21 23 1 ; CA-CT-HC # + 22 21 24 1 ; CA-CT-HC # + 23 21 24 1 ; HC-CT-HC # CHARMM 22 parameter file + 21 22 37 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 21 22 29 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 29 22 37 1 ; CA-CA-CA # PHE(OL) + 22 29 31 1 ; CA-CA-CA # PHE(OL) + 22 29 30 1 ; CA-CA-HA # + 31 29 30 1 ; CA-CA-HA # + 29 31 33 1 ; CA-CA-CA # PHE(OL) + 29 31 32 1 ; CA-CA-HA # + 33 31 32 1 ; CA-CA-HA # + 31 33 35 1 ; CA-CA-CA # PHE(OL) + 31 33 34 1 ; CA-CA-HA # + 35 33 34 1 ; CA-CA-HA # + 33 35 37 1 ; CA-CA-CA # PHE(OL) + 33 35 36 1 ; CA-CA-HA # + 37 35 36 1 ; CA-CA-HA # + 22 37 35 1 ; CA-CA-CA # PHE(OL) + 22 37 38 1 ; CA-CA-HA # + 35 37 38 1 ; CA-CA-HA # + 2 3 10 1 ; SY-N-CT # + 2 3 6 1 ; SY-N-CT # + 10 3 6 1 ; CT-N-CT # PRO(OL) DETAR JACS 99,1232 + 3 10 11 1 ; N-CT-HC # (HC-CT-N) + 3 10 12 1 ; N-CT-HC # (HC-CT-N) + 3 10 13 1 ; N-CT-HC # (HC-CT-N) + 11 10 12 1 ; HC-CT-HC # CHARMM 22 parameter file + 11 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 12 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 3 6 7 1 ; N-CT-HC # (HC-CT-N) + 3 6 8 1 ; N-CT-HC # (HC-CT-N) + 3 6 9 1 ; N-CT-HC # (HC-CT-N) + 7 6 8 1 ; HC-CT-HC # CHARMM 22 parameter file + 7 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + 8 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 5 28 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 5 39 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 5 28 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 3 2 5 39 3 -15.611 0.703 20.506 -5.598 -0.000 0.000 ; N-SY-N-H # LigParGen + 4 2 5 28 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 5 39 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 5 2 3 10 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 5 2 3 6 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 4 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 5 28 18 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 28 15 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 28 25 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 39 5 28 18 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 39 5 28 15 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 39 5 28 25 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 5 28 18 14 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-S # (S-CT-CT-N) adapted from CT-CT-CT-N : N-propylformamide + 5 28 18 19 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 28 18 20 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 15 28 18 14 3 ; CT-CT-CT-S # sulfide all-atom + 15 28 18 19 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 15 28 18 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 25 28 18 14 3 ; CT-CT-CT-S # sulfide all-atom + 25 28 18 19 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 25 28 18 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 28 15 14 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-S # (S-CT-CT-N) adapted from CT-CT-CT-N : N-propylformamide + 5 28 15 16 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 28 15 17 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 18 28 15 14 3 ; CT-CT-CT-S # sulfide all-atom + 18 28 15 16 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 18 28 15 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 25 28 15 14 3 ; CT-CT-CT-S # sulfide all-atom + 25 28 15 16 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 25 28 15 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 28 25 21 3 ; N-CT-CT-CT # (CT-CT-CT-N) N-propylformamide + 5 28 25 26 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 28 25 27 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 18 28 25 21 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 18 28 25 26 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 18 28 25 27 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 15 28 25 21 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 15 28 25 26 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 15 28 25 27 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 28 15 14 18 3 ; CT-CT-S-CT # sulfide all-atom + 16 15 14 18 3 ; HC-CT-S-CT # (CT-S-CT-HC) sulfide all-atom + 17 15 14 18 3 ; HC-CT-S-CT # (CT-S-CT-HC) sulfide all-atom + 15 14 18 28 3 ; CT-S-CT-CT # (CT-CT-S-CT) sulfide all-atom + 15 14 18 19 3 ; CT-S-CT-HC # sulfide all-atom + 15 14 18 20 3 ; CT-S-CT-HC # sulfide all-atom + 28 25 21 22 3 ; CT-CT-CT-CA # (CA-CT-CT-CT) + 28 25 21 23 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 28 25 21 24 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 26 25 21 22 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 26 25 21 23 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 26 25 21 24 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 27 25 21 22 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 27 25 21 23 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 27 25 21 24 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 25 21 22 37 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 25 21 22 29 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 23 21 22 37 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 23 21 22 29 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 24 21 22 37 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 24 21 22 29 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 21 22 37 35 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 22 37 38 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 22 37 35 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 22 37 38 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 22 29 31 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 22 29 30 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 37 22 29 31 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 37 22 29 30 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 29 31 33 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 29 31 32 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 29 31 33 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 29 31 32 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 31 33 35 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 31 33 34 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 31 33 35 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 31 33 34 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 33 35 37 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 33 35 36 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 33 35 37 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 33 35 36 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 35 37 22 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 35 37 38 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 36 35 37 22 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 36 35 37 38 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 10 11 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 12 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 13 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 6 3 10 11 3 ; CT-N-CT-HC # tert. amide + 6 3 10 12 3 ; CT-N-CT-HC # tert. amide + 6 3 10 13 3 ; CT-N-CT-HC # tert. amide + 2 3 6 7 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 8 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 9 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 10 3 6 7 3 ; CT-N-CT-HC # tert. amide + 10 3 6 8 3 ; CT-N-CT-HC # tert. amide + 10 3 6 9 3 ; CT-N-CT-HC # tert. amide + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 2 39 5 28 1 improper_Z_N_X_Y ; SY-H-N-CT + 37 29 22 21 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 31 30 29 22 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 33 32 31 29 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 35 34 33 31 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 37 36 35 33 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 35 38 37 22 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 2 6 3 10 1 improper_Z_N_X_Y ; SY-CT-N-CT + +[ pairs ] +; ai aj funct + 1 28 1 + 1 39 1 + 1 10 1 + 1 6 1 + 2 18 1 + 2 15 1 + 2 25 1 + 2 11 1 + 2 12 1 + 2 13 1 + 2 7 1 + 2 8 1 + 2 9 1 + 5 10 1 + 5 6 1 + 5 14 1 + 5 19 1 + 5 20 1 + 5 16 1 + 5 17 1 + 5 21 1 + 5 26 1 + 5 27 1 + 28 3 1 + 28 4 1 + 28 22 1 + 28 23 1 + 28 24 1 + 15 39 1 + 15 19 1 + 15 20 1 + 15 21 1 + 15 26 1 + 15 27 1 + 14 25 1 + 18 39 1 + 18 16 1 + 18 17 1 + 18 21 1 + 18 26 1 + 18 27 1 + 25 39 1 + 25 19 1 + 25 20 1 + 25 16 1 + 25 17 1 + 25 37 1 + 25 29 1 + 21 35 1 + 21 38 1 + 21 31 1 + 21 30 1 + 22 26 1 + 22 27 1 + 22 33 1 + 22 36 1 + 22 32 1 + 29 23 1 + 29 24 1 + 29 35 1 + 29 38 1 + 29 34 1 + 31 37 1 + 31 36 1 + 33 30 1 + 33 38 1 + 35 32 1 + 37 23 1 + 37 24 1 + 37 30 1 + 37 34 1 + 3 39 1 + 10 4 1 + 10 7 1 + 10 8 1 + 10 9 1 + 6 4 1 + 6 11 1 + 6 12 1 + 6 13 1 + 4 39 1 + 26 23 1 + 26 24 1 + 27 23 1 + 27 24 1 + 30 32 1 + 32 34 1 + 34 36 1 + 36 38 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 5 1 1000 1000 1000 + 28 1 1000 1000 1000 + 15 1 1000 1000 1000 + 14 1 1000 1000 1000 + 18 1 1000 1000 1000 + 25 1 1000 1000 1000 + 21 1 1000 1000 1000 + 22 1 1000 1000 1000 + 29 1 1000 1000 1000 + 31 1 1000 1000 1000 + 33 1 1000 1000 1000 + 35 1 1000 1000 1000 + 37 1 1000 1000 1000 + 3 1 1000 1000 1000 + 10 1 1000 1000 1000 + 6 1 1000 1000 1000 + 4 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM34/SM34.mol2.1.pdb b/top/oplsaa/SM34/SM34.mol2.1.pdb new file mode 100644 index 0000000..fbe9784 --- /dev/null +++ b/top/oplsaa/SM34/SM34.mol2.1.pdb @@ -0,0 +1,40 @@ +HETATM 1 O1 UNK 1 -0.439 0.604 -3.982 1.00 20.00 +HETATM 2 S2 UNK 1 0.321 1.022 -2.856 1.00 20.00 +HETATM 3 N16 UNK 1 0.953 2.503 -3.243 1.00 20.00 +HETATM 4 O19 UNK 1 -0.229 1.149 -1.552 1.00 20.00 +HETATM 5 N3 UNK 1 1.589 -0.035 -2.728 1.00 20.00 +HETATM 6 C18 UNK 1 0.874 3.607 -2.284 1.00 20.00 +HETATM 7 H37 UNK 1 0.285 3.297 -1.421 1.00 20.00 +HETATM 8 H38 UNK 1 1.878 3.880 -1.960 1.00 20.00 +HETATM 9 H39 UNK 1 0.399 4.466 -2.757 1.00 20.00 +HETATM 10 C17 UNK 1 1.593 2.709 -4.545 1.00 20.00 +HETATM 11 H34 UNK 1 0.847 3.042 -5.268 1.00 20.00 +HETATM 12 H35 UNK 1 2.372 3.465 -4.452 1.00 20.00 +HETATM 13 H36 UNK 1 2.035 1.772 -4.885 1.00 20.00 +HETATM 14 S6 UNK 1 1.719 1.731 -0.322 1.00 20.00 +HETATM 15 C5 UNK 1 1.694 -0.098 -0.242 1.00 20.00 +HETATM 16 H21 UNK 1 2.267 -0.520 0.584 1.00 20.00 +HETATM 17 H22 UNK 1 0.703 -0.540 -0.352 1.00 20.00 +HETATM 18 C7 UNK 1 3.127 1.455 -1.458 1.00 20.00 +HETATM 19 H23 UNK 1 3.088 2.043 -2.375 1.00 20.00 +HETATM 20 H24 UNK 1 4.105 1.470 -0.975 1.00 20.00 +HETATM 21 C9 UNK 1 4.332 -0.877 -2.993 1.00 20.00 +HETATM 22 C10 UNK 1 5.398 -1.938 -3.091 1.00 20.00 +HETATM 23 H27 UNK 1 3.639 -0.981 -3.828 1.00 20.00 +HETATM 24 H28 UNK 1 4.796 0.108 -3.026 1.00 20.00 +HETATM 25 C8 UNK 1 3.571 -1.039 -1.675 1.00 20.00 +HETATM 26 H25 UNK 1 4.265 -0.936 -0.840 1.00 20.00 +HETATM 27 H26 UNK 1 3.107 -2.025 -1.642 1.00 20.00 +HETATM 28 C4 UNK 1 2.489 0.038 -1.575 1.00 20.00 +HETATM 29 C11 UNK 1 6.667 -1.691 -2.602 1.00 20.00 +HETATM 30 H29 UNK 1 6.894 -0.737 -2.150 1.00 20.00 +HETATM 31 C12 UNK 1 7.643 -2.665 -2.688 1.00 20.00 +HETATM 32 H30 UNK 1 8.633 -2.473 -2.303 1.00 20.00 +HETATM 33 C13 UNK 1 7.353 -3.884 -3.273 1.00 20.00 +HETATM 34 H31 UNK 1 8.117 -4.644 -3.344 1.00 20.00 +HETATM 35 C14 UNK 1 6.086 -4.130 -3.766 1.00 20.00 +HETATM 36 H32 UNK 1 5.859 -5.082 -4.223 1.00 20.00 +HETATM 37 C15 UNK 1 5.108 -3.157 -3.676 1.00 20.00 +HETATM 38 H33 UNK 1 4.118 -3.349 -4.062 1.00 20.00 +HETATM 39 H20 UNK 1 1.736 -0.701 -3.417 1.00 20.00 +END diff --git a/top/oplsaa/SM34/SM34.pdb b/top/oplsaa/SM34/SM34.pdb new file mode 120000 index 0000000..b84c0fe --- /dev/null +++ b/top/oplsaa/SM34/SM34.pdb @@ -0,0 +1 @@ +SM34.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM35/SM35.itp b/top/oplsaa/SM35/SM35.itp new file mode 120000 index 0000000..6c1f368 --- /dev/null +++ b/top/oplsaa/SM35/SM35.itp @@ -0,0 +1 @@ +SM35.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM35/SM35.mol2 b/top/oplsaa/SM35/SM35.mol2 new file mode 100644 index 0000000..f12083c --- /dev/null +++ b/top/oplsaa/SM35/SM35.mol2 @@ -0,0 +1,92 @@ +# Name: SM35 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 35 36 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 C1 -1.4668 -1.5581 -1.5447 C.3 + 2 S2 -2.5562 -0.1930 -2.0348 S.o2 + 3 N3 -2.3180 0.9632 -0.8735 N.am + 4 C4 -0.9959 1.5719 -0.7061 C.3 + 5 C5 0.0114 0.6443 -0.0227 C.3 + 6 S6 -0.6567 1.1155 1.5969 S.o + 7 O7 -2.0188 0.4366 1.6161 O.3 + 8 C8 -0.9201 2.5274 0.4870 C.3 + 9 C9 -0.4652 2.1848 -2.0036 C.3 + 10 C10 -1.5189 3.1253 -2.5918 C.3 + 11 C11 -0.9499 3.8248 -3.7992 C.ar + 12 C12 -0.2951 5.0334 -3.6531 C.ar + 13 C13 0.2310 5.6727 -4.7601 C.ar + 14 C14 0.0932 5.1086 -6.0145 C.ar + 15 C15 -0.5663 3.9025 -6.1613 C.ar + 16 C16 -1.0878 3.2607 -5.0537 C.ar + 17 O17 -3.9195 -0.5646 -1.8850 O.2 + 18 O18 -2.0892 0.4121 -3.2327 O.2 + 19 H19 -1.6485 -1.8109 -0.5001 H + 20 H20 -1.6703 -2.4277 -2.1696 H + 21 H21 -0.4270 -1.2561 -1.6698 H + 22 H22 -3.0538 1.2374 -0.3040 H + 23 H23 -0.1448 -0.4078 -0.2609 H + 24 H24 1.0462 0.9552 -0.1663 H + 25 H25 -0.0649 3.2017 0.4422 H + 26 H26 -1.8562 3.0530 0.6752 H + 27 H27 0.4460 2.7453 -1.7945 H + 28 H28 -0.2475 1.3909 -2.7180 H + 29 H29 -2.3965 2.5494 -2.8855 H + 30 H30 -1.8035 3.8653 -1.8437 H + 31 H31 -0.1912 5.4764 -2.6736 H + 32 H32 0.7459 6.6152 -4.6455 H + 33 H33 0.5003 5.6102 -6.8800 H + 34 H34 -0.6743 3.4620 -7.1414 H + 35 H35 -1.6033 2.3186 -5.1684 H +@BOND + 1 1 2 1 + 2 1 19 1 + 3 1 20 1 + 4 1 21 1 + 5 2 3 am + 6 2 17 2 + 7 2 18 2 + 8 3 4 1 + 9 3 22 1 + 10 4 8 1 + 11 4 5 1 + 12 4 9 1 + 13 5 6 1 + 14 5 23 1 + 15 5 24 1 + 16 6 7 1 + 17 6 8 1 + 18 8 25 1 + 19 8 26 1 + 20 9 10 1 + 21 9 27 1 + 22 9 28 1 + 23 10 11 1 + 24 10 29 1 + 25 10 30 1 + 26 11 16 ar + 27 11 12 ar + 28 12 13 ar + 29 12 31 1 + 30 13 14 ar + 31 13 32 1 + 32 14 15 ar + 33 14 33 1 + 34 15 16 ar + 35 15 34 1 + 36 16 35 1 + +# End of record + diff --git a/top/oplsaa/SM35/SM35.mol2.1.itp b/top/oplsaa/SM35/SM35.mol2.1.itp new file mode 100644 index 0000000..2de31c3 --- /dev/null +++ b/top/oplsaa/SM35/SM35.mol2.1.itp @@ -0,0 +1,378 @@ +; input pdb SMILES : C[S](N[C@]1(C[S@+](C1)[O-])CCC2=CC=CC=C2)(=O)=O +; Script arguments : SM35.mol2 "5 opls_499" "8 opls_499" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_474 1 UNK S2 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 2 opls_475 1 UNK O17 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 3 opls_475 1 UNK O18 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 4 opls_476 1 UNK C1 3 -0.540 12.01100 ; CT # CH3 attached to S of sulfonamide + 5 opls_477 1 UNK H19 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 6 opls_477 1 UNK H20 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 7 opls_477 1 UNK H21 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 8 opls_480 1 UNK N3 15 -0.800 14.00670 ; N # N secondary amide of sulfonamide + 9 opls_139 1 UNK C4 15 0.270 12.01100 ; CT # adapted alpha C-N of sulfonamide + 10 opls_481 1 UNK H22 15 0.410 1.00800 ; H # H on N: secondary sulfonamide + 11 opls_496 1 UNK S6 27 0.130 32.06000 ; SZ # sulfoxide - all atom + 12 opls_497 1 UNK O7 27 -0.420 15.99940 ; OY # sulfoxide - all atom + 13 opls_499 1 UNK C5 29 0.025 12.01100 ; CT # CH2 all-atom C: sulfoxide ### user-defined OPLS atom type (opls_499) + 14 opls_140 1 UNK H23 29 0.060 1.00800 ; HC # alkane H. + 15 opls_140 1 UNK H24 29 0.060 1.00800 ; HC # alkane H. + 16 opls_499 1 UNK C8 31 0.025 12.01100 ; CT # CH2 all-atom C: sulfoxide ### user-defined OPLS atom type (opls_499) + 17 opls_140 1 UNK H25 31 0.060 1.00800 ; HC # alkane H. + 18 opls_140 1 UNK H26 31 0.060 1.00800 ; HC # alkane H. + 19 opls_149 1 UNK C10 33 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 20 opls_145 1 UNK C11 33 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 21 opls_140 1 UNK H29 33 0.060 1.00800 ; HC # alkane H. + 22 opls_140 1 UNK H30 33 0.060 1.00800 ; HC # alkane H. + 23 opls_136 1 UNK C9 51 -0.120 12.01100 ; CT # alkane CH2 + 24 opls_140 1 UNK H27 51 0.060 1.00800 ; HC # alkane H. + 25 opls_140 1 UNK H28 51 0.060 1.00800 ; HC # alkane H. + 26 opls_145 1 UNK C12 79 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 27 opls_146 1 UNK H31 79 0.115 1.00800 ; HA # Benzene H - 12 site. + 28 opls_145 1 UNK C13 81 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 29 opls_146 1 UNK H32 81 0.115 1.00800 ; HA # Benzene H - 12 site. + 30 opls_145 1 UNK C14 83 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 31 opls_146 1 UNK H33 83 0.115 1.00800 ; HA # Benzene H - 12 site. + 32 opls_145 1 UNK C15 85 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 33 opls_146 1 UNK H34 85 0.115 1.00800 ; HA # Benzene H - 12 site. + 34 opls_145 1 UNK C16 87 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 35 opls_146 1 UNK H35 87 0.115 1.00800 ; HA # Benzene H - 12 site. +; Total charge : -0.000 ### Number of unassigned atoms : 0/35 + +[ bonds ] +; ai aj funct r k + 4 1 1 ; CT-SY # (SY-CT) + 4 5 1 ; CT-HC # CHARMM 22 parameter file + 4 6 1 ; CT-HC # CHARMM 22 parameter file + 4 7 1 ; CT-HC # CHARMM 22 parameter file + 1 8 1 ; SY-N # + 1 2 1 ; SY-OY # + 1 3 1 ; SY-OY # + 8 9 1 ; N-CT # (CT-N) + 8 10 1 ; N-H # (H-N) + 9 16 1 ; CT-CT # CHARMM 22 parameter file + 9 13 1 ; CT-CT # CHARMM 22 parameter file + 9 23 1 ; CT-CT # CHARMM 22 parameter file + 13 11 1 ; CT-SZ # (SZ-CT) + 13 14 1 ; CT-HC # CHARMM 22 parameter file + 13 15 1 ; CT-HC # CHARMM 22 parameter file + 11 12 1 ; SZ-OY # + 11 16 1 ; SZ-CT # + 16 17 1 ; CT-HC # CHARMM 22 parameter file + 16 18 1 ; CT-HC # CHARMM 22 parameter file + 23 19 1 ; CT-CT # CHARMM 22 parameter file + 23 24 1 ; CT-HC # CHARMM 22 parameter file + 23 25 1 ; CT-HC # CHARMM 22 parameter file + 19 20 1 ; CT-CA # (CA-CT) PHE,TYR + 19 21 1 ; CT-HC # CHARMM 22 parameter file + 19 22 1 ; CT-HC # CHARMM 22 parameter file + 20 34 1 ; CA-CA # TRP,TYR,PHE + 20 26 1 ; CA-CA # TRP,TYR,PHE + 26 28 1 ; CA-CA # TRP,TYR,PHE + 26 27 1 ; CA-HA # PHE, etc. + 28 30 1 ; CA-CA # TRP,TYR,PHE + 28 29 1 ; CA-HA # PHE, etc. + 30 32 1 ; CA-CA # TRP,TYR,PHE + 30 31 1 ; CA-HA # PHE, etc. + 32 34 1 ; CA-CA # TRP,TYR,PHE + 32 33 1 ; CA-HA # PHE, etc. + 34 35 1 ; CA-HA # PHE, etc. + +[ angles ] +; ai aj ak funct theta cth + 1 4 5 1 ; SY-CT-HC # + 1 4 6 1 ; SY-CT-HC # + 1 4 7 1 ; SY-CT-HC # + 5 4 6 1 ; HC-CT-HC # CHARMM 22 parameter file + 5 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + 6 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + 4 1 8 1 ; CT-SY-N # (N-SY-CT) + 4 1 2 1 ; CT-SY-OY # (OY-SY-CT) + 4 1 3 1 ; CT-SY-OY # (OY-SY-CT) + 8 1 2 1 ; N-SY-OY # (OY-SY-N) + 8 1 3 1 ; N-SY-OY # (OY-SY-N) + 2 1 3 1 ; OY-SY-OY # + 1 8 9 1 ; SY-N-CT # + 1 8 10 1 ; SY-N-H # (H-N-SY) + 9 8 10 1 ; CT-N-H # + 8 9 16 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 8 9 13 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 8 9 23 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 16 9 23 1 ; CT-CT-CT # CHARMM 22 parameter file + 13 9 16 1 ; CT-CT-CT # CHARMM 22 parameter file + 13 9 23 1 ; CT-CT-CT # CHARMM 22 parameter file + 9 13 11 1 ; CT-CT-SZ # + 9 13 14 1 ; CT-CT-HC # CHARMM 22 parameter file + 9 13 15 1 ; CT-CT-HC # CHARMM 22 parameter file + 11 13 14 1 ; SZ-CT-HC # + 11 13 15 1 ; SZ-CT-HC # + 14 13 15 1 ; HC-CT-HC # CHARMM 22 parameter file + 13 11 12 1 ; CT-SZ-OY # (OY-SZ-CT) + 13 11 16 1 ; CT-SZ-CT # + 12 11 16 1 ; OY-SZ-CT # + 9 16 11 1 ; CT-CT-SZ # + 9 16 17 1 ; CT-CT-HC # CHARMM 22 parameter file + 9 16 18 1 ; CT-CT-HC # CHARMM 22 parameter file + 11 16 17 1 ; SZ-CT-HC # + 11 16 18 1 ; SZ-CT-HC # + 17 16 18 1 ; HC-CT-HC # CHARMM 22 parameter file + 9 23 19 1 ; CT-CT-CT # CHARMM 22 parameter file + 9 23 24 1 ; CT-CT-HC # CHARMM 22 parameter file + 9 23 25 1 ; CT-CT-HC # CHARMM 22 parameter file + 19 23 24 1 ; CT-CT-HC # CHARMM 22 parameter file + 19 23 25 1 ; CT-CT-HC # CHARMM 22 parameter file + 24 23 25 1 ; HC-CT-HC # CHARMM 22 parameter file + 23 19 20 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 23 19 21 1 ; CT-CT-HC # CHARMM 22 parameter file + 23 19 22 1 ; CT-CT-HC # CHARMM 22 parameter file + 20 19 21 1 ; CA-CT-HC # + 20 19 22 1 ; CA-CT-HC # + 21 19 22 1 ; HC-CT-HC # CHARMM 22 parameter file + 19 20 34 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 19 20 26 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 26 20 34 1 ; CA-CA-CA # PHE(OL) + 20 26 28 1 ; CA-CA-CA # PHE(OL) + 20 26 27 1 ; CA-CA-HA # + 28 26 27 1 ; CA-CA-HA # + 26 28 30 1 ; CA-CA-CA # PHE(OL) + 26 28 29 1 ; CA-CA-HA # + 30 28 29 1 ; CA-CA-HA # + 28 30 32 1 ; CA-CA-CA # PHE(OL) + 28 30 31 1 ; CA-CA-HA # + 32 30 31 1 ; CA-CA-HA # + 30 32 34 1 ; CA-CA-CA # PHE(OL) + 30 32 33 1 ; CA-CA-HA # + 34 32 33 1 ; CA-CA-HA # + 20 34 32 1 ; CA-CA-CA # PHE(OL) + 20 34 35 1 ; CA-CA-HA # + 32 34 35 1 ; CA-CA-HA # + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 5 4 1 8 3 ; HC-CT-SY-N # sulfonamide + 5 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 5 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 6 4 1 8 3 ; HC-CT-SY-N # sulfonamide + 6 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 6 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 7 4 1 8 3 ; HC-CT-SY-N # sulfonamide + 7 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 7 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 4 1 8 9 3 ; CT-SY-N-CT # (CT-N-SY-CT) sulfonamide + 4 1 8 10 3 ; CT-SY-N-H # sulfonamide + 2 1 8 9 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 1 8 10 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 1 8 9 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 1 8 10 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 8 9 16 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 1 8 9 13 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 1 8 9 23 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 10 8 9 16 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 10 8 9 13 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 10 8 9 23 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 8 9 16 11 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-SZ # adapted from CT-CT-CT-N : N-propylformamide + 8 9 16 17 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 8 9 16 18 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 13 9 16 11 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 13 9 16 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 13 9 16 18 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 23 9 16 11 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 23 9 16 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 23 9 16 18 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 8 9 13 11 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-SZ # adapted from CT-CT-CT-N : N-propylformamide + 8 9 13 14 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 8 9 13 15 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 16 9 13 11 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 16 9 13 14 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 16 9 13 15 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 23 9 13 11 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 23 9 13 14 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 23 9 13 15 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 8 9 23 19 3 ; N-CT-CT-CT # (CT-CT-CT-N) N-propylformamide + 8 9 23 24 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 8 9 23 25 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 16 9 23 19 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 16 9 23 24 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 16 9 23 25 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 13 9 23 19 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 13 9 23 24 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 13 9 23 25 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 9 13 11 12 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CT-CT-SZ-OY # adapted from CT-CT-SH2-OY : sulfone + 9 13 11 16 3 0.94140 2.31375 2.40999 -5.66514 0.00000 0.00000 ; CT-CT-SZ-CT # adapted from CT-CT-S-CT : sulfide all-atom + 14 13 11 12 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; HC-CT-SZ-OY # adapted from HC-CT-SH2-OY : sulfone + 14 13 11 16 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; HC-CT-SZ-CT # adapted from HC-CT-S-CT : sulfide all-atom + 15 13 11 12 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; HC-CT-SZ-OY # adapted from HC-CT-SH2-OY : sulfone + 15 13 11 16 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; HC-CT-SZ-CT # adapted from HC-CT-S-CT : sulfide all-atom + 13 11 16 9 3 0.94140 2.31375 2.40999 -5.66514 0.00000 0.00000 ; CT-SZ-CT-CT # adapted from CT-CT-S-CT : sulfide all-atom + 13 11 16 17 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; CT-SZ-CT-HC # adapted from HC-CT-S-CT : sulfide all-atom + 13 11 16 18 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; CT-SZ-CT-HC # adapted from HC-CT-S-CT : sulfide all-atom + 12 11 16 9 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; OY-SZ-CT-CT # adapted from CT-CT-SH2-OY : sulfone + 12 11 16 17 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; OY-SZ-CT-HC # adapted from HC-CT-SH2-OY : sulfone + 12 11 16 18 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; OY-SZ-CT-HC # adapted from HC-CT-SH2-OY : sulfone + 9 23 19 20 3 ; CT-CT-CT-CA # (CA-CT-CT-CT) + 9 23 19 21 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 9 23 19 22 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 24 23 19 20 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 24 23 19 21 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 24 23 19 22 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 25 23 19 20 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 25 23 19 21 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 25 23 19 22 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 23 19 20 34 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 23 19 20 26 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 21 19 20 34 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 21 19 20 26 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 22 19 20 34 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 22 19 20 26 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 19 20 34 32 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 20 34 35 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 20 34 32 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 20 34 35 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 20 26 28 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 20 26 27 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 20 26 28 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 20 26 27 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 20 26 28 30 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 20 26 28 29 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 26 28 30 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 26 28 29 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 28 30 32 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 28 30 31 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 28 30 32 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 28 30 31 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 30 32 34 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 30 32 33 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 30 32 34 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 30 32 33 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 32 34 20 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 32 34 35 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 32 34 20 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 32 34 35 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 1 10 8 9 1 improper_Z_N_X_Y ; SY-H-N-CT + 34 26 20 19 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 28 27 26 20 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 30 29 28 26 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 32 31 30 28 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 34 33 32 30 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 32 35 34 20 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + +[ pairs ] +; ai aj funct + 4 9 1 + 4 10 1 + 1 16 1 + 1 13 1 + 1 23 1 + 8 5 1 + 8 6 1 + 8 7 1 + 8 11 1 + 8 17 1 + 8 18 1 + 8 14 1 + 8 15 1 + 8 19 1 + 8 24 1 + 8 25 1 + 9 2 1 + 9 3 1 + 9 12 1 + 9 20 1 + 9 21 1 + 9 22 1 + 13 10 1 + 13 17 1 + 13 18 1 + 13 19 1 + 13 24 1 + 13 25 1 + 11 23 1 + 12 14 1 + 12 15 1 + 12 17 1 + 12 18 1 + 16 10 1 + 16 14 1 + 16 15 1 + 16 19 1 + 16 24 1 + 16 25 1 + 23 10 1 + 23 17 1 + 23 18 1 + 23 14 1 + 23 15 1 + 23 34 1 + 23 26 1 + 19 32 1 + 19 35 1 + 19 28 1 + 19 27 1 + 20 24 1 + 20 25 1 + 20 30 1 + 20 33 1 + 20 29 1 + 26 21 1 + 26 22 1 + 26 32 1 + 26 35 1 + 26 31 1 + 28 34 1 + 28 33 1 + 30 27 1 + 30 35 1 + 32 29 1 + 34 21 1 + 34 22 1 + 34 27 1 + 34 31 1 + 2 5 1 + 2 6 1 + 2 7 1 + 2 10 1 + 3 5 1 + 3 6 1 + 3 7 1 + 3 10 1 + 24 21 1 + 24 22 1 + 25 21 1 + 25 22 1 + 27 29 1 + 29 31 1 + 31 33 1 + 33 35 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 4 1 1000 1000 1000 + 1 1 1000 1000 1000 + 8 1 1000 1000 1000 + 9 1 1000 1000 1000 + 13 1 1000 1000 1000 + 11 1 1000 1000 1000 + 12 1 1000 1000 1000 + 16 1 1000 1000 1000 + 23 1 1000 1000 1000 + 19 1 1000 1000 1000 + 20 1 1000 1000 1000 + 26 1 1000 1000 1000 + 28 1 1000 1000 1000 + 30 1 1000 1000 1000 + 32 1 1000 1000 1000 + 34 1 1000 1000 1000 + 2 1 1000 1000 1000 + 3 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM35/SM35.mol2.1.pdb b/top/oplsaa/SM35/SM35.mol2.1.pdb new file mode 100644 index 0000000..3337799 --- /dev/null +++ b/top/oplsaa/SM35/SM35.mol2.1.pdb @@ -0,0 +1,36 @@ +HETATM 1 S2 UNK 1 -2.556 -0.193 -2.035 1.00 20.00 +HETATM 2 O17 UNK 1 -3.920 -0.565 -1.885 1.00 20.00 +HETATM 3 O18 UNK 1 -2.089 0.412 -3.233 1.00 20.00 +HETATM 4 C1 UNK 1 -1.467 -1.558 -1.545 1.00 20.00 +HETATM 5 H19 UNK 1 -1.649 -1.811 -0.500 1.00 20.00 +HETATM 6 H20 UNK 1 -1.670 -2.428 -2.170 1.00 20.00 +HETATM 7 H21 UNK 1 -0.427 -1.256 -1.670 1.00 20.00 +HETATM 8 N3 UNK 1 -2.318 0.963 -0.874 1.00 20.00 +HETATM 9 C4 UNK 1 -0.996 1.572 -0.706 1.00 20.00 +HETATM 10 H22 UNK 1 -3.054 1.237 -0.304 1.00 20.00 +HETATM 11 S6 UNK 1 -0.657 1.115 1.597 1.00 20.00 +HETATM 12 O7 UNK 1 -2.019 0.437 1.616 1.00 20.00 +HETATM 13 C5 UNK 1 0.011 0.644 -0.023 1.00 20.00 +HETATM 14 H23 UNK 1 -0.145 -0.408 -0.261 1.00 20.00 +HETATM 15 H24 UNK 1 1.046 0.955 -0.166 1.00 20.00 +HETATM 16 C8 UNK 1 -0.920 2.527 0.487 1.00 20.00 +HETATM 17 H25 UNK 1 -0.065 3.202 0.442 1.00 20.00 +HETATM 18 H26 UNK 1 -1.856 3.053 0.675 1.00 20.00 +HETATM 19 C10 UNK 1 -1.519 3.125 -2.592 1.00 20.00 +HETATM 20 C11 UNK 1 -0.950 3.825 -3.799 1.00 20.00 +HETATM 21 H29 UNK 1 -2.397 2.549 -2.885 1.00 20.00 +HETATM 22 H30 UNK 1 -1.804 3.865 -1.844 1.00 20.00 +HETATM 23 C9 UNK 1 -0.465 2.185 -2.004 1.00 20.00 +HETATM 24 H27 UNK 1 0.446 2.745 -1.794 1.00 20.00 +HETATM 25 H28 UNK 1 -0.247 1.391 -2.718 1.00 20.00 +HETATM 26 C12 UNK 1 -0.295 5.033 -3.653 1.00 20.00 +HETATM 27 H31 UNK 1 -0.191 5.476 -2.674 1.00 20.00 +HETATM 28 C13 UNK 1 0.231 5.673 -4.760 1.00 20.00 +HETATM 29 H32 UNK 1 0.746 6.615 -4.646 1.00 20.00 +HETATM 30 C14 UNK 1 0.093 5.109 -6.014 1.00 20.00 +HETATM 31 H33 UNK 1 0.500 5.610 -6.880 1.00 20.00 +HETATM 32 C15 UNK 1 -0.566 3.902 -6.161 1.00 20.00 +HETATM 33 H34 UNK 1 -0.674 3.462 -7.141 1.00 20.00 +HETATM 34 C16 UNK 1 -1.088 3.261 -5.054 1.00 20.00 +HETATM 35 H35 UNK 1 -1.603 2.319 -5.168 1.00 20.00 +END diff --git a/top/oplsaa/SM35/SM35.pdb b/top/oplsaa/SM35/SM35.pdb new file mode 120000 index 0000000..e29c111 --- /dev/null +++ b/top/oplsaa/SM35/SM35.pdb @@ -0,0 +1 @@ +SM35.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM36/SM36.itp b/top/oplsaa/SM36/SM36.itp new file mode 120000 index 0000000..b83a38f --- /dev/null +++ b/top/oplsaa/SM36/SM36.itp @@ -0,0 +1 @@ +SM36.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM36/SM36.mol2 b/top/oplsaa/SM36/SM36.mol2 new file mode 100644 index 0000000..7429188 --- /dev/null +++ b/top/oplsaa/SM36/SM36.mol2 @@ -0,0 +1,107 @@ +# Name: SM36 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 42 44 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 0.6047 1.8005 1.2454 O.2 + 2 S2 1.2791 0.5760 1.5007 S.o2 + 3 N3 0.1137 -0.5999 1.5420 N.am + 4 C4 -1.0987 -0.4019 2.3402 C.3 + 5 C5 -2.3393 -1.0494 1.7207 C.3 + 6 S6 -3.3721 0.2672 2.4235 S.o + 7 O7 -4.1649 0.7600 1.2214 O.3 + 8 C8 -1.7269 0.9803 2.1475 C.3 + 9 C9 -0.8980 -0.7717 3.8112 C.3 + 10 C10 -0.1582 -2.1077 3.9048 C.3 + 11 C11 0.0394 -2.4720 5.3537 C.ar + 12 C12 1.1799 -2.0638 6.0196 C.ar + 13 C13 1.3590 -2.3938 7.3500 C.ar + 14 C14 0.4024 -3.1410 8.0115 C.ar + 15 C15 -0.7356 -3.5537 7.3441 C.ar + 16 C16 -0.9171 -3.2192 6.0152 C.ar + 17 C17 1.9472 0.7054 3.1259 C.ar + 18 C18 1.3851 1.5802 4.0367 C.ar + 19 C19 1.9063 1.6782 5.3133 C.ar + 20 C20 2.9961 0.9090 5.6758 C.ar + 21 C21 3.5616 0.0380 4.7634 C.ar + 22 C22 3.0371 -0.0638 3.4884 C.ar + 23 O23 2.3233 0.0772 0.6761 O.2 + 24 H24 0.2338 -1.4197 1.0376 H + 25 H25 -2.3250 -1.0471 0.6308 H + 26 H26 -2.5600 -2.0340 2.1332 H + 27 H27 -1.4349 1.6947 2.9172 H + 28 H28 -1.5937 1.3749 1.1402 H + 29 H29 -0.3115 0.0037 4.3040 H + 30 H30 -1.8686 -0.8588 4.2996 H + 31 H31 -0.7447 -2.8831 3.4119 H + 32 H32 0.8123 -2.0206 3.4164 H + 33 H33 1.9293 -1.4838 5.5015 H + 34 H34 2.2483 -2.0717 7.8713 H + 35 H35 0.5444 -3.4026 9.0497 H + 36 H36 -1.4828 -4.1377 7.8609 H + 37 H37 -1.8061 -3.5419 5.4937 H + 38 H38 0.5363 2.1844 3.7521 H + 39 H39 1.4647 2.3589 6.0261 H + 40 H40 3.4061 0.9888 6.6718 H + 41 H41 4.4133 -0.5627 5.0465 H + 42 H42 3.4791 -0.7441 2.7754 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 17 1 + 4 2 23 2 + 5 3 4 1 + 6 3 24 1 + 7 4 8 1 + 8 4 5 1 + 9 4 9 1 + 10 5 6 1 + 11 5 25 1 + 12 5 26 1 + 13 6 7 1 + 14 6 8 1 + 15 8 27 1 + 16 8 28 1 + 17 9 10 1 + 18 9 29 1 + 19 9 30 1 + 20 10 11 1 + 21 10 31 1 + 22 10 32 1 + 23 11 16 ar + 24 11 12 ar + 25 12 13 ar + 26 12 33 1 + 27 13 14 ar + 28 13 34 1 + 29 14 15 ar + 30 14 35 1 + 31 15 16 ar + 32 15 36 1 + 33 16 37 1 + 34 17 22 ar + 35 17 18 ar + 36 18 19 ar + 37 18 38 1 + 38 19 20 ar + 39 19 39 1 + 40 20 21 ar + 41 20 40 1 + 42 21 22 ar + 43 21 41 1 + 44 22 42 1 + +# End of record + diff --git a/top/oplsaa/SM36/SM36.mol2.1.itp b/top/oplsaa/SM36/SM36.mol2.1.itp new file mode 100644 index 0000000..bb575fa --- /dev/null +++ b/top/oplsaa/SM36/SM36.mol2.1.itp @@ -0,0 +1,455 @@ +; input pdb SMILES : O=[S](N[C@]1(C[S@](C1)[O])CCC2=CC=CC=C2)(C3=CC=CC=C3)=O +; Script arguments : SM36.mol2 "5 opls_499" "8 opls_499" "6 opls_496" "7 opls_497" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 2 opls_474 1 UNK S2 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 3 opls_488 1 UNK C17 1 0.000 12.01100 ; CA # The charge for this atom has been adjusted to take into account contributions from:`CA (opls_488)' AND `CA (opls_488)' + 4 opls_475 1 UNK O23 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 5 opls_480 1 UNK N3 3 -0.800 14.00670 ; N # N secondary amide of sulfonamide + 6 opls_139 1 UNK C4 3 0.270 12.01100 ; CT # adapted alpha C-N of sulfonamide + 7 opls_481 1 UNK H24 3 0.410 1.00800 ; H # H on N: secondary sulfonamide + 8 opls_149 1 UNK C10 15 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 9 opls_145 1 UNK C11 15 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 10 opls_140 1 UNK H31 15 0.060 1.00800 ; HC # alkane H. + 11 opls_140 1 UNK H32 15 0.060 1.00800 ; HC # alkane H. + 12 opls_499 1 UNK C5 19 0.025 12.01100 ; CT # CH2 all-atom C: sulfoxide ### user-defined OPLS atom type (opls_499) + 13 opls_140 1 UNK H25 19 0.060 1.00800 ; HC # alkane H. + 14 opls_140 1 UNK H26 19 0.060 1.00800 ; HC # alkane H. + 15 opls_499 1 UNK C8 23 0.025 12.01100 ; CT # CH2 all-atom C: sulfoxide ### user-defined OPLS atom type (opls_499) + 16 opls_140 1 UNK H27 23 0.060 1.00800 ; HC # alkane H. + 17 opls_140 1 UNK H28 23 0.060 1.00800 ; HC # alkane H. + 18 opls_136 1 UNK C9 27 -0.120 12.01100 ; CT # alkane CH2 + 19 opls_140 1 UNK H29 27 0.060 1.00800 ; HC # alkane H. + 20 opls_140 1 UNK H30 27 0.060 1.00800 ; HC # alkane H. + 21 opls_145 1 UNK C12 55 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 22 opls_146 1 UNK H33 55 0.115 1.00800 ; HA # Benzene H - 12 site. + 23 opls_145 1 UNK C13 57 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 24 opls_146 1 UNK H34 57 0.115 1.00800 ; HA # Benzene H - 12 site. + 25 opls_145 1 UNK C14 59 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 26 opls_146 1 UNK H35 59 0.115 1.00800 ; HA # Benzene H - 12 site. + 27 opls_145 1 UNK C15 61 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 28 opls_146 1 UNK H36 61 0.115 1.00800 ; HA # Benzene H - 12 site. + 29 opls_145 1 UNK C16 63 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 30 opls_146 1 UNK H37 63 0.115 1.00800 ; HA # Benzene H - 12 site. + 31 opls_145 1 UNK C18 65 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 32 opls_146 1 UNK H38 65 0.115 1.00800 ; HA # Benzene H - 12 site. + 33 opls_145 1 UNK C19 67 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 34 opls_146 1 UNK H39 67 0.115 1.00800 ; HA # Benzene H - 12 site. + 35 opls_145 1 UNK C20 69 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 36 opls_146 1 UNK H40 69 0.115 1.00800 ; HA # Benzene H - 12 site. + 37 opls_145 1 UNK C21 71 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 38 opls_146 1 UNK H41 71 0.115 1.00800 ; HA # Benzene H - 12 site. + 39 opls_145 1 UNK C22 73 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 40 opls_146 1 UNK H42 73 0.115 1.00800 ; HA # Benzene H - 12 site. + 41 opls_496 1 UNK S6 75 0.130 32.06000 ; SZ # sulfoxide - all atom ### user-defined OPLS atom type (opls_496) + 42 opls_497 1 UNK O7 75 -0.420 15.99940 ; OY # sulfoxide - all atom ### user-defined OPLS atom type (opls_497) +; Total charge : 0.000 ### Number of unassigned atoms : 0/42 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 5 1 ; SY-N # + 2 3 1 ; SY-CA # + 2 4 1 ; SY-OY # + 5 6 1 ; N-CT # (CT-N) + 5 7 1 ; N-H # (H-N) + 6 15 1 ; CT-CT # CHARMM 22 parameter file + 6 12 1 ; CT-CT # CHARMM 22 parameter file + 6 18 1 ; CT-CT # CHARMM 22 parameter file + 12 41 1 ; CT-SZ # (SZ-CT) + 12 13 1 ; CT-HC # CHARMM 22 parameter file + 12 14 1 ; CT-HC # CHARMM 22 parameter file + 41 42 1 ; SZ-OY # + 41 15 1 ; SZ-CT # + 15 16 1 ; CT-HC # CHARMM 22 parameter file + 15 17 1 ; CT-HC # CHARMM 22 parameter file + 18 8 1 ; CT-CT # CHARMM 22 parameter file + 18 19 1 ; CT-HC # CHARMM 22 parameter file + 18 20 1 ; CT-HC # CHARMM 22 parameter file + 8 9 1 ; CT-CA # (CA-CT) PHE,TYR + 8 10 1 ; CT-HC # CHARMM 22 parameter file + 8 11 1 ; CT-HC # CHARMM 22 parameter file + 9 29 1 ; CA-CA # TRP,TYR,PHE + 9 21 1 ; CA-CA # TRP,TYR,PHE + 21 23 1 ; CA-CA # TRP,TYR,PHE + 21 22 1 ; CA-HA # PHE, etc. + 23 25 1 ; CA-CA # TRP,TYR,PHE + 23 24 1 ; CA-HA # PHE, etc. + 25 27 1 ; CA-CA # TRP,TYR,PHE + 25 26 1 ; CA-HA # PHE, etc. + 27 29 1 ; CA-CA # TRP,TYR,PHE + 27 28 1 ; CA-HA # PHE, etc. + 29 30 1 ; CA-HA # PHE, etc. + 3 39 1 ; CA-CA # TRP,TYR,PHE + 3 31 1 ; CA-CA # TRP,TYR,PHE + 31 33 1 ; CA-CA # TRP,TYR,PHE + 31 32 1 ; CA-HA # PHE, etc. + 33 35 1 ; CA-CA # TRP,TYR,PHE + 33 34 1 ; CA-HA # PHE, etc. + 35 37 1 ; CA-CA # TRP,TYR,PHE + 35 36 1 ; CA-HA # PHE, etc. + 37 39 1 ; CA-CA # TRP,TYR,PHE + 37 38 1 ; CA-HA # PHE, etc. + 39 40 1 ; CA-HA # PHE, etc. + +[ angles ] +; ai aj ak funct theta cth + 1 2 5 1 ; OY-SY-N # + 1 2 3 1 ; OY-SY-CA # + 1 2 4 1 ; OY-SY-OY # + 5 2 3 1 ; N-SY-CA # + 5 2 4 1 ; N-SY-OY # (OY-SY-N) + 3 2 4 1 ; CA-SY-OY # (OY-SY-CA) + 2 5 6 1 ; SY-N-CT # + 2 5 7 1 ; SY-N-H # (H-N-SY) + 6 5 7 1 ; CT-N-H # + 5 6 15 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 6 12 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 6 18 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 15 6 18 1 ; CT-CT-CT # CHARMM 22 parameter file + 12 6 15 1 ; CT-CT-CT # CHARMM 22 parameter file + 12 6 18 1 ; CT-CT-CT # CHARMM 22 parameter file + 6 12 41 1 ; CT-CT-SZ # + 6 12 13 1 ; CT-CT-HC # CHARMM 22 parameter file + 6 12 14 1 ; CT-CT-HC # CHARMM 22 parameter file + 41 12 13 1 ; SZ-CT-HC # + 41 12 14 1 ; SZ-CT-HC # + 13 12 14 1 ; HC-CT-HC # CHARMM 22 parameter file + 12 41 42 1 ; CT-SZ-OY # (OY-SZ-CT) + 12 41 15 1 ; CT-SZ-CT # + 42 41 15 1 ; OY-SZ-CT # + 6 15 41 1 ; CT-CT-SZ # + 6 15 16 1 ; CT-CT-HC # CHARMM 22 parameter file + 6 15 17 1 ; CT-CT-HC # CHARMM 22 parameter file + 41 15 16 1 ; SZ-CT-HC # + 41 15 17 1 ; SZ-CT-HC # + 16 15 17 1 ; HC-CT-HC # CHARMM 22 parameter file + 6 18 8 1 ; CT-CT-CT # CHARMM 22 parameter file + 6 18 19 1 ; CT-CT-HC # CHARMM 22 parameter file + 6 18 20 1 ; CT-CT-HC # CHARMM 22 parameter file + 8 18 19 1 ; CT-CT-HC # CHARMM 22 parameter file + 8 18 20 1 ; CT-CT-HC # CHARMM 22 parameter file + 19 18 20 1 ; HC-CT-HC # CHARMM 22 parameter file + 18 8 9 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 18 8 10 1 ; CT-CT-HC # CHARMM 22 parameter file + 18 8 11 1 ; CT-CT-HC # CHARMM 22 parameter file + 9 8 10 1 ; CA-CT-HC # + 9 8 11 1 ; CA-CT-HC # + 10 8 11 1 ; HC-CT-HC # CHARMM 22 parameter file + 8 9 29 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 8 9 21 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 21 9 29 1 ; CA-CA-CA # PHE(OL) + 9 21 23 1 ; CA-CA-CA # PHE(OL) + 9 21 22 1 ; CA-CA-HA # + 23 21 22 1 ; CA-CA-HA # + 21 23 25 1 ; CA-CA-CA # PHE(OL) + 21 23 24 1 ; CA-CA-HA # + 25 23 24 1 ; CA-CA-HA # + 23 25 27 1 ; CA-CA-CA # PHE(OL) + 23 25 26 1 ; CA-CA-HA # + 27 25 26 1 ; CA-CA-HA # + 25 27 29 1 ; CA-CA-CA # PHE(OL) + 25 27 28 1 ; CA-CA-HA # + 29 27 28 1 ; CA-CA-HA # + 9 29 27 1 ; CA-CA-CA # PHE(OL) + 9 29 30 1 ; CA-CA-HA # + 27 29 30 1 ; CA-CA-HA # + 2 3 39 1 ; SY-CA-CA # + 2 3 31 1 ; SY-CA-CA # + 31 3 39 1 ; CA-CA-CA # PHE(OL) + 3 31 33 1 ; CA-CA-CA # PHE(OL) + 3 31 32 1 ; CA-CA-HA # + 33 31 32 1 ; CA-CA-HA # + 31 33 35 1 ; CA-CA-CA # PHE(OL) + 31 33 34 1 ; CA-CA-HA # + 35 33 34 1 ; CA-CA-HA # + 33 35 37 1 ; CA-CA-CA # PHE(OL) + 33 35 36 1 ; CA-CA-HA # + 37 35 36 1 ; CA-CA-HA # + 35 37 39 1 ; CA-CA-CA # PHE(OL) + 35 37 38 1 ; CA-CA-HA # + 39 37 38 1 ; CA-CA-HA # + 3 39 37 1 ; CA-CA-CA # PHE(OL) + 3 39 40 1 ; CA-CA-HA # + 37 39 40 1 ; CA-CA-HA # + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 5 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 5 7 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 5 6 3 ; CA-SY-N-CT # sulfonamide + 3 2 5 7 3 ; CA-SY-N-H # sulfonamide + 4 2 5 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 5 7 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 39 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 1 2 3 31 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 5 2 3 39 3 ; N-SY-CA-CA # (CA-CA-SY-N) sulfonamide + 5 2 3 31 3 ; N-SY-CA-CA # (CA-CA-SY-N) sulfonamide + 4 2 3 39 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 4 2 3 31 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 2 5 6 15 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 6 12 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 6 18 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 7 5 6 15 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 7 5 6 12 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 7 5 6 18 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 5 6 15 41 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-SZ # adapted from CT-CT-CT-N : N-propylformamide + 5 6 15 16 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 6 15 17 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 12 6 15 41 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 12 6 15 16 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 12 6 15 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 18 6 15 41 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 18 6 15 16 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 18 6 15 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 6 12 41 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-SZ # adapted from CT-CT-CT-N : N-propylformamide + 5 6 12 13 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 6 12 14 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 15 6 12 41 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 15 6 12 13 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 15 6 12 14 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 18 6 12 41 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 18 6 12 13 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 18 6 12 14 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 6 18 8 3 ; N-CT-CT-CT # (CT-CT-CT-N) N-propylformamide + 5 6 18 19 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 6 18 20 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 15 6 18 8 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 15 6 18 19 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 15 6 18 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 12 6 18 8 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 12 6 18 19 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 12 6 18 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 6 12 41 42 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CT-CT-SZ-OY # adapted from CT-CT-SH2-OY : sulfone + 6 12 41 15 3 0.94140 2.31375 2.40999 -5.66514 0.00000 0.00000 ; CT-CT-SZ-CT # adapted from CT-CT-S-CT : sulfide all-atom + 13 12 41 42 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; HC-CT-SZ-OY # adapted from HC-CT-SH2-OY : sulfone + 13 12 41 15 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; HC-CT-SZ-CT # adapted from HC-CT-S-CT : sulfide all-atom + 14 12 41 42 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; HC-CT-SZ-OY # adapted from HC-CT-SH2-OY : sulfone + 14 12 41 15 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; HC-CT-SZ-CT # adapted from HC-CT-S-CT : sulfide all-atom + 12 41 15 6 3 0.94140 2.31375 2.40999 -5.66514 0.00000 0.00000 ; CT-SZ-CT-CT # adapted from CT-CT-S-CT : sulfide all-atom + 12 41 15 16 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; CT-SZ-CT-HC # adapted from HC-CT-S-CT : sulfide all-atom + 12 41 15 17 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; CT-SZ-CT-HC # adapted from HC-CT-S-CT : sulfide all-atom + 42 41 15 6 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; OY-SZ-CT-CT # adapted from CT-CT-SH2-OY : sulfone + 42 41 15 16 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; OY-SZ-CT-HC # adapted from HC-CT-SH2-OY : sulfone + 42 41 15 17 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; OY-SZ-CT-HC # adapted from HC-CT-SH2-OY : sulfone + 6 18 8 9 3 ; CT-CT-CT-CA # (CA-CT-CT-CT) + 6 18 8 10 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 6 18 8 11 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 19 18 8 9 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 19 18 8 10 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 19 18 8 11 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 20 18 8 9 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 20 18 8 10 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 20 18 8 11 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 18 8 9 29 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 18 8 9 21 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 10 8 9 29 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 10 8 9 21 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 11 8 9 29 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 11 8 9 21 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 8 9 29 27 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 8 9 29 30 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 9 29 27 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 9 29 30 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 8 9 21 23 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 8 9 21 22 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 9 21 23 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 9 21 22 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 9 21 23 25 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 9 21 23 24 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 21 23 25 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 21 23 24 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 23 25 27 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 23 25 26 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 27 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 26 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 25 27 29 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 25 27 28 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 25 27 29 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 25 27 28 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 27 29 9 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 27 29 30 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 27 29 9 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 27 29 30 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 39 37 3 ; SY-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 39 40 3 ; SY-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 3 39 37 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 3 39 40 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 31 33 3 ; SY-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 31 32 3 ; SY-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 39 3 31 33 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 39 3 31 32 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 3 31 33 35 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 3 31 33 34 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 31 33 35 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 31 33 34 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 33 35 37 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 33 35 36 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 33 35 37 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 33 35 36 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 35 37 39 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 35 37 38 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 36 35 37 39 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 36 35 37 38 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 35 37 39 3 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 35 37 39 40 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 38 37 39 3 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 38 37 39 40 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 2 7 5 6 1 improper_Z_N_X_Y ; SY-H-N-CT + 29 21 9 8 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 23 22 21 9 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 25 24 23 21 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 27 26 25 23 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 29 28 27 25 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 27 30 29 9 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 39 31 3 2 1 improper_Z_CA_X_Y ; CA-CA-CA-SY + 33 32 31 3 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 35 34 33 31 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 37 36 35 33 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 39 38 37 35 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 37 40 39 3 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + +[ pairs ] +; ai aj funct + 1 6 1 + 1 7 1 + 1 39 1 + 1 31 1 + 2 15 1 + 2 12 1 + 2 18 1 + 2 37 1 + 2 40 1 + 2 33 1 + 2 32 1 + 5 39 1 + 5 31 1 + 5 41 1 + 5 16 1 + 5 17 1 + 5 13 1 + 5 14 1 + 5 8 1 + 5 19 1 + 5 20 1 + 6 3 1 + 6 4 1 + 6 42 1 + 6 9 1 + 6 10 1 + 6 11 1 + 12 7 1 + 12 16 1 + 12 17 1 + 12 8 1 + 12 19 1 + 12 20 1 + 41 18 1 + 42 13 1 + 42 14 1 + 42 16 1 + 42 17 1 + 15 7 1 + 15 13 1 + 15 14 1 + 15 8 1 + 15 19 1 + 15 20 1 + 18 7 1 + 18 16 1 + 18 17 1 + 18 13 1 + 18 14 1 + 18 29 1 + 18 21 1 + 8 27 1 + 8 30 1 + 8 23 1 + 8 22 1 + 9 19 1 + 9 20 1 + 9 25 1 + 9 28 1 + 9 24 1 + 21 10 1 + 21 11 1 + 21 27 1 + 21 30 1 + 21 26 1 + 23 29 1 + 23 28 1 + 25 22 1 + 25 30 1 + 27 24 1 + 29 10 1 + 29 11 1 + 29 22 1 + 29 26 1 + 3 7 1 + 3 35 1 + 3 38 1 + 3 34 1 + 31 4 1 + 31 37 1 + 31 40 1 + 31 36 1 + 33 39 1 + 33 38 1 + 35 32 1 + 35 40 1 + 37 34 1 + 39 4 1 + 39 32 1 + 39 36 1 + 4 7 1 + 19 10 1 + 19 11 1 + 20 10 1 + 20 11 1 + 22 24 1 + 24 26 1 + 26 28 1 + 28 30 1 + 32 34 1 + 34 36 1 + 36 38 1 + 38 40 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 5 1 1000 1000 1000 + 6 1 1000 1000 1000 + 12 1 1000 1000 1000 + 41 1 1000 1000 1000 + 42 1 1000 1000 1000 + 15 1 1000 1000 1000 + 18 1 1000 1000 1000 + 8 1 1000 1000 1000 + 9 1 1000 1000 1000 + 21 1 1000 1000 1000 + 23 1 1000 1000 1000 + 25 1 1000 1000 1000 + 27 1 1000 1000 1000 + 29 1 1000 1000 1000 + 3 1 1000 1000 1000 + 31 1 1000 1000 1000 + 33 1 1000 1000 1000 + 35 1 1000 1000 1000 + 37 1 1000 1000 1000 + 39 1 1000 1000 1000 + 4 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM36/SM36.mol2.1.pdb b/top/oplsaa/SM36/SM36.mol2.1.pdb new file mode 100644 index 0000000..91d610f --- /dev/null +++ b/top/oplsaa/SM36/SM36.mol2.1.pdb @@ -0,0 +1,43 @@ +HETATM 1 O1 UNK 1 0.605 1.800 1.245 1.00 20.00 +HETATM 2 S2 UNK 1 1.279 0.576 1.501 1.00 20.00 +HETATM 3 C17 UNK 1 1.947 0.705 3.126 1.00 20.00 +HETATM 4 O23 UNK 1 2.323 0.077 0.676 1.00 20.00 +HETATM 5 N3 UNK 1 0.114 -0.600 1.542 1.00 20.00 +HETATM 6 C4 UNK 1 -1.099 -0.402 2.340 1.00 20.00 +HETATM 7 H24 UNK 1 0.234 -1.420 1.038 1.00 20.00 +HETATM 8 C10 UNK 1 -0.158 -2.108 3.905 1.00 20.00 +HETATM 9 C11 UNK 1 0.039 -2.472 5.354 1.00 20.00 +HETATM 10 H31 UNK 1 -0.745 -2.883 3.412 1.00 20.00 +HETATM 11 H32 UNK 1 0.812 -2.021 3.416 1.00 20.00 +HETATM 12 C5 UNK 1 -2.339 -1.049 1.721 1.00 20.00 +HETATM 13 H25 UNK 1 -2.325 -1.047 0.631 1.00 20.00 +HETATM 14 H26 UNK 1 -2.560 -2.034 2.133 1.00 20.00 +HETATM 15 C8 UNK 1 -1.727 0.980 2.147 1.00 20.00 +HETATM 16 H27 UNK 1 -1.435 1.695 2.917 1.00 20.00 +HETATM 17 H28 UNK 1 -1.594 1.375 1.140 1.00 20.00 +HETATM 18 C9 UNK 1 -0.898 -0.772 3.811 1.00 20.00 +HETATM 19 H29 UNK 1 -0.311 0.004 4.304 1.00 20.00 +HETATM 20 H30 UNK 1 -1.869 -0.859 4.300 1.00 20.00 +HETATM 21 C12 UNK 1 1.180 -2.064 6.020 1.00 20.00 +HETATM 22 H33 UNK 1 1.929 -1.484 5.502 1.00 20.00 +HETATM 23 C13 UNK 1 1.359 -2.394 7.350 1.00 20.00 +HETATM 24 H34 UNK 1 2.248 -2.072 7.871 1.00 20.00 +HETATM 25 C14 UNK 1 0.402 -3.141 8.011 1.00 20.00 +HETATM 26 H35 UNK 1 0.544 -3.403 9.050 1.00 20.00 +HETATM 27 C15 UNK 1 -0.736 -3.554 7.344 1.00 20.00 +HETATM 28 H36 UNK 1 -1.483 -4.138 7.861 1.00 20.00 +HETATM 29 C16 UNK 1 -0.917 -3.219 6.015 1.00 20.00 +HETATM 30 H37 UNK 1 -1.806 -3.542 5.494 1.00 20.00 +HETATM 31 C18 UNK 1 1.385 1.580 4.037 1.00 20.00 +HETATM 32 H38 UNK 1 0.536 2.184 3.752 1.00 20.00 +HETATM 33 C19 UNK 1 1.906 1.678 5.313 1.00 20.00 +HETATM 34 H39 UNK 1 1.465 2.359 6.026 1.00 20.00 +HETATM 35 C20 UNK 1 2.996 0.909 5.676 1.00 20.00 +HETATM 36 H40 UNK 1 3.406 0.989 6.672 1.00 20.00 +HETATM 37 C21 UNK 1 3.562 0.038 4.763 1.00 20.00 +HETATM 38 H41 UNK 1 4.413 -0.563 5.046 1.00 20.00 +HETATM 39 C22 UNK 1 3.037 -0.064 3.488 1.00 20.00 +HETATM 40 H42 UNK 1 3.479 -0.744 2.775 1.00 20.00 +HETATM 41 S6 UNK 1 -3.372 0.267 2.424 1.00 20.00 +HETATM 42 O7 UNK 1 -4.165 0.760 1.221 1.00 20.00 +END diff --git a/top/oplsaa/SM36/SM36.pdb b/top/oplsaa/SM36/SM36.pdb new file mode 120000 index 0000000..2216837 --- /dev/null +++ b/top/oplsaa/SM36/SM36.pdb @@ -0,0 +1 @@ +SM36.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM37/SM37.itp b/top/oplsaa/SM37/SM37.itp new file mode 120000 index 0000000..c9fabfd --- /dev/null +++ b/top/oplsaa/SM37/SM37.itp @@ -0,0 +1 @@ +SM37.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM37/SM37.mol2 b/top/oplsaa/SM37/SM37.mol2 new file mode 100644 index 0000000..b675f83 --- /dev/null +++ b/top/oplsaa/SM37/SM37.mol2 @@ -0,0 +1,102 @@ +# Name: SM37 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 40 41 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -3.0677 -1.6105 -2.4976 O.2 + 2 S2 -1.9084 -0.8634 -2.1555 S.o2 + 3 N3 -2.4411 0.6199 -1.6472 N.am + 4 C4 -1.4824 1.6158 -1.1622 C.3 + 5 C5 -0.8180 1.2184 0.1580 C.3 + 6 S6 -2.2599 1.8386 1.0678 S.o + 7 O7 -3.3353 0.8103 0.7472 O.3 + 8 C8 -2.1486 2.8042 -0.4651 C.3 + 9 C9 -0.4788 2.0350 -2.2384 C.3 + 10 C10 -1.2299 2.4130 -3.5166 C.3 + 11 C11 -0.2415 2.8259 -4.5766 C.ar + 12 C12 0.1376 4.1504 -4.6898 C.ar + 13 C13 1.0480 4.5283 -5.6590 C.ar + 14 C14 1.5712 3.5835 -6.5217 C.ar + 15 C15 1.1881 2.2598 -6.4119 C.ar + 16 C16 0.2818 1.8810 -5.4393 C.ar + 17 N17 -1.2356 -1.6185 -0.8442 N.am + 18 C18 -2.0957 -2.2682 0.1480 C.3 + 19 C19 0.2196 -1.6367 -0.6763 C.3 + 20 O20 -0.8455 -0.6176 -3.0661 O.2 + 21 H21 -3.3879 0.8293 -1.6706 H + 22 H22 -0.6773 0.1424 0.2600 H + 23 H23 0.0932 1.7796 0.3651 H + 24 H24 -1.4942 3.6716 -0.3777 H + 25 H25 -3.1220 3.0569 -0.8854 H + 26 H26 0.0942 2.8928 -1.8864 H + 27 H27 0.1982 1.2064 -2.4464 H + 28 H28 -1.8030 1.5552 -3.8685 H + 29 H29 -1.9069 3.2416 -3.3086 H + 30 H30 -0.2745 4.8893 -4.0186 H + 31 H31 1.3470 5.5625 -5.7450 H + 32 H32 2.2791 3.8795 -7.2818 H + 33 H33 1.5967 1.5217 -7.0861 H + 34 H34 -0.0178 0.8469 -5.3537 H + 35 H35 -2.2587 -3.3074 -0.1374 H + 36 H36 -1.6150 -2.2309 1.1255 H + 37 H37 -3.0533 -1.7495 0.1940 H + 38 H38 0.6825 -1.0264 -1.4518 H + 39 H39 0.4773 -1.2356 0.3039 H + 40 H40 0.5817 -2.6617 -0.7561 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 17 am + 4 2 20 2 + 5 3 4 1 + 6 3 21 1 + 7 4 8 1 + 8 4 5 1 + 9 4 9 1 + 10 5 6 1 + 11 5 22 1 + 12 5 23 1 + 13 6 7 1 + 14 6 8 1 + 15 8 24 1 + 16 8 25 1 + 17 9 10 1 + 18 9 26 1 + 19 9 27 1 + 20 10 11 1 + 21 10 28 1 + 22 10 29 1 + 23 11 16 ar + 24 11 12 ar + 25 12 13 ar + 26 12 30 1 + 27 13 14 ar + 28 13 31 1 + 29 14 15 ar + 30 14 32 1 + 31 15 16 ar + 32 15 33 1 + 33 16 34 1 + 34 17 18 1 + 35 17 19 1 + 36 18 35 1 + 37 18 36 1 + 38 18 37 1 + 39 19 38 1 + 40 19 39 1 + 41 19 40 1 + +# End of record + diff --git a/top/oplsaa/SM37/SM37.mol2.1.itp b/top/oplsaa/SM37/SM37.mol2.1.itp new file mode 100644 index 0000000..d20fcf0 --- /dev/null +++ b/top/oplsaa/SM37/SM37.mol2.1.itp @@ -0,0 +1,418 @@ +; input pdb SMILES : O=[S](N[C@]1(C[S@+](C1)[O-])CCC2=CC=CC=C2)(N(C)C)=O +; Script arguments : SM37.mol2 "5 opls_499" "8 opls_499" "21 opls_241 0.482" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 2 opls_474 1 UNK S2 1 0.852 32.06000 ; SY # S in sulfamide, S(=O)2(NR2) + 3 opls_480 1 UNK N17 1 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 4 opls_475 1 UNK O20 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 5 opls_480 1 UNK N3 3 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 6 opls_482 1 UNK C19 5 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 7 opls_483 1 UNK H38 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 8 opls_483 1 UNK H39 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 9 opls_483 1 UNK H40 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 10 opls_482 1 UNK C18 11 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 11 opls_483 1 UNK H35 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 12 opls_483 1 UNK H36 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 13 opls_483 1 UNK H37 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 14 opls_496 1 UNK S6 29 0.130 32.06000 ; SZ # sulfoxide - all atom + 15 opls_497 1 UNK O7 29 -0.420 15.99940 ; OY # sulfoxide - all atom + 16 opls_499 1 UNK C5 31 0.025 12.01100 ; CT # CH2 all-atom C: sulfoxide ### user-defined OPLS atom type (opls_499) + 17 opls_140 1 UNK H22 31 0.060 1.00800 ; HC # alkane H. + 18 opls_140 1 UNK H23 31 0.060 1.00800 ; HC # alkane H. + 19 opls_499 1 UNK C8 33 0.025 12.01100 ; CT # CH2 all-atom C: sulfoxide ### user-defined OPLS atom type (opls_499) + 20 opls_140 1 UNK H24 33 0.060 1.00800 ; HC # alkane H. + 21 opls_140 1 UNK H25 33 0.060 1.00800 ; HC # alkane H. + 22 opls_149 1 UNK C10 35 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 23 opls_145 1 UNK C11 35 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 24 opls_140 1 UNK H28 35 0.060 1.00800 ; HC # alkane H. + 25 opls_140 1 UNK H29 35 0.060 1.00800 ; HC # alkane H. + 26 opls_136 1 UNK C9 59 -0.120 12.01100 ; CT # alkane CH2 + 27 opls_140 1 UNK H26 59 0.060 1.00800 ; HC # alkane H. + 28 opls_140 1 UNK H27 59 0.060 1.00800 ; HC # alkane H. + 29 opls_139 1 UNK C4 63 0.000 12.01100 ; CT # alkane C + 30 opls_145 1 UNK C12 87 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 31 opls_146 1 UNK H30 87 0.115 1.00800 ; HA # Benzene H - 12 site. + 32 opls_145 1 UNK C13 89 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 33 opls_146 1 UNK H31 89 0.115 1.00800 ; HA # Benzene H - 12 site. + 34 opls_145 1 UNK C14 91 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 35 opls_146 1 UNK H32 91 0.115 1.00800 ; HA # Benzene H - 12 site. + 36 opls_145 1 UNK C15 93 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 37 opls_146 1 UNK H33 93 0.115 1.00800 ; HA # Benzene H - 12 site. + 38 opls_145 1 UNK C16 95 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 39 opls_146 1 UNK H34 95 0.115 1.00800 ; HA # Benzene H - 12 site. + 40 opls_241 1 UNK H21 97 0.482 1.00800 ; H # H on N: secondary amide ### user-defined OPLS atom type (opls_241) atom charge (0.482) +; Total charge : 0.000 ### Number of unassigned atoms : 0/40 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 5 1 ; SY-N # + 2 3 1 ; SY-N # + 2 4 1 ; SY-OY # + 5 29 1 ; N-CT # (CT-N) + 5 40 1 ; N-H # (H-N) + 29 19 1 ; CT-CT # CHARMM 22 parameter file + 29 16 1 ; CT-CT # CHARMM 22 parameter file + 29 26 1 ; CT-CT # CHARMM 22 parameter file + 16 14 1 ; CT-SZ # (SZ-CT) + 16 17 1 ; CT-HC # CHARMM 22 parameter file + 16 18 1 ; CT-HC # CHARMM 22 parameter file + 14 15 1 ; SZ-OY # + 14 19 1 ; SZ-CT # + 19 20 1 ; CT-HC # CHARMM 22 parameter file + 19 21 1 ; CT-HC # CHARMM 22 parameter file + 26 22 1 ; CT-CT # CHARMM 22 parameter file + 26 27 1 ; CT-HC # CHARMM 22 parameter file + 26 28 1 ; CT-HC # CHARMM 22 parameter file + 22 23 1 ; CT-CA # (CA-CT) PHE,TYR + 22 24 1 ; CT-HC # CHARMM 22 parameter file + 22 25 1 ; CT-HC # CHARMM 22 parameter file + 23 38 1 ; CA-CA # TRP,TYR,PHE + 23 30 1 ; CA-CA # TRP,TYR,PHE + 30 32 1 ; CA-CA # TRP,TYR,PHE + 30 31 1 ; CA-HA # PHE, etc. + 32 34 1 ; CA-CA # TRP,TYR,PHE + 32 33 1 ; CA-HA # PHE, etc. + 34 36 1 ; CA-CA # TRP,TYR,PHE + 34 35 1 ; CA-HA # PHE, etc. + 36 38 1 ; CA-CA # TRP,TYR,PHE + 36 37 1 ; CA-HA # PHE, etc. + 38 39 1 ; CA-HA # PHE, etc. + 3 10 1 ; N-CT # (CT-N) + 3 6 1 ; N-CT # (CT-N) + 10 11 1 ; CT-HC # CHARMM 22 parameter file + 10 12 1 ; CT-HC # CHARMM 22 parameter file + 10 13 1 ; CT-HC # CHARMM 22 parameter file + 6 7 1 ; CT-HC # CHARMM 22 parameter file + 6 8 1 ; CT-HC # CHARMM 22 parameter file + 6 9 1 ; CT-HC # CHARMM 22 parameter file + +[ angles ] +; ai aj ak funct theta cth + 1 2 5 1 ; OY-SY-N # + 1 2 3 1 ; OY-SY-N # + 1 2 4 1 ; OY-SY-OY # + 5 2 3 1 107.000 1004.160 ; N-SY-N # by analogy from OY-SY-N : + 5 2 4 1 ; N-SY-OY # (OY-SY-N) + 3 2 4 1 ; N-SY-OY # (OY-SY-N) + 2 5 29 1 ; SY-N-CT # + 2 5 40 1 ; SY-N-H # (H-N-SY) + 29 5 40 1 ; CT-N-H # + 5 29 19 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 29 16 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 29 26 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 19 29 26 1 ; CT-CT-CT # CHARMM 22 parameter file + 16 29 19 1 ; CT-CT-CT # CHARMM 22 parameter file + 16 29 26 1 ; CT-CT-CT # CHARMM 22 parameter file + 29 16 14 1 ; CT-CT-SZ # + 29 16 17 1 ; CT-CT-HC # CHARMM 22 parameter file + 29 16 18 1 ; CT-CT-HC # CHARMM 22 parameter file + 14 16 17 1 ; SZ-CT-HC # + 14 16 18 1 ; SZ-CT-HC # + 17 16 18 1 ; HC-CT-HC # CHARMM 22 parameter file + 16 14 15 1 ; CT-SZ-OY # (OY-SZ-CT) + 16 14 19 1 ; CT-SZ-CT # + 15 14 19 1 ; OY-SZ-CT # + 29 19 14 1 ; CT-CT-SZ # + 29 19 20 1 ; CT-CT-HC # CHARMM 22 parameter file + 29 19 21 1 ; CT-CT-HC # CHARMM 22 parameter file + 14 19 20 1 ; SZ-CT-HC # + 14 19 21 1 ; SZ-CT-HC # + 20 19 21 1 ; HC-CT-HC # CHARMM 22 parameter file + 29 26 22 1 ; CT-CT-CT # CHARMM 22 parameter file + 29 26 27 1 ; CT-CT-HC # CHARMM 22 parameter file + 29 26 28 1 ; CT-CT-HC # CHARMM 22 parameter file + 22 26 27 1 ; CT-CT-HC # CHARMM 22 parameter file + 22 26 28 1 ; CT-CT-HC # CHARMM 22 parameter file + 27 26 28 1 ; HC-CT-HC # CHARMM 22 parameter file + 26 22 23 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 26 22 24 1 ; CT-CT-HC # CHARMM 22 parameter file + 26 22 25 1 ; CT-CT-HC # CHARMM 22 parameter file + 23 22 24 1 ; CA-CT-HC # + 23 22 25 1 ; CA-CT-HC # + 24 22 25 1 ; HC-CT-HC # CHARMM 22 parameter file + 22 23 38 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 22 23 30 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 30 23 38 1 ; CA-CA-CA # PHE(OL) + 23 30 32 1 ; CA-CA-CA # PHE(OL) + 23 30 31 1 ; CA-CA-HA # + 32 30 31 1 ; CA-CA-HA # + 30 32 34 1 ; CA-CA-CA # PHE(OL) + 30 32 33 1 ; CA-CA-HA # + 34 32 33 1 ; CA-CA-HA # + 32 34 36 1 ; CA-CA-CA # PHE(OL) + 32 34 35 1 ; CA-CA-HA # + 36 34 35 1 ; CA-CA-HA # + 34 36 38 1 ; CA-CA-CA # PHE(OL) + 34 36 37 1 ; CA-CA-HA # + 38 36 37 1 ; CA-CA-HA # + 23 38 36 1 ; CA-CA-CA # PHE(OL) + 23 38 39 1 ; CA-CA-HA # + 36 38 39 1 ; CA-CA-HA # + 2 3 10 1 ; SY-N-CT # + 2 3 6 1 ; SY-N-CT # + 10 3 6 1 ; CT-N-CT # PRO(OL) DETAR JACS 99,1232 + 3 10 11 1 ; N-CT-HC # (HC-CT-N) + 3 10 12 1 ; N-CT-HC # (HC-CT-N) + 3 10 13 1 ; N-CT-HC # (HC-CT-N) + 11 10 12 1 ; HC-CT-HC # CHARMM 22 parameter file + 11 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 12 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 3 6 7 1 ; N-CT-HC # (HC-CT-N) + 3 6 8 1 ; N-CT-HC # (HC-CT-N) + 3 6 9 1 ; N-CT-HC # (HC-CT-N) + 7 6 8 1 ; HC-CT-HC # CHARMM 22 parameter file + 7 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + 8 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 5 29 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 5 40 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 5 29 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 3 2 5 40 3 -15.611 0.703 20.506 -5.598 -0.000 0.000 ; N-SY-N-H # LigParGen + 4 2 5 29 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 5 40 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 5 2 3 10 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 5 2 3 6 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 4 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 5 29 19 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 29 16 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 29 26 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 40 5 29 19 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 40 5 29 16 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 40 5 29 26 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 5 29 19 14 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-SZ # adapted from CT-CT-CT-N : N-propylformamide + 5 29 19 20 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 29 19 21 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 16 29 19 14 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 16 29 19 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 16 29 19 21 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 26 29 19 14 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 26 29 19 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 26 29 19 21 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 29 16 14 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-SZ # adapted from CT-CT-CT-N : N-propylformamide + 5 29 16 17 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 29 16 18 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 19 29 16 14 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 19 29 16 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 19 29 16 18 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 26 29 16 14 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-SZ # adapted from CT-CT-CT-SY2 : + 26 29 16 17 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 26 29 16 18 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 29 26 22 3 ; N-CT-CT-CT # (CT-CT-CT-N) N-propylformamide + 5 29 26 27 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 29 26 28 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 19 29 26 22 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 19 29 26 27 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 19 29 26 28 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 16 29 26 22 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 16 29 26 27 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 16 29 26 28 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 29 16 14 15 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CT-CT-SZ-OY # adapted from CT-CT-SH2-OY : sulfone + 29 16 14 19 3 0.94140 2.31375 2.40999 -5.66514 0.00000 0.00000 ; CT-CT-SZ-CT # adapted from CT-CT-S-CT : sulfide all-atom + 17 16 14 15 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; HC-CT-SZ-OY # adapted from HC-CT-SH2-OY : sulfone + 17 16 14 19 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; HC-CT-SZ-CT # adapted from HC-CT-S-CT : sulfide all-atom + 18 16 14 15 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; HC-CT-SZ-OY # adapted from HC-CT-SH2-OY : sulfone + 18 16 14 19 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; HC-CT-SZ-CT # adapted from HC-CT-S-CT : sulfide all-atom + 16 14 19 29 3 0.94140 2.31375 2.40999 -5.66514 0.00000 0.00000 ; CT-SZ-CT-CT # adapted from CT-CT-S-CT : sulfide all-atom + 16 14 19 20 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; CT-SZ-CT-HC # adapted from HC-CT-S-CT : sulfide all-atom + 16 14 19 21 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; CT-SZ-CT-HC # adapted from HC-CT-S-CT : sulfide all-atom + 15 14 19 29 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; OY-SZ-CT-CT # adapted from CT-CT-SH2-OY : sulfone + 15 14 19 20 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; OY-SZ-CT-HC # adapted from HC-CT-SH2-OY : sulfone + 15 14 19 21 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; OY-SZ-CT-HC # adapted from HC-CT-SH2-OY : sulfone + 29 26 22 23 3 ; CT-CT-CT-CA # (CA-CT-CT-CT) + 29 26 22 24 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 29 26 22 25 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 27 26 22 23 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 27 26 22 24 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 27 26 22 25 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 28 26 22 23 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 28 26 22 24 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 28 26 22 25 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 26 22 23 38 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 26 22 23 30 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 24 22 23 38 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 24 22 23 30 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 25 22 23 38 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 25 22 23 30 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 22 23 38 36 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 23 38 39 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 23 38 36 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 23 38 39 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 23 30 32 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 23 30 31 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 38 23 30 32 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 38 23 30 31 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 30 32 34 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 30 32 33 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 30 32 34 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 30 32 33 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 32 34 36 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 32 34 35 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 32 34 36 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 32 34 35 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 34 36 38 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 34 36 37 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 35 34 36 38 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 35 34 36 37 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 36 38 23 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 36 38 39 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 37 36 38 23 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 37 36 38 39 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 10 11 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 12 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 13 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 6 3 10 11 3 ; CT-N-CT-HC # tert. amide + 6 3 10 12 3 ; CT-N-CT-HC # tert. amide + 6 3 10 13 3 ; CT-N-CT-HC # tert. amide + 2 3 6 7 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 8 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 9 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 10 3 6 7 3 ; CT-N-CT-HC # tert. amide + 10 3 6 8 3 ; CT-N-CT-HC # tert. amide + 10 3 6 9 3 ; CT-N-CT-HC # tert. amide + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 2 40 5 29 1 improper_Z_N_X_Y ; SY-H-N-CT + 38 30 23 22 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 32 31 30 23 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 34 33 32 30 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 36 35 34 32 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 38 37 36 34 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 36 39 38 23 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 2 6 3 10 1 improper_Z_N_X_Y ; SY-CT-N-CT + +[ pairs ] +; ai aj funct + 1 29 1 + 1 40 1 + 1 10 1 + 1 6 1 + 2 19 1 + 2 16 1 + 2 26 1 + 2 11 1 + 2 12 1 + 2 13 1 + 2 7 1 + 2 8 1 + 2 9 1 + 5 10 1 + 5 6 1 + 5 14 1 + 5 20 1 + 5 21 1 + 5 17 1 + 5 18 1 + 5 22 1 + 5 27 1 + 5 28 1 + 29 3 1 + 29 4 1 + 29 15 1 + 29 23 1 + 29 24 1 + 29 25 1 + 16 40 1 + 16 20 1 + 16 21 1 + 16 22 1 + 16 27 1 + 16 28 1 + 14 26 1 + 15 17 1 + 15 18 1 + 15 20 1 + 15 21 1 + 19 40 1 + 19 17 1 + 19 18 1 + 19 22 1 + 19 27 1 + 19 28 1 + 26 40 1 + 26 20 1 + 26 21 1 + 26 17 1 + 26 18 1 + 26 38 1 + 26 30 1 + 22 36 1 + 22 39 1 + 22 32 1 + 22 31 1 + 23 27 1 + 23 28 1 + 23 34 1 + 23 37 1 + 23 33 1 + 30 24 1 + 30 25 1 + 30 36 1 + 30 39 1 + 30 35 1 + 32 38 1 + 32 37 1 + 34 31 1 + 34 39 1 + 36 33 1 + 38 24 1 + 38 25 1 + 38 31 1 + 38 35 1 + 3 40 1 + 10 4 1 + 10 7 1 + 10 8 1 + 10 9 1 + 6 4 1 + 6 11 1 + 6 12 1 + 6 13 1 + 4 40 1 + 27 24 1 + 27 25 1 + 28 24 1 + 28 25 1 + 31 33 1 + 33 35 1 + 35 37 1 + 37 39 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 5 1 1000 1000 1000 + 29 1 1000 1000 1000 + 16 1 1000 1000 1000 + 14 1 1000 1000 1000 + 15 1 1000 1000 1000 + 19 1 1000 1000 1000 + 26 1 1000 1000 1000 + 22 1 1000 1000 1000 + 23 1 1000 1000 1000 + 30 1 1000 1000 1000 + 32 1 1000 1000 1000 + 34 1 1000 1000 1000 + 36 1 1000 1000 1000 + 38 1 1000 1000 1000 + 3 1 1000 1000 1000 + 10 1 1000 1000 1000 + 6 1 1000 1000 1000 + 4 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM37/SM37.mol2.1.pdb b/top/oplsaa/SM37/SM37.mol2.1.pdb new file mode 100644 index 0000000..10668e6 --- /dev/null +++ b/top/oplsaa/SM37/SM37.mol2.1.pdb @@ -0,0 +1,41 @@ +HETATM 1 O1 UNK 1 -3.068 -1.611 -2.498 1.00 20.00 +HETATM 2 S2 UNK 1 -1.908 -0.863 -2.155 1.00 20.00 +HETATM 3 N17 UNK 1 -1.236 -1.619 -0.844 1.00 20.00 +HETATM 4 O20 UNK 1 -0.846 -0.618 -3.066 1.00 20.00 +HETATM 5 N3 UNK 1 -2.441 0.620 -1.647 1.00 20.00 +HETATM 6 C19 UNK 1 0.220 -1.637 -0.676 1.00 20.00 +HETATM 7 H38 UNK 1 0.682 -1.026 -1.452 1.00 20.00 +HETATM 8 H39 UNK 1 0.477 -1.236 0.304 1.00 20.00 +HETATM 9 H40 UNK 1 0.582 -2.662 -0.756 1.00 20.00 +HETATM 10 C18 UNK 1 -2.096 -2.268 0.148 1.00 20.00 +HETATM 11 H35 UNK 1 -2.259 -3.307 -0.137 1.00 20.00 +HETATM 12 H36 UNK 1 -1.615 -2.231 1.125 1.00 20.00 +HETATM 13 H37 UNK 1 -3.053 -1.750 0.194 1.00 20.00 +HETATM 14 S6 UNK 1 -2.260 1.839 1.068 1.00 20.00 +HETATM 15 O7 UNK 1 -3.335 0.810 0.747 1.00 20.00 +HETATM 16 C5 UNK 1 -0.818 1.218 0.158 1.00 20.00 +HETATM 17 H22 UNK 1 -0.677 0.142 0.260 1.00 20.00 +HETATM 18 H23 UNK 1 0.093 1.780 0.365 1.00 20.00 +HETATM 19 C8 UNK 1 -2.149 2.804 -0.465 1.00 20.00 +HETATM 20 H24 UNK 1 -1.494 3.672 -0.378 1.00 20.00 +HETATM 21 H25 UNK 1 -3.122 3.057 -0.885 1.00 20.00 +HETATM 22 C10 UNK 1 -1.230 2.413 -3.517 1.00 20.00 +HETATM 23 C11 UNK 1 -0.241 2.826 -4.577 1.00 20.00 +HETATM 24 H28 UNK 1 -1.803 1.555 -3.869 1.00 20.00 +HETATM 25 H29 UNK 1 -1.907 3.242 -3.309 1.00 20.00 +HETATM 26 C9 UNK 1 -0.479 2.035 -2.238 1.00 20.00 +HETATM 27 H26 UNK 1 0.094 2.893 -1.886 1.00 20.00 +HETATM 28 H27 UNK 1 0.198 1.206 -2.446 1.00 20.00 +HETATM 29 C4 UNK 1 -1.482 1.616 -1.162 1.00 20.00 +HETATM 30 C12 UNK 1 0.138 4.150 -4.690 1.00 20.00 +HETATM 31 H30 UNK 1 -0.275 4.889 -4.019 1.00 20.00 +HETATM 32 C13 UNK 1 1.048 4.528 -5.659 1.00 20.00 +HETATM 33 H31 UNK 1 1.347 5.562 -5.745 1.00 20.00 +HETATM 34 C14 UNK 1 1.571 3.583 -6.522 1.00 20.00 +HETATM 35 H32 UNK 1 2.279 3.880 -7.282 1.00 20.00 +HETATM 36 C15 UNK 1 1.188 2.260 -6.412 1.00 20.00 +HETATM 37 H33 UNK 1 1.597 1.522 -7.086 1.00 20.00 +HETATM 38 C16 UNK 1 0.282 1.881 -5.439 1.00 20.00 +HETATM 39 H34 UNK 1 -0.018 0.847 -5.354 1.00 20.00 +HETATM 40 H21 UNK 1 -3.388 0.829 -1.671 1.00 20.00 +END diff --git a/top/oplsaa/SM37/SM37.pdb b/top/oplsaa/SM37/SM37.pdb new file mode 120000 index 0000000..81b95d3 --- /dev/null +++ b/top/oplsaa/SM37/SM37.pdb @@ -0,0 +1 @@ +SM37.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM38/SM38.mol2 b/top/oplsaa/SM38/SM38.mol2 deleted file mode 120000 index a710ac8..0000000 --- a/top/oplsaa/SM38/SM38.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM38/SM38.mol2 \ No newline at end of file diff --git a/top/oplsaa/SM38/SM38.mol2 b/top/oplsaa/SM38/SM38.mol2 new file mode 100644 index 0000000..d939314 --- /dev/null +++ b/top/oplsaa/SM38/SM38.mol2 @@ -0,0 +1,94 @@ +# Name: SM38 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 36 37 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 C1 1.1665 0.0871 -2.7901 C.3 + 2 S2 -0.3339 -0.4110 -1.9004 S.o2 + 3 N3 -0.0566 0.0475 -0.3335 N.am + 4 C4 0.1352 1.4628 -0.0074 C.3 + 5 C5 -0.3702 1.8324 1.3891 C.3 + 6 S6 -0.7943 3.4928 0.7914 S.o2 + 7 C7 -0.9261 2.3729 -0.6298 C.3 + 8 O8 0.3347 4.3521 0.7111 O.2 + 9 O9 -2.0598 3.9408 1.2574 O.2 + 10 C10 1.5653 1.9364 -0.2744 C.3 + 11 C11 2.5493 1.0343 0.4732 C.3 + 12 C12 3.9602 1.4272 0.1183 C.ar + 13 C13 4.5948 0.8301 -0.9549 C.ar + 14 C14 5.8873 1.1939 -1.2834 C.ar + 15 C15 6.5490 2.1473 -0.5323 C.ar + 16 C16 5.9163 2.7406 0.5441 C.ar + 17 C17 4.6219 2.3805 0.8694 C.ar + 18 O18 -0.4303 -1.8274 -1.8393 O.2 + 19 O19 -1.4410 0.3818 -2.3069 O.2 + 20 H20 2.0289 -0.4246 -2.3629 H + 21 H21 1.0703 -0.1796 -3.8425 H + 22 H22 1.3018 1.1649 -2.6993 H + 23 H23 -0.0212 -0.6211 0.3684 H + 24 H24 -1.2404 1.2527 1.6971 H + 25 H25 0.4172 1.8359 2.1427 H + 26 H26 -0.6040 2.8288 -1.5660 H + 27 H27 -1.9036 1.8976 -0.7116 H + 28 H28 1.7699 1.8894 -1.3440 H + 29 H29 1.6786 2.9636 0.0724 H + 30 H30 2.4004 1.1456 1.5472 H + 31 H31 2.3787 -0.0039 0.1884 H + 32 H32 4.0794 0.0820 -1.5390 H + 33 H33 6.3818 0.7302 -2.1241 H + 34 H34 7.5604 2.4284 -0.7862 H + 35 H35 6.4334 3.4852 1.1312 H + 36 H36 4.1277 2.8438 1.7106 H +@BOND + 1 1 2 1 + 2 1 20 1 + 3 1 21 1 + 4 1 22 1 + 5 2 3 am + 6 2 18 2 + 7 2 19 2 + 8 3 4 1 + 9 3 23 1 + 10 4 7 1 + 11 4 5 1 + 12 4 10 1 + 13 5 6 1 + 14 5 24 1 + 15 5 25 1 + 16 6 7 1 + 17 6 8 2 + 18 6 9 2 + 19 7 26 1 + 20 7 27 1 + 21 10 11 1 + 22 10 28 1 + 23 10 29 1 + 24 11 12 1 + 25 11 30 1 + 26 11 31 1 + 27 12 17 ar + 28 12 13 ar + 29 13 14 ar + 30 13 32 1 + 31 14 15 ar + 32 14 33 1 + 33 15 16 ar + 34 15 34 1 + 35 16 17 ar + 36 16 35 1 + 37 17 36 1 + +# End of record + diff --git a/top/oplsaa/SM39/SM39.mol2 b/top/oplsaa/SM39/SM39.mol2 deleted file mode 120000 index 74b8b55..0000000 --- a/top/oplsaa/SM39/SM39.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM39/SM39.mol2 \ No newline at end of file diff --git a/top/oplsaa/SM39/SM39.mol2 b/top/oplsaa/SM39/SM39.mol2 new file mode 100644 index 0000000..487ec68 --- /dev/null +++ b/top/oplsaa/SM39/SM39.mol2 @@ -0,0 +1,109 @@ +# Name: SM39 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 43 45 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 0.5370 7.7981 -3.4612 O.2 + 2 S2 0.4485 7.8090 -2.0430 S.o2 + 3 N3 -0.0324 6.2897 -1.5928 N.am + 4 C4 -1.1748 5.6563 -2.2561 C.3 + 5 C5 -1.0831 4.1289 -2.2847 C.3 + 6 S6 -1.9677 4.1098 -3.8694 S.o2 + 7 C7 -1.0777 5.6884 -3.7831 C.3 + 8 O8 -3.3722 4.2616 -3.7158 O.2 + 9 O9 -1.3981 3.2084 -4.8087 O.2 + 10 C10 -2.5162 6.1686 -1.7278 C.3 + 11 C11 -2.6392 5.8349 -0.2397 C.3 + 12 C12 -4.0108 6.2220 0.2502 C.ar + 13 C13 -4.2314 7.4885 0.7583 C.ar + 14 C14 -5.4907 7.8451 1.2032 C.ar + 15 C15 -6.5269 6.9317 1.1497 C.ar + 16 C16 -6.3052 5.6635 0.6464 C.ar + 17 C17 -5.0471 5.3086 0.1966 C.ar + 18 C18 -0.8624 8.9133 -1.6348 C.ar + 19 C19 -0.9680 9.4164 -0.3516 C.ar + 20 C20 -1.9967 10.2825 -0.0312 C.ar + 21 C21 -2.9198 10.6454 -0.9941 C.ar + 22 C22 -2.8173 10.1381 -2.2759 C.ar + 23 C23 -1.7855 9.2763 -2.5977 C.ar + 24 O24 1.5391 8.1513 -1.1988 O.2 + 25 H25 0.4424 5.8190 -0.8900 H + 26 H26 -0.0594 3.7625 -2.3611 H + 27 H27 -1.6385 3.6511 -1.4777 H + 28 H28 -1.6286 6.5159 -4.2302 H + 29 H29 -0.0529 5.6231 -4.1488 H + 30 H30 -2.5718 7.2486 -1.8638 H + 31 H31 -3.3287 5.6912 -2.2755 H + 32 H32 -2.4897 4.7652 -0.0936 H + 33 H33 -1.8843 6.3871 0.3201 H + 34 H34 -3.4207 8.2006 0.8043 H + 35 H35 -5.6639 8.8358 1.5968 H + 36 H36 -7.5097 7.2089 1.5013 H + 37 H37 -7.1147 4.9498 0.6048 H + 38 H38 -4.8737 4.3177 -0.1963 H + 39 H39 -0.2470 9.1326 0.4007 H + 40 H40 -2.0795 10.6752 0.9714 H + 41 H41 -3.7237 11.3217 -0.7437 H + 42 H42 -3.5411 10.4182 -3.0270 H + 43 H43 -1.7032 8.8829 -3.6001 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 18 1 + 4 2 24 2 + 5 3 4 1 + 6 3 25 1 + 7 4 7 1 + 8 4 5 1 + 9 4 10 1 + 10 5 6 1 + 11 5 26 1 + 12 5 27 1 + 13 6 7 1 + 14 6 8 2 + 15 6 9 2 + 16 7 28 1 + 17 7 29 1 + 18 10 11 1 + 19 10 30 1 + 20 10 31 1 + 21 11 12 1 + 22 11 32 1 + 23 11 33 1 + 24 12 17 ar + 25 12 13 ar + 26 13 14 ar + 27 13 34 1 + 28 14 15 ar + 29 14 35 1 + 30 15 16 ar + 31 15 36 1 + 32 16 17 ar + 33 16 37 1 + 34 17 38 1 + 35 18 23 ar + 36 18 19 ar + 37 19 20 ar + 38 19 39 1 + 39 20 21 ar + 40 20 40 1 + 41 21 22 ar + 42 21 41 1 + 43 22 23 ar + 44 22 42 1 + 45 23 43 1 + +# End of record + diff --git a/top/oplsaa/SM40/SM40.itp b/top/oplsaa/SM40/SM40.itp new file mode 120000 index 0000000..38508f4 --- /dev/null +++ b/top/oplsaa/SM40/SM40.itp @@ -0,0 +1 @@ +SM40.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM40/SM40.mol2 b/top/oplsaa/SM40/SM40.mol2 new file mode 100644 index 0000000..56ea1f3 --- /dev/null +++ b/top/oplsaa/SM40/SM40.mol2 @@ -0,0 +1,104 @@ +# Name: SM40 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 41 42 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -0.9745 -1.8878 -1.8995 O.2 + 2 S2 -0.6777 -0.4981 -1.8950 S.o2 + 3 N3 -0.1691 -0.1336 -0.3618 N.am + 4 C4 0.3322 1.2086 -0.0561 C.3 + 5 C5 0.0297 1.6519 1.3772 C.3 + 6 S6 -0.0967 3.3726 0.8137 S.o2 + 7 C7 -0.5703 2.3239 -0.5889 C.3 + 8 O8 1.1725 3.9867 0.6369 O.2 + 9 O9 -1.2019 4.0602 1.3837 O.2 + 10 C10 1.8015 1.3871 -0.4435 C.3 + 11 C11 2.6429 0.3039 0.2345 C.3 + 12 C12 4.1030 0.5565 -0.0402 C.ar + 13 C13 4.7045 -0.0046 -1.1511 C.ar + 14 C14 6.0426 0.2311 -1.4057 C.ar + 15 C15 6.7817 1.0194 -0.5437 C.ar + 16 C16 6.1815 1.5763 0.5701 C.ar + 17 C17 4.8421 1.3448 0.8218 C.ar + 18 N18 0.6198 -0.2937 -2.9035 N.am + 19 C19 1.6299 -1.3483 -3.0203 C.3 + 20 C20 0.7574 0.9417 -3.6788 C.3 + 21 O21 -1.6243 0.4999 -2.2517 O.2 + 22 H22 -0.2031 -0.8087 0.3339 H + 23 H23 -0.9113 1.2557 1.7587 H + 24 H24 0.8612 1.4848 2.0619 H + 25 H25 -0.2411 2.7192 -1.5499 H + 26 H26 -1.6273 2.0574 -0.5870 H + 27 H27 1.9047 1.3033 -1.5254 H + 28 H28 2.1456 2.3696 -0.1207 H + 29 H29 2.4663 0.3265 1.3098 H + 30 H30 2.3629 -0.6732 -0.1592 H + 31 H31 4.1280 -0.6241 -1.8223 H + 32 H32 6.5116 -0.2043 -2.2757 H + 33 H33 7.8282 1.1999 -0.7401 H + 34 H34 6.7591 2.1919 1.2438 H + 35 H35 4.3732 1.7796 1.6922 H + 36 H36 1.3486 -2.0340 -3.8196 H + 37 H37 2.5973 -0.9010 -3.2490 H + 38 H38 1.6955 -1.8945 -2.0793 H + 39 H39 1.3822 1.6469 -3.1306 H + 40 H40 1.2198 0.7177 -4.6401 H + 41 H41 -0.2272 1.3796 -3.8424 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 18 am + 4 2 21 2 + 5 3 4 1 + 6 3 22 1 + 7 4 7 1 + 8 4 5 1 + 9 4 10 1 + 10 5 6 1 + 11 5 23 1 + 12 5 24 1 + 13 6 7 1 + 14 6 8 2 + 15 6 9 2 + 16 7 25 1 + 17 7 26 1 + 18 10 11 1 + 19 10 27 1 + 20 10 28 1 + 21 11 12 1 + 22 11 29 1 + 23 11 30 1 + 24 12 17 ar + 25 12 13 ar + 26 13 14 ar + 27 13 31 1 + 28 14 15 ar + 29 14 32 1 + 30 15 16 ar + 31 15 33 1 + 32 16 17 ar + 33 16 34 1 + 34 17 35 1 + 35 18 19 1 + 36 18 20 1 + 37 19 36 1 + 38 19 37 1 + 39 19 38 1 + 40 20 39 1 + 41 20 40 1 + 42 20 41 1 + +# End of record + diff --git a/top/oplsaa/SM40/SM40.mol2.1.itp b/top/oplsaa/SM40/SM40.mol2.1.itp new file mode 100644 index 0000000..a857589 --- /dev/null +++ b/top/oplsaa/SM40/SM40.mol2.1.itp @@ -0,0 +1,435 @@ +; input pdb SMILES : O=[S](NC1(C[S](C1)(=O)=O)CCC2=CC=CC=C2)(N(C)C)=O +; Script arguments : SM40.mol2 "22 opls_241 0.482" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 2 opls_474 1 UNK S2 1 0.852 32.06000 ; SY # S in sulfamide, S(=O)2(NR2) + 3 opls_480 1 UNK N18 1 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 4 opls_475 1 UNK O21 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 5 opls_480 1 UNK N3 3 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 6 opls_482 1 UNK C20 5 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 7 opls_483 1 UNK H39 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 8 opls_483 1 UNK H40 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 9 opls_483 1 UNK H41 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 10 opls_482 1 UNK C19 11 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 11 opls_483 1 UNK H36 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 12 opls_483 1 UNK H37 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 13 opls_483 1 UNK H38 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 14 opls_493 1 UNK S6 29 1.374 32.06000 ; SY2 # S in sulfone + 15 opls_494 1 UNK O8 29 -0.687 15.99940 ; OY # O in sulfone + 16 opls_494 1 UNK O9 29 -0.687 15.99940 ; OY # O in sulfone + 17 opls_149 1 UNK C11 33 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 18 opls_145 1 UNK C12 33 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 19 opls_140 1 UNK H29 33 0.060 1.00800 ; HC # alkane H. + 20 opls_140 1 UNK H30 33 0.060 1.00800 ; HC # alkane H. + 21 opls_136 1 UNK C5 49 -0.120 12.01100 ; CT # alkane CH2 + 22 opls_140 1 UNK H23 49 0.060 1.00800 ; HC # alkane H. + 23 opls_140 1 UNK H24 49 0.060 1.00800 ; HC # alkane H. + 24 opls_136 1 UNK C7 53 -0.120 12.01100 ; CT # alkane CH2 + 25 opls_140 1 UNK H25 53 0.060 1.00800 ; HC # alkane H. + 26 opls_140 1 UNK H26 53 0.060 1.00800 ; HC # alkane H. + 27 opls_136 1 UNK C10 57 -0.120 12.01100 ; CT # alkane CH2 + 28 opls_140 1 UNK H27 57 0.060 1.00800 ; HC # alkane H. + 29 opls_140 1 UNK H28 57 0.060 1.00800 ; HC # alkane H. + 30 opls_139 1 UNK C4 61 0.000 12.01100 ; CT # alkane C + 31 opls_145 1 UNK C13 85 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 32 opls_146 1 UNK H31 85 0.115 1.00800 ; HA # Benzene H - 12 site. + 33 opls_145 1 UNK C14 87 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 34 opls_146 1 UNK H32 87 0.115 1.00800 ; HA # Benzene H - 12 site. + 35 opls_145 1 UNK C15 89 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 36 opls_146 1 UNK H33 89 0.115 1.00800 ; HA # Benzene H - 12 site. + 37 opls_145 1 UNK C16 91 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 38 opls_146 1 UNK H34 91 0.115 1.00800 ; HA # Benzene H - 12 site. + 39 opls_145 1 UNK C17 93 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 40 opls_146 1 UNK H35 93 0.115 1.00800 ; HA # Benzene H - 12 site. + 41 opls_241 1 UNK H22 95 0.482 1.00800 ; H # H on N: secondary amide ### user-defined OPLS atom type (opls_241) atom charge (0.482) +; Total charge : 0.000 ### Number of unassigned atoms : 0/41 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 5 1 ; SY-N # + 2 3 1 ; SY-N # + 2 4 1 ; SY-OY # + 5 30 1 ; N-CT # (CT-N) + 5 41 1 ; N-H # (H-N) + 30 24 1 ; CT-CT # CHARMM 22 parameter file + 30 21 1 ; CT-CT # CHARMM 22 parameter file + 30 27 1 ; CT-CT # CHARMM 22 parameter file + 21 14 1 0.17700 284512.0 ; CT-SY2 # (SY2-CT) by analogy from SY-CT + 21 22 1 ; CT-HC # CHARMM 22 parameter file + 21 23 1 ; CT-HC # CHARMM 22 parameter file + 14 24 1 0.17700 284512.0 ; SY2-CT # by analogy from SY-CT + 14 15 1 0.14400 585760.0 ; SY2-OY # by analogy from SY-OY + 14 16 1 0.14400 585760.0 ; SY2-OY # by analogy from SY-OY + 24 25 1 ; CT-HC # CHARMM 22 parameter file + 24 26 1 ; CT-HC # CHARMM 22 parameter file + 27 17 1 ; CT-CT # CHARMM 22 parameter file + 27 28 1 ; CT-HC # CHARMM 22 parameter file + 27 29 1 ; CT-HC # CHARMM 22 parameter file + 17 18 1 ; CT-CA # (CA-CT) PHE,TYR + 17 19 1 ; CT-HC # CHARMM 22 parameter file + 17 20 1 ; CT-HC # CHARMM 22 parameter file + 18 39 1 ; CA-CA # TRP,TYR,PHE + 18 31 1 ; CA-CA # TRP,TYR,PHE + 31 33 1 ; CA-CA # TRP,TYR,PHE + 31 32 1 ; CA-HA # PHE, etc. + 33 35 1 ; CA-CA # TRP,TYR,PHE + 33 34 1 ; CA-HA # PHE, etc. + 35 37 1 ; CA-CA # TRP,TYR,PHE + 35 36 1 ; CA-HA # PHE, etc. + 37 39 1 ; CA-CA # TRP,TYR,PHE + 37 38 1 ; CA-HA # PHE, etc. + 39 40 1 ; CA-HA # PHE, etc. + 3 10 1 ; N-CT # (CT-N) + 3 6 1 ; N-CT # (CT-N) + 10 11 1 ; CT-HC # CHARMM 22 parameter file + 10 12 1 ; CT-HC # CHARMM 22 parameter file + 10 13 1 ; CT-HC # CHARMM 22 parameter file + 6 7 1 ; CT-HC # CHARMM 22 parameter file + 6 8 1 ; CT-HC # CHARMM 22 parameter file + 6 9 1 ; CT-HC # CHARMM 22 parameter file + +[ angles ] +; ai aj ak funct theta cth + 1 2 5 1 ; OY-SY-N # + 1 2 3 1 ; OY-SY-N # + 1 2 4 1 ; OY-SY-OY # + 5 2 3 1 107.000 1004.160 ; N-SY-N # by analogy from OY-SY-N : + 5 2 4 1 ; N-SY-OY # (OY-SY-N) + 3 2 4 1 ; N-SY-OY # (OY-SY-N) + 2 5 30 1 ; SY-N-CT # + 2 5 41 1 ; SY-N-H # (H-N-SY) + 30 5 41 1 ; CT-N-H # + 5 30 24 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 30 21 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 5 30 27 1 ; N-CT-CT # (CT-CT-N) ALA JACS 94, 2657 + 24 30 27 1 ; CT-CT-CT # CHARMM 22 parameter file + 21 30 24 1 ; CT-CT-CT # CHARMM 22 parameter file + 21 30 27 1 ; CT-CT-CT # CHARMM 22 parameter file + 30 21 14 1 128.000 460.240 ; CT-CT-SY2 # LigParGen + 30 21 22 1 ; CT-CT-HC # CHARMM 22 parameter file + 30 21 23 1 ; CT-CT-HC # CHARMM 22 parameter file + 14 21 22 1 117.200 313.800 ; SY2-CT-HC # LigParGen + 14 21 23 1 117.200 313.800 ; SY2-CT-HC # LigParGen + 22 21 23 1 ; HC-CT-HC # CHARMM 22 parameter file + 21 14 24 1 102.000 518.816 ; CT-SY2-CT # LigParGen + 21 14 15 1 108.900 619.232 ; CT-SY2-OY # (OY-SY2-CT) LigParGen + 21 14 16 1 108.900 619.232 ; CT-SY2-OY # (OY-SY2-CT) LigParGen + 24 14 15 1 108.900 619.232 ; CT-SY2-OY # (OY-SY2-CT) LigParGen + 24 14 16 1 108.900 619.232 ; CT-SY2-OY # (OY-SY2-CT) LigParGen + 15 14 16 1 119.000 870.272 ; OY-SY2-OY # LigParGen + 30 24 14 1 128.000 460.240 ; CT-CT-SY2 # LigParGen + 30 24 25 1 ; CT-CT-HC # CHARMM 22 parameter file + 30 24 26 1 ; CT-CT-HC # CHARMM 22 parameter file + 14 24 25 1 117.200 313.800 ; SY2-CT-HC # LigParGen + 14 24 26 1 117.200 313.800 ; SY2-CT-HC # LigParGen + 25 24 26 1 ; HC-CT-HC # CHARMM 22 parameter file + 30 27 17 1 ; CT-CT-CT # CHARMM 22 parameter file + 30 27 28 1 ; CT-CT-HC # CHARMM 22 parameter file + 30 27 29 1 ; CT-CT-HC # CHARMM 22 parameter file + 17 27 28 1 ; CT-CT-HC # CHARMM 22 parameter file + 17 27 29 1 ; CT-CT-HC # CHARMM 22 parameter file + 28 27 29 1 ; HC-CT-HC # CHARMM 22 parameter file + 27 17 18 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 27 17 19 1 ; CT-CT-HC # CHARMM 22 parameter file + 27 17 20 1 ; CT-CT-HC # CHARMM 22 parameter file + 18 17 19 1 ; CA-CT-HC # + 18 17 20 1 ; CA-CT-HC # + 19 17 20 1 ; HC-CT-HC # CHARMM 22 parameter file + 17 18 39 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 17 18 31 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 31 18 39 1 ; CA-CA-CA # PHE(OL) + 18 31 33 1 ; CA-CA-CA # PHE(OL) + 18 31 32 1 ; CA-CA-HA # + 33 31 32 1 ; CA-CA-HA # + 31 33 35 1 ; CA-CA-CA # PHE(OL) + 31 33 34 1 ; CA-CA-HA # + 35 33 34 1 ; CA-CA-HA # + 33 35 37 1 ; CA-CA-CA # PHE(OL) + 33 35 36 1 ; CA-CA-HA # + 37 35 36 1 ; CA-CA-HA # + 35 37 39 1 ; CA-CA-CA # PHE(OL) + 35 37 38 1 ; CA-CA-HA # + 39 37 38 1 ; CA-CA-HA # + 18 39 37 1 ; CA-CA-CA # PHE(OL) + 18 39 40 1 ; CA-CA-HA # + 37 39 40 1 ; CA-CA-HA # + 2 3 10 1 ; SY-N-CT # + 2 3 6 1 ; SY-N-CT # + 10 3 6 1 ; CT-N-CT # PRO(OL) DETAR JACS 99,1232 + 3 10 11 1 ; N-CT-HC # (HC-CT-N) + 3 10 12 1 ; N-CT-HC # (HC-CT-N) + 3 10 13 1 ; N-CT-HC # (HC-CT-N) + 11 10 12 1 ; HC-CT-HC # CHARMM 22 parameter file + 11 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 12 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 3 6 7 1 ; N-CT-HC # (HC-CT-N) + 3 6 8 1 ; N-CT-HC # (HC-CT-N) + 3 6 9 1 ; N-CT-HC # (HC-CT-N) + 7 6 8 1 ; HC-CT-HC # CHARMM 22 parameter file + 7 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + 8 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 5 30 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 5 41 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 5 30 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 3 2 5 41 3 -15.611 0.703 20.506 -5.598 -0.000 0.000 ; N-SY-N-H # LigParGen + 4 2 5 30 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 5 41 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 5 2 3 10 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 5 2 3 6 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 4 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 5 30 24 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 30 21 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 2 5 30 27 3 ; SY-N-CT-CT # (CT-CT-N-SY) sulfonamide + 41 5 30 24 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 41 5 30 21 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 41 5 30 27 3 ; H-N-CT-CT # (CT-CT-N-H) N-ethylformamide, peptides + 5 30 24 14 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-SY2 # by analogy from N-CT-CT-CT + 5 30 24 25 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 30 24 26 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 21 30 24 14 3 ; CT-CT-CT-SY2 # + 21 30 24 25 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 21 30 24 26 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 27 30 24 14 3 ; CT-CT-CT-SY2 # + 27 30 24 25 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 27 30 24 26 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 30 21 14 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-CT-CT-SY2 # by analogy from N-CT-CT-CT + 5 30 21 22 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 30 21 23 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 24 30 21 14 3 ; CT-CT-CT-SY2 # + 24 30 21 22 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 24 30 21 23 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 27 30 21 14 3 ; CT-CT-CT-SY2 # + 27 30 21 22 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 27 30 21 23 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 5 30 27 17 3 ; N-CT-CT-CT # (CT-CT-CT-N) N-propylformamide + 5 30 27 28 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 5 30 27 29 3 ; N-CT-CT-HC # (HC-CT-CT-N) N-ethylformamide + 24 30 27 17 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 24 30 27 28 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 24 30 27 29 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 21 30 27 17 3 ; CT-CT-CT-CT # hydrocarbon all-atom + 21 30 27 28 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 21 30 27 29 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 30 21 14 24 3 ; CT-CT-SY2-CT # sulfone + 30 21 14 15 3 ; CT-CT-SY2-OY # sulfone + 30 21 14 16 3 ; CT-CT-SY2-OY # sulfone + 22 21 14 24 3 ; HC-CT-SY2-CT # (CT-SY2-CT-HC) sulfone + 22 21 14 15 3 ; HC-CT-SY2-OY # sulfone + 22 21 14 16 3 ; HC-CT-SY2-OY # sulfone + 23 21 14 24 3 ; HC-CT-SY2-CT # (CT-SY2-CT-HC) sulfone + 23 21 14 15 3 ; HC-CT-SY2-OY # sulfone + 23 21 14 16 3 ; HC-CT-SY2-OY # sulfone + 21 14 24 30 3 ; CT-SY2-CT-CT # (CT-CT-SY2-CT) sulfone + 21 14 24 25 3 ; CT-SY2-CT-HC # sulfone + 21 14 24 26 3 ; CT-SY2-CT-HC # sulfone + 15 14 24 30 3 ; OY-SY2-CT-CT # (CT-CT-SY2-OY) sulfone + 15 14 24 25 3 ; OY-SY2-CT-HC # (HC-CT-SY2-OY) sulfone + 15 14 24 26 3 ; OY-SY2-CT-HC # (HC-CT-SY2-OY) sulfone + 16 14 24 30 3 ; OY-SY2-CT-CT # (CT-CT-SY2-OY) sulfone + 16 14 24 25 3 ; OY-SY2-CT-HC # (HC-CT-SY2-OY) sulfone + 16 14 24 26 3 ; OY-SY2-CT-HC # (HC-CT-SY2-OY) sulfone + 30 27 17 18 3 ; CT-CT-CT-CA # (CA-CT-CT-CT) + 30 27 17 19 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 30 27 17 20 3 ; CT-CT-CT-HC # hydrocarbon all-atom + 28 27 17 18 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 28 27 17 19 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 28 27 17 20 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 29 27 17 18 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 29 27 17 19 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 29 27 17 20 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 27 17 18 39 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 27 17 18 31 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 19 17 18 39 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 19 17 18 31 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 20 17 18 39 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 20 17 18 31 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 17 18 39 37 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 18 39 40 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 18 39 37 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 18 39 40 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 18 31 33 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 18 31 32 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 39 18 31 33 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 39 18 31 32 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 31 33 35 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 31 33 34 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 31 33 35 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 31 33 34 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 33 35 37 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 33 35 36 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 33 35 37 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 34 33 35 36 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 35 37 39 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 33 35 37 38 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 36 35 37 39 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 36 35 37 38 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 35 37 39 18 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 35 37 39 40 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 38 37 39 18 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 38 37 39 40 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 10 11 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 12 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 13 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 6 3 10 11 3 ; CT-N-CT-HC # tert. amide + 6 3 10 12 3 ; CT-N-CT-HC # tert. amide + 6 3 10 13 3 ; CT-N-CT-HC # tert. amide + 2 3 6 7 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 8 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 9 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 10 3 6 7 3 ; CT-N-CT-HC # tert. amide + 10 3 6 8 3 ; CT-N-CT-HC # tert. amide + 10 3 6 9 3 ; CT-N-CT-HC # tert. amide + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 2 41 5 30 1 improper_Z_N_X_Y ; SY-H-N-CT + 39 31 18 17 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 33 32 31 18 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 35 34 33 31 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 37 36 35 33 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 39 38 37 35 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 37 40 39 18 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 2 6 3 10 1 improper_Z_N_X_Y ; SY-CT-N-CT + +[ pairs ] +; ai aj funct + 1 30 1 + 1 41 1 + 1 10 1 + 1 6 1 + 2 24 1 + 2 21 1 + 2 27 1 + 2 11 1 + 2 12 1 + 2 13 1 + 2 7 1 + 2 8 1 + 2 9 1 + 5 10 1 + 5 6 1 + 5 14 1 + 5 25 1 + 5 26 1 + 5 22 1 + 5 23 1 + 5 17 1 + 5 28 1 + 5 29 1 + 30 3 1 + 30 4 1 + 30 15 1 + 30 16 1 + 30 18 1 + 30 19 1 + 30 20 1 + 21 41 1 + 21 25 1 + 21 26 1 + 21 17 1 + 21 28 1 + 21 29 1 + 14 27 1 + 24 41 1 + 24 22 1 + 24 23 1 + 24 17 1 + 24 28 1 + 24 29 1 + 15 22 1 + 15 23 1 + 15 25 1 + 15 26 1 + 16 22 1 + 16 23 1 + 16 25 1 + 16 26 1 + 27 41 1 + 27 25 1 + 27 26 1 + 27 22 1 + 27 23 1 + 27 39 1 + 27 31 1 + 17 37 1 + 17 40 1 + 17 33 1 + 17 32 1 + 18 28 1 + 18 29 1 + 18 35 1 + 18 38 1 + 18 34 1 + 31 19 1 + 31 20 1 + 31 37 1 + 31 40 1 + 31 36 1 + 33 39 1 + 33 38 1 + 35 32 1 + 35 40 1 + 37 34 1 + 39 19 1 + 39 20 1 + 39 32 1 + 39 36 1 + 3 41 1 + 10 4 1 + 10 7 1 + 10 8 1 + 10 9 1 + 6 4 1 + 6 11 1 + 6 12 1 + 6 13 1 + 4 41 1 + 28 19 1 + 28 20 1 + 29 19 1 + 29 20 1 + 32 34 1 + 34 36 1 + 36 38 1 + 38 40 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 5 1 1000 1000 1000 + 30 1 1000 1000 1000 + 21 1 1000 1000 1000 + 14 1 1000 1000 1000 + 24 1 1000 1000 1000 + 15 1 1000 1000 1000 + 16 1 1000 1000 1000 + 27 1 1000 1000 1000 + 17 1 1000 1000 1000 + 18 1 1000 1000 1000 + 31 1 1000 1000 1000 + 33 1 1000 1000 1000 + 35 1 1000 1000 1000 + 37 1 1000 1000 1000 + 39 1 1000 1000 1000 + 3 1 1000 1000 1000 + 10 1 1000 1000 1000 + 6 1 1000 1000 1000 + 4 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM40/SM40.mol2.1.pdb b/top/oplsaa/SM40/SM40.mol2.1.pdb new file mode 100644 index 0000000..d56dd0c --- /dev/null +++ b/top/oplsaa/SM40/SM40.mol2.1.pdb @@ -0,0 +1,42 @@ +HETATM 1 O1 UNK 1 -0.975 -1.888 -1.899 1.00 20.00 +HETATM 2 S2 UNK 1 -0.678 -0.498 -1.895 1.00 20.00 +HETATM 3 N18 UNK 1 0.620 -0.294 -2.904 1.00 20.00 +HETATM 4 O21 UNK 1 -1.624 0.500 -2.252 1.00 20.00 +HETATM 5 N3 UNK 1 -0.169 -0.134 -0.362 1.00 20.00 +HETATM 6 C20 UNK 1 0.757 0.942 -3.679 1.00 20.00 +HETATM 7 H39 UNK 1 1.382 1.647 -3.131 1.00 20.00 +HETATM 8 H40 UNK 1 1.220 0.718 -4.640 1.00 20.00 +HETATM 9 H41 UNK 1 -0.227 1.380 -3.842 1.00 20.00 +HETATM 10 C19 UNK 1 1.630 -1.348 -3.020 1.00 20.00 +HETATM 11 H36 UNK 1 1.349 -2.034 -3.820 1.00 20.00 +HETATM 12 H37 UNK 1 2.597 -0.901 -3.249 1.00 20.00 +HETATM 13 H38 UNK 1 1.696 -1.895 -2.079 1.00 20.00 +HETATM 14 S6 UNK 1 -0.097 3.373 0.814 1.00 20.00 +HETATM 15 O8 UNK 1 1.173 3.987 0.637 1.00 20.00 +HETATM 16 O9 UNK 1 -1.202 4.060 1.384 1.00 20.00 +HETATM 17 C11 UNK 1 2.643 0.304 0.234 1.00 20.00 +HETATM 18 C12 UNK 1 4.103 0.556 -0.040 1.00 20.00 +HETATM 19 H29 UNK 1 2.466 0.327 1.310 1.00 20.00 +HETATM 20 H30 UNK 1 2.363 -0.673 -0.159 1.00 20.00 +HETATM 21 C5 UNK 1 0.030 1.652 1.377 1.00 20.00 +HETATM 22 H23 UNK 1 -0.911 1.256 1.759 1.00 20.00 +HETATM 23 H24 UNK 1 0.861 1.485 2.062 1.00 20.00 +HETATM 24 C7 UNK 1 -0.570 2.324 -0.589 1.00 20.00 +HETATM 25 H25 UNK 1 -0.241 2.719 -1.550 1.00 20.00 +HETATM 26 H26 UNK 1 -1.627 2.057 -0.587 1.00 20.00 +HETATM 27 C10 UNK 1 1.802 1.387 -0.444 1.00 20.00 +HETATM 28 H27 UNK 1 1.905 1.303 -1.525 1.00 20.00 +HETATM 29 H28 UNK 1 2.146 2.370 -0.121 1.00 20.00 +HETATM 30 C4 UNK 1 0.332 1.209 -0.056 1.00 20.00 +HETATM 31 C13 UNK 1 4.705 -0.005 -1.151 1.00 20.00 +HETATM 32 H31 UNK 1 4.128 -0.624 -1.822 1.00 20.00 +HETATM 33 C14 UNK 1 6.043 0.231 -1.406 1.00 20.00 +HETATM 34 H32 UNK 1 6.512 -0.204 -2.276 1.00 20.00 +HETATM 35 C15 UNK 1 6.782 1.019 -0.544 1.00 20.00 +HETATM 36 H33 UNK 1 7.828 1.200 -0.740 1.00 20.00 +HETATM 37 C16 UNK 1 6.181 1.576 0.570 1.00 20.00 +HETATM 38 H34 UNK 1 6.759 2.192 1.244 1.00 20.00 +HETATM 39 C17 UNK 1 4.842 1.345 0.822 1.00 20.00 +HETATM 40 H35 UNK 1 4.373 1.780 1.692 1.00 20.00 +HETATM 41 H22 UNK 1 -0.203 -0.809 0.334 1.00 20.00 +END diff --git a/top/oplsaa/SM40/SM40.pdb b/top/oplsaa/SM40/SM40.pdb new file mode 120000 index 0000000..a28712d --- /dev/null +++ b/top/oplsaa/SM40/SM40.pdb @@ -0,0 +1 @@ +SM40.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM41/SM41.itp b/top/oplsaa/SM41/SM41.itp new file mode 120000 index 0000000..0e6dc5b --- /dev/null +++ b/top/oplsaa/SM41/SM41.itp @@ -0,0 +1 @@ +SM41.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM41/SM41.mol2 b/top/oplsaa/SM41/SM41.mol2 new file mode 100644 index 0000000..9f4054f --- /dev/null +++ b/top/oplsaa/SM41/SM41.mol2 @@ -0,0 +1,74 @@ +# Name: SM41 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 26 27 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -2.4342 0.7435 0.0434 O.2 + 2 S2 -1.4563 1.7742 0.0186 S.o2 + 3 N3 -0.0111 0.9658 0.0074 N.am + 4 C4 1.1844 1.6779 -0.0002 C.2 + 5 N5 1.3219 2.9792 0.0059 N.2 + 6 O6 2.4853 3.3075 -0.0032 O.3 + 7 C7 3.3026 2.2389 -0.0169 C.2 + 8 C8 4.7812 2.2538 -0.0308 C.ar + 9 C9 5.4940 1.0541 -0.0379 C.ar + 10 C10 6.8734 1.0750 -0.0552 C.ar + 11 C11 7.5501 2.2818 -0.0557 C.ar + 12 C12 6.8493 3.4746 -0.0433 C.ar + 13 C13 5.4698 3.4676 -0.0309 C.ar + 14 C14 2.4948 1.1375 -0.0099 C.2 + 15 C15 -1.4964 2.6518 -1.5685 C.3 + 16 O16 -1.3346 2.6947 1.0943 O.2 + 17 H17 0.0021 -0.0041 0.0020 H + 18 H18 4.9670 0.1115 -0.0337 H + 19 H19 7.4263 0.1473 -0.0645 H + 20 H20 8.6300 2.2926 -0.0654 H + 21 H21 7.3834 4.4133 -0.0438 H + 22 H22 4.9239 4.3995 -0.0216 H + 23 H23 2.7864 0.0976 -0.0129 H + 24 H24 -1.4399 1.9306 -2.3839 H + 25 H25 -2.4248 3.2175 -1.6475 H + 26 H26 -0.6488 3.3344 -1.6278 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 1 + 4 2 16 2 + 5 3 4 1 + 6 3 17 1 + 7 4 14 1 + 8 4 5 2 + 9 5 6 1 + 10 6 7 1 + 11 7 8 1 + 12 7 14 2 + 13 8 13 ar + 14 8 9 ar + 15 9 10 ar + 16 9 18 1 + 17 10 11 ar + 18 10 19 1 + 19 11 12 ar + 20 11 20 1 + 21 12 13 ar + 22 12 21 1 + 23 13 22 1 + 24 14 23 1 + 25 15 24 1 + 26 15 25 1 + 27 15 26 1 + +# End of record + diff --git a/top/oplsaa/SM41/SM41.mol2.1.itp b/top/oplsaa/SM41/SM41.mol2.1.itp new file mode 100644 index 0000000..b54ecc7 --- /dev/null +++ b/top/oplsaa/SM41/SM41.mol2.1.itp @@ -0,0 +1,267 @@ +; input pdb SMILES : O=[S](NC1=NOC(=C1)C2=CC=CC=C2)(C)=O +; Script arguments : SM41.mol2 "4 opls_581 0.728" "7 opls_583 0.348" "8 opls_147" "3 opls_480" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 2 opls_474 1 UNK S2 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 3 opls_475 1 UNK O16 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 4 opls_476 1 UNK C15 3 -0.540 12.01100 ; CT # CH3 attached to S of sulfonamide + 5 opls_477 1 UNK H24 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 6 opls_477 1 UNK H25 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 7 opls_477 1 UNK H26 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 8 opls_480 1 UNK N3 15 -0.800 14.00670 ; N # N secondary amide of sulfonamide ### user-defined OPLS atom type (opls_480) + 9 opls_581 1 UNK C4 15 0.728 12.01100 ; CU # C3 in isoxazole ### user-defined OPLS atom type (opls_581) atom charge (0.728) + 10 opls_481 1 UNK H17 15 0.410 1.00800 ; H # H on N: secondary sulfonamide + 11 opls_582 1 UNK C14 17 -0.455 12.01100 ; CA # C4 in isoxazole + 12 opls_585 1 UNK H23 17 0.184 1.00800 ; HA # H4 in isoxazole + 13 opls_583 1 UNK C7 19 0.348 12.01100 ; CW # C5 in isoxazole ### user-defined OPLS atom type (opls_583) atom charge (0.348) + 14 opls_147 1 UNK C8 19 0.000 12.01100 ; CA # Naphthalene fusion C (C9) ### user-defined OPLS atom type (opls_147) + 15 opls_580 1 UNK N5 20 -0.413 14.00670 ; NB # N in isoxazole + 16 opls_579 1 UNK O6 20 -0.122 15.99940 ; OS # O in isoxazole + 17 opls_145 1 UNK C9 27 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 18 opls_146 1 UNK H18 27 0.115 1.00800 ; HA # Benzene H - 12 site. + 19 opls_145 1 UNK C10 29 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 20 opls_146 1 UNK H19 29 0.115 1.00800 ; HA # Benzene H - 12 site. + 21 opls_145 1 UNK C11 31 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 22 opls_146 1 UNK H20 31 0.115 1.00800 ; HA # Benzene H - 12 site. + 23 opls_145 1 UNK C12 33 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 24 opls_146 1 UNK H21 33 0.115 1.00800 ; HA # Benzene H - 12 site. + 25 opls_145 1 UNK C13 35 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 26 opls_146 1 UNK H22 35 0.115 1.00800 ; HA # Benzene H - 12 site. +; Total charge : -0.000 ### Number of unassigned atoms : 0/26 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 8 1 ; SY-N # + 2 4 1 ; SY-CT # + 2 3 1 ; SY-OY # + 8 9 1 0.1381 357313.600 ; N-CU # LigParGen + 8 10 1 ; N-H # (H-N) + 9 11 1 ; CU-CA # -idem- + 9 15 1 ; CU-NB # -idem- + 15 16 1 ; NB-OS # (OS-NB) -idem- + 16 13 1 ; OS-CW # (CW-OS) Furan - wlj 4/97 + 13 14 1 ; CW-CA # (CA-CW) pyrrole- wlj + 13 11 1 ; CW-CA # (CA-CW) pyrrole- wlj + 14 25 1 ; CA-CA # TRP,TYR,PHE + 14 17 1 ; CA-CA # TRP,TYR,PHE + 17 19 1 ; CA-CA # TRP,TYR,PHE + 17 18 1 ; CA-HA # PHE, etc. + 19 21 1 ; CA-CA # TRP,TYR,PHE + 19 20 1 ; CA-HA # PHE, etc. + 21 23 1 ; CA-CA # TRP,TYR,PHE + 21 22 1 ; CA-HA # PHE, etc. + 23 25 1 ; CA-CA # TRP,TYR,PHE + 23 24 1 ; CA-HA # PHE, etc. + 25 26 1 ; CA-HA # PHE, etc. + 11 12 1 ; CA-HA # PHE, etc. + 4 5 1 ; CT-HC # CHARMM 22 parameter file + 4 6 1 ; CT-HC # CHARMM 22 parameter file + 4 7 1 ; CT-HC # CHARMM 22 parameter file + +[ angles ] +; ai aj ak funct theta cth + 1 2 8 1 ; OY-SY-N # + 1 2 4 1 ; OY-SY-CT # + 1 2 3 1 ; OY-SY-OY # + 8 2 4 1 ; N-SY-CT # + 8 2 3 1 ; N-SY-OY # (OY-SY-N) + 4 2 3 1 ; CT-SY-OY # (OY-SY-CT) + 2 8 9 1 118.330 404.760 ; SY-N-CU # LigParGen + 2 8 10 1 ; SY-N-H # (H-N-SY) + 9 8 10 1 119.800 292.880 ; CU-N-H # LigParGen + 8 9 11 1 119.440 468.608 ; N-CU-CA # LigParGen + 8 9 15 1 119.440 468.608 ; N-CU-NB # LigParGen + 15 9 11 1 ; NB-CU-CA # -idem- + 9 15 16 1 ; CU-NB-OS # -idem- + 15 16 13 1 ; NB-OS-CW # (CW-OS-NB) -idem- + 16 13 14 1 ; OS-CW-CA # wlj + 16 13 11 1 ; OS-CW-CA # wlj + 14 13 11 1 132.100 585.760 ; CA-CW-CA # LigParGen + 13 14 25 1 ; CW-CA-CA # (CA-CA-CW) wlj 1/97 based on pyrrole + 13 14 17 1 ; CW-CA-CA # (CA-CA-CW) wlj 1/97 based on pyrrole + 17 14 25 1 ; CA-CA-CA # PHE(OL) + 14 17 19 1 ; CA-CA-CA # PHE(OL) + 14 17 18 1 ; CA-CA-HA # + 19 17 18 1 ; CA-CA-HA # + 17 19 21 1 ; CA-CA-CA # PHE(OL) + 17 19 20 1 ; CA-CA-HA # + 21 19 20 1 ; CA-CA-HA # + 19 21 23 1 ; CA-CA-CA # PHE(OL) + 19 21 22 1 ; CA-CA-HA # + 23 21 22 1 ; CA-CA-HA # + 21 23 25 1 ; CA-CA-CA # PHE(OL) + 21 23 24 1 ; CA-CA-HA # + 25 23 24 1 ; CA-CA-HA # + 14 25 23 1 ; CA-CA-CA # PHE(OL) + 14 25 26 1 ; CA-CA-HA # + 23 25 26 1 ; CA-CA-HA # + 9 11 13 1 ; CU-CA-CW # -idem- + 9 11 12 1 ; CU-CA-HA # -idem- + 13 11 12 1 ; CW-CA-HA # (HA-CA-CW) wlj - pyrrole + 2 4 5 1 ; SY-CT-HC # + 2 4 6 1 ; SY-CT-HC # + 2 4 7 1 ; SY-CT-HC # + 5 4 6 1 ; HC-CT-HC # CHARMM 22 parameter file + 5 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + 6 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 8 9 3 ; OY-SY-N-CU # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 8 10 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 8 9 3 -2.897 11.182 12.410 -20.694 -0.000 0.000 ; CT-SY-N-CU # LigParGen + 4 2 8 10 3 ; CT-SY-N-H # sulfonamide + 3 2 8 9 3 ; OY-SY-N-CU # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 8 10 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 4 5 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 1 2 4 6 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 1 2 4 7 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 8 2 4 5 3 ; N-SY-CT-HC # (HC-CT-SY-N) sulfonamide + 8 2 4 6 3 ; N-SY-CT-HC # (HC-CT-SY-N) sulfonamide + 8 2 4 7 3 ; N-SY-CT-HC # (HC-CT-SY-N) sulfonamide + 3 2 4 5 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 3 2 4 6 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 3 2 4 7 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 2 8 9 11 3 -3.431 -3.008 10.598 -4.159 -0.000 0.000 ; SY-N-CU-CA # LigParGen + 2 8 9 15 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; SY-N-CU-NB # LigParGen + 10 8 9 11 3 20.502 0.000 -20.502 -0.000 -0.000 0.000 ; H-N-CU-CA # LigParGen + 10 8 9 15 3 8.786 0.000 -8.786 -0.000 -0.000 0.000 ; H-N-CU-NB # LigParGen + 8 9 11 13 3 ; N-CU-CA-CW # (X-CA-CU-X generic proper dihedral) aromatic ring + 8 9 11 12 3 ; N-CU-CA-HA # (X-CA-CU-X generic proper dihedral) aromatic ring + 15 9 11 13 3 ; NB-CU-CA-CW # (X-CA-CU-X generic proper dihedral) aromatic ring + 15 9 11 12 3 ; NB-CU-CA-HA # (X-CA-CU-X generic proper dihedral) aromatic ring + 8 9 15 16 3 ; N-CU-NB-OS # (X-CU-NB-X generic proper dihedral) aromatic ring + 11 9 15 16 3 ; CA-CU-NB-OS # (X-CU-NB-X generic proper dihedral) aromatic ring + 9 15 16 13 3 ; CU-NB-OS-CW # (X-NB-OS-X generic proper dihedral) aromatic ring isoxazole + 15 16 13 14 3 ; NB-OS-CW-CA # (X-CW-OS-X generic proper dihedral) aromatic ring furan + 15 16 13 11 3 ; NB-OS-CW-CA # (X-CW-OS-X generic proper dihedral) aromatic ring furan + 16 13 14 25 3 ; OS-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 16 13 14 17 3 ; OS-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 11 13 14 25 3 ; CA-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 11 13 14 17 3 ; CA-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 16 13 11 9 3 ; OS-CW-CA-CU # (X-CA-CW-X generic proper dihedral) aromatic ring + 16 13 11 12 3 ; OS-CW-CA-HA # (X-CA-CW-X generic proper dihedral) aromatic ring + 14 13 11 9 3 ; CA-CW-CA-CU # (X-CA-CW-X generic proper dihedral) aromatic ring + 14 13 11 12 3 ; CA-CW-CA-HA # (X-CA-CW-X generic proper dihedral) aromatic ring + 13 14 25 23 3 ; CW-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 13 14 25 26 3 ; CW-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 14 25 23 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 14 25 26 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 13 14 17 19 3 ; CW-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 13 14 17 18 3 ; CW-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 14 17 19 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 14 17 18 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 17 19 21 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 17 19 20 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 17 19 21 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 17 19 20 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 19 21 23 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 19 21 22 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 20 19 21 23 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 20 19 21 22 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 21 23 25 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 21 23 24 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 21 23 25 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 21 23 24 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 23 25 14 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 23 25 26 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 14 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 26 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 9 10 8 2 1 improper_Z_N_X_Y ; CU-H-N-SY + 11 15 9 8 1 improper_N2_X_N2_N2 ; CA-NB-CU-N + 16 14 13 11 1 improper_Z_CM_X_Y ; OS-CA-CW-CA + 25 17 14 13 1 improper_Z_CA_X_Y ; CA-CA-CA-CW + 19 18 17 14 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 21 20 19 17 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 23 22 21 19 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 25 24 23 21 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 23 26 25 14 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 13 12 11 9 1 improper_Z_CM_X_Y ; CW-HA-CA-CU + +[ pairs ] +; ai aj funct + 1 9 1 + 1 10 1 + 1 5 1 + 1 6 1 + 1 7 1 + 2 11 1 + 2 15 1 + 8 5 1 + 8 6 1 + 8 7 1 + 8 13 1 + 8 12 1 + 8 16 1 + 9 4 1 + 9 3 1 + 9 14 1 + 15 10 1 + 15 12 1 + 15 14 1 + 16 25 1 + 16 17 1 + 16 12 1 + 13 23 1 + 13 26 1 + 13 19 1 + 13 18 1 + 14 12 1 + 14 21 1 + 14 24 1 + 14 20 1 + 17 11 1 + 17 23 1 + 17 26 1 + 17 22 1 + 19 25 1 + 19 24 1 + 21 18 1 + 21 26 1 + 23 20 1 + 25 11 1 + 25 18 1 + 25 22 1 + 11 10 1 + 4 10 1 + 3 10 1 + 3 5 1 + 3 6 1 + 3 7 1 + 18 20 1 + 20 22 1 + 22 24 1 + 24 26 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 8 1 1000 1000 1000 + 9 1 1000 1000 1000 + 15 1 1000 1000 1000 + 16 1 1000 1000 1000 + 13 1 1000 1000 1000 + 14 1 1000 1000 1000 + 17 1 1000 1000 1000 + 19 1 1000 1000 1000 + 21 1 1000 1000 1000 + 23 1 1000 1000 1000 + 25 1 1000 1000 1000 + 11 1 1000 1000 1000 + 4 1 1000 1000 1000 + 3 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM41/SM41.mol2.1.pdb b/top/oplsaa/SM41/SM41.mol2.1.pdb new file mode 100644 index 0000000..d03d3d4 --- /dev/null +++ b/top/oplsaa/SM41/SM41.mol2.1.pdb @@ -0,0 +1,27 @@ +HETATM 1 O1 UNK 1 -2.434 0.744 0.043 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 O16 UNK 1 -1.335 2.695 1.094 1.00 20.00 +HETATM 4 C15 UNK 1 -1.496 2.652 -1.569 1.00 20.00 +HETATM 5 H24 UNK 1 -1.440 1.931 -2.384 1.00 20.00 +HETATM 6 H25 UNK 1 -2.425 3.217 -1.647 1.00 20.00 +HETATM 7 H26 UNK 1 -0.649 3.334 -1.628 1.00 20.00 +HETATM 8 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 9 C4 UNK 1 1.184 1.678 -0.000 1.00 20.00 +HETATM 10 H17 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 11 C14 UNK 1 2.495 1.137 -0.010 1.00 20.00 +HETATM 12 H23 UNK 1 2.786 0.098 -0.013 1.00 20.00 +HETATM 13 C7 UNK 1 3.303 2.239 -0.017 1.00 20.00 +HETATM 14 C8 UNK 1 4.781 2.254 -0.031 1.00 20.00 +HETATM 15 N5 UNK 1 1.322 2.979 0.006 1.00 20.00 +HETATM 16 O6 UNK 1 2.485 3.308 -0.003 1.00 20.00 +HETATM 17 C9 UNK 1 5.494 1.054 -0.038 1.00 20.00 +HETATM 18 H18 UNK 1 4.967 0.112 -0.034 1.00 20.00 +HETATM 19 C10 UNK 1 6.873 1.075 -0.055 1.00 20.00 +HETATM 20 H19 UNK 1 7.426 0.147 -0.065 1.00 20.00 +HETATM 21 C11 UNK 1 7.550 2.282 -0.056 1.00 20.00 +HETATM 22 H20 UNK 1 8.630 2.293 -0.065 1.00 20.00 +HETATM 23 C12 UNK 1 6.849 3.475 -0.043 1.00 20.00 +HETATM 24 H21 UNK 1 7.383 4.413 -0.044 1.00 20.00 +HETATM 25 C13 UNK 1 5.470 3.468 -0.031 1.00 20.00 +HETATM 26 H22 UNK 1 4.924 4.399 -0.022 1.00 20.00 +END diff --git a/top/oplsaa/SM41/SM41.pdb b/top/oplsaa/SM41/SM41.pdb new file mode 120000 index 0000000..57f927b --- /dev/null +++ b/top/oplsaa/SM41/SM41.pdb @@ -0,0 +1 @@ +SM41.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM42/SM42.itp b/top/oplsaa/SM42/SM42.itp new file mode 120000 index 0000000..36ddff1 --- /dev/null +++ b/top/oplsaa/SM42/SM42.itp @@ -0,0 +1 @@ +SM42.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM42/SM42.mol2 b/top/oplsaa/SM42/SM42.mol2 new file mode 100644 index 0000000..57f0bc8 --- /dev/null +++ b/top/oplsaa/SM42/SM42.mol2 @@ -0,0 +1,89 @@ +# Name: SM42 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 33 35 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 1.1325 -2.1978 0.0147 O.2 + 2 S2 1.4473 -0.8125 -0.0155 S.o2 + 3 N3 0.0021 -0.0041 0.0020 N.am + 4 C4 -0.0168 1.3873 0.0097 C.2 + 5 N5 1.0201 2.1855 0.0041 N.2 + 6 O6 0.6910 3.3487 0.0135 O.3 + 7 C7 -0.6473 3.4859 0.0270 C.2 + 8 C8 -1.4084 4.7536 0.0406 C.ar + 9 C9 -2.8037 4.7332 0.0476 C.ar + 10 C10 -3.5079 5.9195 0.0662 C.ar + 11 C11 -2.8337 7.1276 0.0668 C.ar + 12 C12 -1.4505 7.1548 0.0537 C.ar + 13 C13 -0.7344 5.9756 0.0408 C.ar + 14 C14 -1.1631 2.2211 0.0189 C.2 + 15 C15 2.2636 -0.4545 1.5044 C.ar + 16 C16 3.1132 0.6323 1.5934 C.ar + 17 C17 3.7499 0.9159 2.7872 C.ar + 18 C18 3.5451 0.1067 3.8890 C.ar + 19 C19 2.6995 -0.9831 3.7986 C.ar + 20 C20 2.0587 -1.2637 2.6063 C.ar + 21 O21 2.2287 -0.2152 -1.0411 O.2 + 22 H22 -0.8313 -0.5004 0.0069 H + 23 H23 -3.3312 3.7908 0.0430 H + 24 H24 -4.5877 5.9051 0.0765 H + 25 H25 -3.3895 8.0535 0.0772 H + 26 H26 -0.9301 8.1012 0.0538 H + 27 H27 0.3453 5.9981 0.0313 H + 28 H28 -2.2018 1.9253 0.0212 H + 29 H29 3.2767 1.2619 0.7313 H + 30 H30 4.4108 1.7671 2.8577 H + 31 H31 4.0459 0.3257 4.8205 H + 32 H32 2.5397 -1.6156 4.6593 H + 33 H33 1.3983 -2.1154 2.5355 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 1 + 4 2 21 2 + 5 3 4 1 + 6 3 22 1 + 7 4 14 1 + 8 4 5 2 + 9 5 6 1 + 10 6 7 1 + 11 7 8 1 + 12 7 14 2 + 13 8 13 ar + 14 8 9 ar + 15 9 10 ar + 16 9 23 1 + 17 10 11 ar + 18 10 24 1 + 19 11 12 ar + 20 11 25 1 + 21 12 13 ar + 22 12 26 1 + 23 13 27 1 + 24 14 28 1 + 25 15 20 ar + 26 15 16 ar + 27 16 17 ar + 28 16 29 1 + 29 17 18 ar + 30 17 30 1 + 31 18 19 ar + 32 18 31 1 + 33 19 20 ar + 34 19 32 1 + 35 20 33 1 + +# End of record + diff --git a/top/oplsaa/SM42/SM42.mol2.1.itp b/top/oplsaa/SM42/SM42.mol2.1.itp new file mode 100644 index 0000000..f48804c --- /dev/null +++ b/top/oplsaa/SM42/SM42.mol2.1.itp @@ -0,0 +1,344 @@ +; input pdb SMILES : O=[S](NC1=NOC(=C1)C2=CC=CC=C2)(C3=CC=CC=C3)=O +; Script arguments : SM42.mol2 "4 opls_581 0.728" "7 opls_583 0.348" "8 opls_147" "15 opls_147" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 2 opls_474 1 UNK S2 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 3 opls_147 1 UNK C15 1 0.000 12.01100 ; CA # Naphthalene fusion C (C9) ### user-defined OPLS atom type (opls_147) + 4 opls_475 1 UNK O21 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 5 opls_480 1 UNK N3 3 -0.800 14.00670 ; N # N secondary amide of sulfonamide + 6 opls_581 1 UNK C4 3 0.728 12.01100 ; CU # C3 in isoxazole ### user-defined OPLS atom type (opls_581) atom charge (0.728) + 7 opls_481 1 UNK H22 3 0.410 1.00800 ; H # H on N: secondary sulfonamide + 8 opls_582 1 UNK C14 5 -0.455 12.01100 ; CA # C4 in isoxazole + 9 opls_585 1 UNK H28 5 0.184 1.00800 ; HA # H4 in isoxazole + 10 opls_583 1 UNK C7 7 0.348 12.01100 ; CW # C5 in isoxazole ### user-defined OPLS atom type (opls_583) atom charge (0.348) + 11 opls_147 1 UNK C8 7 0.000 12.01100 ; CA # Naphthalene fusion C (C9) ### user-defined OPLS atom type (opls_147) + 12 opls_580 1 UNK N5 8 -0.413 14.00670 ; NB # N in isoxazole + 13 opls_579 1 UNK O6 8 -0.122 15.99940 ; OS # O in isoxazole + 14 opls_145 1 UNK C9 9 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 15 opls_146 1 UNK H23 9 0.115 1.00800 ; HA # Benzene H - 12 site. + 16 opls_145 1 UNK C10 11 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 17 opls_146 1 UNK H24 11 0.115 1.00800 ; HA # Benzene H - 12 site. + 18 opls_145 1 UNK C11 13 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 19 opls_146 1 UNK H25 13 0.115 1.00800 ; HA # Benzene H - 12 site. + 20 opls_145 1 UNK C12 15 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 21 opls_146 1 UNK H26 15 0.115 1.00800 ; HA # Benzene H - 12 site. + 22 opls_145 1 UNK C13 17 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 23 opls_146 1 UNK H27 17 0.115 1.00800 ; HA # Benzene H - 12 site. + 24 opls_145 1 UNK C16 19 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 25 opls_146 1 UNK H29 19 0.115 1.00800 ; HA # Benzene H - 12 site. + 26 opls_145 1 UNK C17 21 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 27 opls_146 1 UNK H30 21 0.115 1.00800 ; HA # Benzene H - 12 site. + 28 opls_145 1 UNK C18 23 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 29 opls_146 1 UNK H31 23 0.115 1.00800 ; HA # Benzene H - 12 site. + 30 opls_145 1 UNK C19 25 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 31 opls_146 1 UNK H32 25 0.115 1.00800 ; HA # Benzene H - 12 site. + 32 opls_145 1 UNK C20 27 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 33 opls_146 1 UNK H33 27 0.115 1.00800 ; HA # Benzene H - 12 site. +; Total charge : -0.000 ### Number of unassigned atoms : 0/33 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 5 1 ; SY-N # + 2 3 1 ; SY-CA # + 2 4 1 ; SY-OY # + 5 6 1 0.1381 357313.600 ; N-CU # LigParGen + 5 7 1 ; N-H # (H-N) + 6 8 1 ; CU-CA # -idem- + 6 12 1 ; CU-NB # -idem- + 12 13 1 ; NB-OS # (OS-NB) -idem- + 13 10 1 ; OS-CW # (CW-OS) Furan - wlj 4/97 + 10 11 1 ; CW-CA # (CA-CW) pyrrole- wlj + 10 8 1 ; CW-CA # (CA-CW) pyrrole- wlj + 11 22 1 ; CA-CA # TRP,TYR,PHE + 11 14 1 ; CA-CA # TRP,TYR,PHE + 14 16 1 ; CA-CA # TRP,TYR,PHE + 14 15 1 ; CA-HA # PHE, etc. + 16 18 1 ; CA-CA # TRP,TYR,PHE + 16 17 1 ; CA-HA # PHE, etc. + 18 20 1 ; CA-CA # TRP,TYR,PHE + 18 19 1 ; CA-HA # PHE, etc. + 20 22 1 ; CA-CA # TRP,TYR,PHE + 20 21 1 ; CA-HA # PHE, etc. + 22 23 1 ; CA-HA # PHE, etc. + 8 9 1 ; CA-HA # PHE, etc. + 3 32 1 ; CA-CA # TRP,TYR,PHE + 3 24 1 ; CA-CA # TRP,TYR,PHE + 24 26 1 ; CA-CA # TRP,TYR,PHE + 24 25 1 ; CA-HA # PHE, etc. + 26 28 1 ; CA-CA # TRP,TYR,PHE + 26 27 1 ; CA-HA # PHE, etc. + 28 30 1 ; CA-CA # TRP,TYR,PHE + 28 29 1 ; CA-HA # PHE, etc. + 30 32 1 ; CA-CA # TRP,TYR,PHE + 30 31 1 ; CA-HA # PHE, etc. + 32 33 1 ; CA-HA # PHE, etc. + +[ angles ] +; ai aj ak funct theta cth + 1 2 5 1 ; OY-SY-N # + 1 2 3 1 ; OY-SY-CA # + 1 2 4 1 ; OY-SY-OY # + 5 2 3 1 ; N-SY-CA # + 5 2 4 1 ; N-SY-OY # (OY-SY-N) + 3 2 4 1 ; CA-SY-OY # (OY-SY-CA) + 2 5 6 1 118.330 404.760 ; SY-N-CU # LigParGen + 2 5 7 1 ; SY-N-H # (H-N-SY) + 6 5 7 1 119.800 292.880 ; CU-N-H # LigParGen + 5 6 8 1 119.440 468.608 ; N-CU-CA # LigParGen + 5 6 12 1 119.440 468.608 ; N-CU-NB # LigParGen + 12 6 8 1 ; NB-CU-CA # -idem- + 6 12 13 1 ; CU-NB-OS # -idem- + 12 13 10 1 ; NB-OS-CW # (CW-OS-NB) -idem- + 13 10 11 1 ; OS-CW-CA # wlj + 13 10 8 1 ; OS-CW-CA # wlj + 11 10 8 1 132.100 585.760 ; CA-CW-CA # LigParGen + 10 11 22 1 ; CW-CA-CA # (CA-CA-CW) wlj 1/97 based on pyrrole + 10 11 14 1 ; CW-CA-CA # (CA-CA-CW) wlj 1/97 based on pyrrole + 14 11 22 1 ; CA-CA-CA # PHE(OL) + 11 14 16 1 ; CA-CA-CA # PHE(OL) + 11 14 15 1 ; CA-CA-HA # + 16 14 15 1 ; CA-CA-HA # + 14 16 18 1 ; CA-CA-CA # PHE(OL) + 14 16 17 1 ; CA-CA-HA # + 18 16 17 1 ; CA-CA-HA # + 16 18 20 1 ; CA-CA-CA # PHE(OL) + 16 18 19 1 ; CA-CA-HA # + 20 18 19 1 ; CA-CA-HA # + 18 20 22 1 ; CA-CA-CA # PHE(OL) + 18 20 21 1 ; CA-CA-HA # + 22 20 21 1 ; CA-CA-HA # + 11 22 20 1 ; CA-CA-CA # PHE(OL) + 11 22 23 1 ; CA-CA-HA # + 20 22 23 1 ; CA-CA-HA # + 6 8 10 1 ; CU-CA-CW # -idem- + 6 8 9 1 ; CU-CA-HA # -idem- + 10 8 9 1 ; CW-CA-HA # (HA-CA-CW) wlj - pyrrole + 2 3 32 1 ; SY-CA-CA # + 2 3 24 1 ; SY-CA-CA # + 24 3 32 1 ; CA-CA-CA # PHE(OL) + 3 24 26 1 ; CA-CA-CA # PHE(OL) + 3 24 25 1 ; CA-CA-HA # + 26 24 25 1 ; CA-CA-HA # + 24 26 28 1 ; CA-CA-CA # PHE(OL) + 24 26 27 1 ; CA-CA-HA # + 28 26 27 1 ; CA-CA-HA # + 26 28 30 1 ; CA-CA-CA # PHE(OL) + 26 28 29 1 ; CA-CA-HA # + 30 28 29 1 ; CA-CA-HA # + 28 30 32 1 ; CA-CA-CA # PHE(OL) + 28 30 31 1 ; CA-CA-HA # + 32 30 31 1 ; CA-CA-HA # + 3 32 30 1 ; CA-CA-CA # PHE(OL) + 3 32 33 1 ; CA-CA-HA # + 30 32 33 1 ; CA-CA-HA # + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 5 6 3 ; OY-SY-N-CU # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 5 7 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 5 6 3 -2.897 11.182 12.410 -20.694 -0.000 0.000 ; CA-SY-N-CU # LigParGen + 3 2 5 7 3 ; CA-SY-N-H # sulfonamide + 4 2 5 6 3 ; OY-SY-N-CU # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 5 7 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 32 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 1 2 3 24 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 5 2 3 32 3 ; N-SY-CA-CA # (CA-CA-SY-N) sulfonamide + 5 2 3 24 3 ; N-SY-CA-CA # (CA-CA-SY-N) sulfonamide + 4 2 3 32 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 4 2 3 24 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 2 5 6 8 3 -3.431 -3.008 10.598 -4.159 -0.000 0.000 ; SY-N-CU-CA # LigParGen + 2 5 6 12 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; SY-N-CU-NB # LigParGen + 7 5 6 8 3 20.502 0.000 -20.502 -0.000 -0.000 0.000 ; H-N-CU-CA # LigParGen + 7 5 6 12 3 8.786 0.000 -8.786 -0.000 -0.000 0.000 ; H-N-CU-NB # LigParGen + 5 6 8 10 3 ; N-CU-CA-CW # (X-CA-CU-X generic proper dihedral) aromatic ring + 5 6 8 9 3 ; N-CU-CA-HA # (X-CA-CU-X generic proper dihedral) aromatic ring + 12 6 8 10 3 ; NB-CU-CA-CW # (X-CA-CU-X generic proper dihedral) aromatic ring + 12 6 8 9 3 ; NB-CU-CA-HA # (X-CA-CU-X generic proper dihedral) aromatic ring + 5 6 12 13 3 ; N-CU-NB-OS # (X-CU-NB-X generic proper dihedral) aromatic ring + 8 6 12 13 3 ; CA-CU-NB-OS # (X-CU-NB-X generic proper dihedral) aromatic ring + 6 12 13 10 3 ; CU-NB-OS-CW # (X-NB-OS-X generic proper dihedral) aromatic ring isoxazole + 12 13 10 11 3 ; NB-OS-CW-CA # (X-CW-OS-X generic proper dihedral) aromatic ring furan + 12 13 10 8 3 ; NB-OS-CW-CA # (X-CW-OS-X generic proper dihedral) aromatic ring furan + 13 10 11 22 3 ; OS-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 13 10 11 14 3 ; OS-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 8 10 11 22 3 ; CA-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 8 10 11 14 3 ; CA-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 13 10 8 6 3 ; OS-CW-CA-CU # (X-CA-CW-X generic proper dihedral) aromatic ring + 13 10 8 9 3 ; OS-CW-CA-HA # (X-CA-CW-X generic proper dihedral) aromatic ring + 11 10 8 6 3 ; CA-CW-CA-CU # (X-CA-CW-X generic proper dihedral) aromatic ring + 11 10 8 9 3 ; CA-CW-CA-HA # (X-CA-CW-X generic proper dihedral) aromatic ring + 10 11 22 20 3 ; CW-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 11 22 23 3 ; CW-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 11 22 20 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 11 22 23 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 11 14 16 3 ; CW-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 11 14 15 3 ; CW-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 11 14 16 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 11 14 15 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 14 16 18 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 14 16 17 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 14 16 18 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 14 16 17 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 16 18 20 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 16 18 19 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 16 18 20 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 16 18 19 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 18 20 22 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 18 20 21 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 18 20 22 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 18 20 21 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 20 22 11 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 20 22 23 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 20 22 11 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 20 22 23 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 32 30 3 ; SY-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 32 33 3 ; SY-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 3 32 30 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 3 32 33 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 24 26 3 ; SY-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 24 25 3 ; SY-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 3 24 26 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 32 3 24 25 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 3 24 26 28 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 3 24 26 27 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 24 26 28 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 24 26 27 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 26 28 30 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 26 28 29 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 26 28 30 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 26 28 29 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 28 30 32 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 28 30 31 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 28 30 32 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 28 30 31 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 30 32 3 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 30 32 33 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 30 32 3 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 30 32 33 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 6 7 5 2 1 improper_Z_N_X_Y ; CU-H-N-SY + 8 12 6 5 1 improper_N2_X_N2_N2 ; CA-NB-CU-N + 13 11 10 8 1 improper_Z_CM_X_Y ; OS-CA-CW-CA + 22 14 11 10 1 improper_Z_CA_X_Y ; CA-CA-CA-CW + 16 15 14 11 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 18 17 16 14 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 20 19 18 16 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 22 21 20 18 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 20 23 22 11 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 10 9 8 6 1 improper_Z_CM_X_Y ; CW-HA-CA-CU + 32 24 3 2 1 improper_Z_CA_X_Y ; CA-CA-CA-SY + 26 25 24 3 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 28 27 26 24 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 30 29 28 26 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 32 31 30 28 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 30 33 32 3 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + +[ pairs ] +; ai aj funct + 1 6 1 + 1 7 1 + 1 32 1 + 1 24 1 + 2 8 1 + 2 12 1 + 2 30 1 + 2 33 1 + 2 26 1 + 2 25 1 + 5 32 1 + 5 24 1 + 5 10 1 + 5 9 1 + 5 13 1 + 6 3 1 + 6 4 1 + 6 11 1 + 12 7 1 + 12 9 1 + 12 11 1 + 13 22 1 + 13 14 1 + 13 9 1 + 10 20 1 + 10 23 1 + 10 16 1 + 10 15 1 + 11 9 1 + 11 18 1 + 11 21 1 + 11 17 1 + 14 8 1 + 14 20 1 + 14 23 1 + 14 19 1 + 16 22 1 + 16 21 1 + 18 15 1 + 18 23 1 + 20 17 1 + 22 8 1 + 22 15 1 + 22 19 1 + 8 7 1 + 3 7 1 + 3 28 1 + 3 31 1 + 3 27 1 + 24 4 1 + 24 30 1 + 24 33 1 + 24 29 1 + 26 32 1 + 26 31 1 + 28 25 1 + 28 33 1 + 30 27 1 + 32 4 1 + 32 25 1 + 32 29 1 + 4 7 1 + 15 17 1 + 17 19 1 + 19 21 1 + 21 23 1 + 25 27 1 + 27 29 1 + 29 31 1 + 31 33 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 5 1 1000 1000 1000 + 6 1 1000 1000 1000 + 12 1 1000 1000 1000 + 13 1 1000 1000 1000 + 10 1 1000 1000 1000 + 11 1 1000 1000 1000 + 14 1 1000 1000 1000 + 16 1 1000 1000 1000 + 18 1 1000 1000 1000 + 20 1 1000 1000 1000 + 22 1 1000 1000 1000 + 8 1 1000 1000 1000 + 3 1 1000 1000 1000 + 24 1 1000 1000 1000 + 26 1 1000 1000 1000 + 28 1 1000 1000 1000 + 30 1 1000 1000 1000 + 32 1 1000 1000 1000 + 4 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM42/SM42.mol2.1.pdb b/top/oplsaa/SM42/SM42.mol2.1.pdb new file mode 100644 index 0000000..e030df0 --- /dev/null +++ b/top/oplsaa/SM42/SM42.mol2.1.pdb @@ -0,0 +1,34 @@ +HETATM 1 O1 UNK 1 1.133 -2.198 0.015 1.00 20.00 +HETATM 2 S2 UNK 1 1.447 -0.812 -0.015 1.00 20.00 +HETATM 3 C15 UNK 1 2.264 -0.455 1.504 1.00 20.00 +HETATM 4 O21 UNK 1 2.229 -0.215 -1.041 1.00 20.00 +HETATM 5 N3 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 6 C4 UNK 1 -0.017 1.387 0.010 1.00 20.00 +HETATM 7 H22 UNK 1 -0.831 -0.500 0.007 1.00 20.00 +HETATM 8 C14 UNK 1 -1.163 2.221 0.019 1.00 20.00 +HETATM 9 H28 UNK 1 -2.202 1.925 0.021 1.00 20.00 +HETATM 10 C7 UNK 1 -0.647 3.486 0.027 1.00 20.00 +HETATM 11 C8 UNK 1 -1.408 4.754 0.041 1.00 20.00 +HETATM 12 N5 UNK 1 1.020 2.186 0.004 1.00 20.00 +HETATM 13 O6 UNK 1 0.691 3.349 0.013 1.00 20.00 +HETATM 14 C9 UNK 1 -2.804 4.733 0.048 1.00 20.00 +HETATM 15 H23 UNK 1 -3.331 3.791 0.043 1.00 20.00 +HETATM 16 C10 UNK 1 -3.508 5.920 0.066 1.00 20.00 +HETATM 17 H24 UNK 1 -4.588 5.905 0.076 1.00 20.00 +HETATM 18 C11 UNK 1 -2.834 7.128 0.067 1.00 20.00 +HETATM 19 H25 UNK 1 -3.389 8.053 0.077 1.00 20.00 +HETATM 20 C12 UNK 1 -1.450 7.155 0.054 1.00 20.00 +HETATM 21 H26 UNK 1 -0.930 8.101 0.054 1.00 20.00 +HETATM 22 C13 UNK 1 -0.734 5.976 0.041 1.00 20.00 +HETATM 23 H27 UNK 1 0.345 5.998 0.031 1.00 20.00 +HETATM 24 C16 UNK 1 3.113 0.632 1.593 1.00 20.00 +HETATM 25 H29 UNK 1 3.277 1.262 0.731 1.00 20.00 +HETATM 26 C17 UNK 1 3.750 0.916 2.787 1.00 20.00 +HETATM 27 H30 UNK 1 4.411 1.767 2.858 1.00 20.00 +HETATM 28 C18 UNK 1 3.545 0.107 3.889 1.00 20.00 +HETATM 29 H31 UNK 1 4.046 0.326 4.821 1.00 20.00 +HETATM 30 C19 UNK 1 2.700 -0.983 3.799 1.00 20.00 +HETATM 31 H32 UNK 1 2.540 -1.616 4.659 1.00 20.00 +HETATM 32 C20 UNK 1 2.059 -1.264 2.606 1.00 20.00 +HETATM 33 H33 UNK 1 1.398 -2.115 2.535 1.00 20.00 +END diff --git a/top/oplsaa/SM42/SM42.pdb b/top/oplsaa/SM42/SM42.pdb new file mode 120000 index 0000000..26a72f8 --- /dev/null +++ b/top/oplsaa/SM42/SM42.pdb @@ -0,0 +1 @@ +SM42.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM43/SM43.itp b/top/oplsaa/SM43/SM43.itp new file mode 120000 index 0000000..2740da5 --- /dev/null +++ b/top/oplsaa/SM43/SM43.itp @@ -0,0 +1 @@ +SM43.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM43/SM43.mol2 b/top/oplsaa/SM43/SM43.mol2 new file mode 100644 index 0000000..bfeece4 --- /dev/null +++ b/top/oplsaa/SM43/SM43.mol2 @@ -0,0 +1,84 @@ +# Name: SM43 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 31 32 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -2.4719 0.7810 -0.0167 O.2 + 2 S2 -1.4563 1.7742 0.0186 S.o2 + 3 N3 -0.0111 0.9658 0.0074 N.am + 4 C4 1.1844 1.6779 -0.0002 C.2 + 5 N5 1.3219 2.9792 0.0059 N.2 + 6 O6 2.4853 3.3075 -0.0032 O.3 + 7 C7 3.3026 2.2389 -0.0169 C.2 + 8 C8 4.7812 2.2538 -0.0308 C.ar + 9 C9 5.4940 1.0541 -0.0379 C.ar + 10 C10 6.8734 1.0750 -0.0552 C.ar + 11 C11 7.5501 2.2818 -0.0557 C.ar + 12 C12 6.8493 3.4746 -0.0433 C.ar + 13 C13 5.4698 3.4676 -0.0309 C.ar + 14 C14 2.4948 1.1375 -0.0099 C.2 + 15 N15 -1.5645 2.6048 -1.4100 N.am + 16 C16 -2.1763 1.9715 -2.5809 C.3 + 17 C17 -1.0485 3.9727 -1.5029 C.3 + 18 O18 -1.3610 2.7523 1.0451 O.2 + 19 H19 0.0021 -0.0041 0.0020 H + 20 H20 4.9670 0.1115 -0.0337 H + 21 H21 7.4263 0.1473 -0.0645 H + 22 H22 8.6300 2.2926 -0.0654 H + 23 H23 7.3834 4.4133 -0.0438 H + 24 H24 4.9239 4.3995 -0.0216 H + 25 H25 2.7864 0.0976 -0.0129 H + 26 H26 -3.2462 2.1800 -2.5892 H + 27 H27 -1.7216 2.3692 -3.4882 H + 28 H28 -2.0164 0.8942 -2.5364 H + 29 H29 -0.0024 3.9465 -1.8080 H + 30 H30 -1.6278 4.5303 -2.2389 H + 31 H31 -1.1314 4.4591 -0.5310 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 am + 4 2 18 2 + 5 3 4 1 + 6 3 19 1 + 7 4 14 1 + 8 4 5 2 + 9 5 6 1 + 10 6 7 1 + 11 7 8 1 + 12 7 14 2 + 13 8 13 ar + 14 8 9 ar + 15 9 10 ar + 16 9 20 1 + 17 10 11 ar + 18 10 21 1 + 19 11 12 ar + 20 11 22 1 + 21 12 13 ar + 22 12 23 1 + 23 13 24 1 + 24 14 25 1 + 25 15 16 1 + 26 15 17 1 + 27 16 26 1 + 28 16 27 1 + 29 16 28 1 + 30 17 29 1 + 31 17 30 1 + 32 17 31 1 + +# End of record + diff --git a/top/oplsaa/SM43/SM43.mol2.1.itp b/top/oplsaa/SM43/SM43.mol2.1.itp new file mode 100644 index 0000000..fc9b4e0 --- /dev/null +++ b/top/oplsaa/SM43/SM43.mol2.1.itp @@ -0,0 +1,307 @@ +; input pdb SMILES : O=[S](NC1=NOC(=C1)C2=CC=CC=C2)(N(C)C)=O +; Script arguments : SM43.mol2 "4 opls_581 0.458" "7 opls_583 0.348" "8 opls_147" "19 opls_241 0.482" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 2 opls_474 1 UNK S2 1 0.852 32.06000 ; SY # S in sulfamide, S(=O)2(NR2) + 3 opls_480 1 UNK N15 1 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 4 opls_475 1 UNK O18 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 5 opls_480 1 UNK N3 3 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 6 opls_482 1 UNK C17 5 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 7 opls_483 1 UNK H29 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 8 opls_483 1 UNK H30 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 9 opls_483 1 UNK H31 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 10 opls_482 1 UNK C16 11 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 11 opls_483 1 UNK H26 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 12 opls_483 1 UNK H27 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 13 opls_483 1 UNK H28 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 14 opls_582 1 UNK C14 29 -0.455 12.01100 ; CA # C4 in isoxazole + 15 opls_585 1 UNK H25 29 0.184 1.00800 ; HA # H4 in isoxazole + 16 opls_581 1 UNK C4 30 0.458 12.01100 ; CU # C3 in isoxazole ### user-defined OPLS atom type (opls_581) atom charge (0.458) + 17 opls_583 1 UNK C7 31 0.348 12.01100 ; CW # C5 in isoxazole ### user-defined OPLS atom type (opls_583) atom charge (0.348) + 18 opls_147 1 UNK C8 31 0.000 12.01100 ; CA # Naphthalene fusion C (C9) ### user-defined OPLS atom type (opls_147) + 19 opls_580 1 UNK N5 32 -0.413 14.00670 ; NB # N in isoxazole + 20 opls_579 1 UNK O6 32 -0.122 15.99940 ; OS # O in isoxazole + 21 opls_145 1 UNK C9 45 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 22 opls_146 1 UNK H20 45 0.115 1.00800 ; HA # Benzene H - 12 site. + 23 opls_145 1 UNK C10 47 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 24 opls_146 1 UNK H21 47 0.115 1.00800 ; HA # Benzene H - 12 site. + 25 opls_145 1 UNK C11 49 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 26 opls_146 1 UNK H22 49 0.115 1.00800 ; HA # Benzene H - 12 site. + 27 opls_145 1 UNK C12 51 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 28 opls_146 1 UNK H23 51 0.115 1.00800 ; HA # Benzene H - 12 site. + 29 opls_145 1 UNK C13 53 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 30 opls_146 1 UNK H24 53 0.115 1.00800 ; HA # Benzene H - 12 site. + 31 opls_241 1 UNK H19 55 0.482 1.00800 ; H # H on N: secondary amide ### user-defined OPLS atom type (opls_241) atom charge (0.482) +; Total charge : -0.000 ### Number of unassigned atoms : 0/31 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 5 1 ; SY-N # + 2 3 1 ; SY-N # + 2 4 1 ; SY-OY # + 5 16 1 0.1381 357313.600 ; N-CU # LigParGen + 5 31 1 ; N-H # (H-N) + 16 14 1 ; CU-CA # -idem- + 16 19 1 ; CU-NB # -idem- + 19 20 1 ; NB-OS # (OS-NB) -idem- + 20 17 1 ; OS-CW # (CW-OS) Furan - wlj 4/97 + 17 18 1 ; CW-CA # (CA-CW) pyrrole- wlj + 17 14 1 ; CW-CA # (CA-CW) pyrrole- wlj + 18 29 1 ; CA-CA # TRP,TYR,PHE + 18 21 1 ; CA-CA # TRP,TYR,PHE + 21 23 1 ; CA-CA # TRP,TYR,PHE + 21 22 1 ; CA-HA # PHE, etc. + 23 25 1 ; CA-CA # TRP,TYR,PHE + 23 24 1 ; CA-HA # PHE, etc. + 25 27 1 ; CA-CA # TRP,TYR,PHE + 25 26 1 ; CA-HA # PHE, etc. + 27 29 1 ; CA-CA # TRP,TYR,PHE + 27 28 1 ; CA-HA # PHE, etc. + 29 30 1 ; CA-HA # PHE, etc. + 14 15 1 ; CA-HA # PHE, etc. + 3 10 1 ; N-CT # (CT-N) + 3 6 1 ; N-CT # (CT-N) + 10 11 1 ; CT-HC # CHARMM 22 parameter file + 10 12 1 ; CT-HC # CHARMM 22 parameter file + 10 13 1 ; CT-HC # CHARMM 22 parameter file + 6 7 1 ; CT-HC # CHARMM 22 parameter file + 6 8 1 ; CT-HC # CHARMM 22 parameter file + 6 9 1 ; CT-HC # CHARMM 22 parameter file + +[ angles ] +; ai aj ak funct theta cth + 1 2 5 1 ; OY-SY-N # + 1 2 3 1 ; OY-SY-N # + 1 2 4 1 ; OY-SY-OY # + 5 2 3 1 107.000 1004.160 ; N-SY-N # by analogy from OY-SY-N : + 5 2 4 1 ; N-SY-OY # (OY-SY-N) + 3 2 4 1 ; N-SY-OY # (OY-SY-N) + 2 5 16 1 118.330 404.760 ; SY-N-CU # LigParGen + 2 5 31 1 ; SY-N-H # (H-N-SY) + 16 5 31 1 119.800 292.880 ; CU-N-H # LigParGen + 5 16 14 1 119.440 468.608 ; N-CU-CA # LigParGen + 5 16 19 1 119.440 468.608 ; N-CU-NB # LigParGen + 19 16 14 1 ; NB-CU-CA # -idem- + 16 19 20 1 ; CU-NB-OS # -idem- + 19 20 17 1 ; NB-OS-CW # (CW-OS-NB) -idem- + 20 17 18 1 ; OS-CW-CA # wlj + 20 17 14 1 ; OS-CW-CA # wlj + 18 17 14 1 132.100 585.760 ; CA-CW-CA # LigParGen + 17 18 29 1 ; CW-CA-CA # (CA-CA-CW) wlj 1/97 based on pyrrole + 17 18 21 1 ; CW-CA-CA # (CA-CA-CW) wlj 1/97 based on pyrrole + 21 18 29 1 ; CA-CA-CA # PHE(OL) + 18 21 23 1 ; CA-CA-CA # PHE(OL) + 18 21 22 1 ; CA-CA-HA # + 23 21 22 1 ; CA-CA-HA # + 21 23 25 1 ; CA-CA-CA # PHE(OL) + 21 23 24 1 ; CA-CA-HA # + 25 23 24 1 ; CA-CA-HA # + 23 25 27 1 ; CA-CA-CA # PHE(OL) + 23 25 26 1 ; CA-CA-HA # + 27 25 26 1 ; CA-CA-HA # + 25 27 29 1 ; CA-CA-CA # PHE(OL) + 25 27 28 1 ; CA-CA-HA # + 29 27 28 1 ; CA-CA-HA # + 18 29 27 1 ; CA-CA-CA # PHE(OL) + 18 29 30 1 ; CA-CA-HA # + 27 29 30 1 ; CA-CA-HA # + 16 14 17 1 ; CU-CA-CW # -idem- + 16 14 15 1 ; CU-CA-HA # -idem- + 17 14 15 1 ; CW-CA-HA # (HA-CA-CW) wlj - pyrrole + 2 3 10 1 ; SY-N-CT # + 2 3 6 1 ; SY-N-CT # + 10 3 6 1 ; CT-N-CT # PRO(OL) DETAR JACS 99,1232 + 3 10 11 1 ; N-CT-HC # (HC-CT-N) + 3 10 12 1 ; N-CT-HC # (HC-CT-N) + 3 10 13 1 ; N-CT-HC # (HC-CT-N) + 11 10 12 1 ; HC-CT-HC # CHARMM 22 parameter file + 11 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 12 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 3 6 7 1 ; N-CT-HC # (HC-CT-N) + 3 6 8 1 ; N-CT-HC # (HC-CT-N) + 3 6 9 1 ; N-CT-HC # (HC-CT-N) + 7 6 8 1 ; HC-CT-HC # CHARMM 22 parameter file + 7 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + 8 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 5 16 3 ; OY-SY-N-CU # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 5 31 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 5 16 3 -2.897 11.182 12.410 -20.694 -0.000 0.000 ; N-SY-N-CU # LigParGen + 3 2 5 31 3 -15.611 0.703 20.506 -5.598 -0.000 0.000 ; N-SY-N-H # LigParGen + 4 2 5 16 3 ; OY-SY-N-CU # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 5 31 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 5 2 3 10 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 5 2 3 6 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 4 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 5 16 14 3 -3.431 -3.008 10.598 -4.159 -0.000 0.000 ; SY-N-CU-CA # LigParGen + 2 5 16 19 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; SY-N-CU-NB # LigParGen + 31 5 16 14 3 20.502 0.000 -20.502 -0.000 -0.000 0.000 ; H-N-CU-CA # LigParGen + 31 5 16 19 3 8.786 0.000 -8.786 -0.000 -0.000 0.000 ; H-N-CU-NB # LigParGen + 5 16 14 17 3 ; N-CU-CA-CW # (X-CA-CU-X generic proper dihedral) aromatic ring + 5 16 14 15 3 ; N-CU-CA-HA # (X-CA-CU-X generic proper dihedral) aromatic ring + 19 16 14 17 3 ; NB-CU-CA-CW # (X-CA-CU-X generic proper dihedral) aromatic ring + 19 16 14 15 3 ; NB-CU-CA-HA # (X-CA-CU-X generic proper dihedral) aromatic ring + 5 16 19 20 3 ; N-CU-NB-OS # (X-CU-NB-X generic proper dihedral) aromatic ring + 14 16 19 20 3 ; CA-CU-NB-OS # (X-CU-NB-X generic proper dihedral) aromatic ring + 16 19 20 17 3 ; CU-NB-OS-CW # (X-NB-OS-X generic proper dihedral) aromatic ring isoxazole + 19 20 17 18 3 ; NB-OS-CW-CA # (X-CW-OS-X generic proper dihedral) aromatic ring furan + 19 20 17 14 3 ; NB-OS-CW-CA # (X-CW-OS-X generic proper dihedral) aromatic ring furan + 20 17 18 29 3 ; OS-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 20 17 18 21 3 ; OS-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 14 17 18 29 3 ; CA-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 14 17 18 21 3 ; CA-CW-CA-CA # (X-CA-CW-X generic proper dihedral) aromatic ring + 20 17 14 16 3 ; OS-CW-CA-CU # (X-CA-CW-X generic proper dihedral) aromatic ring + 20 17 14 15 3 ; OS-CW-CA-HA # (X-CA-CW-X generic proper dihedral) aromatic ring + 18 17 14 16 3 ; CA-CW-CA-CU # (X-CA-CW-X generic proper dihedral) aromatic ring + 18 17 14 15 3 ; CA-CW-CA-HA # (X-CA-CW-X generic proper dihedral) aromatic ring + 17 18 29 27 3 ; CW-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 18 29 30 3 ; CW-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 18 29 27 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 18 29 30 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 18 21 23 3 ; CW-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 18 21 22 3 ; CW-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 18 21 23 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 18 21 22 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 21 23 25 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 21 23 24 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 21 23 25 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 21 23 24 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 23 25 27 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 23 25 26 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 27 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 26 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 25 27 29 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 25 27 28 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 25 27 29 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 25 27 28 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 27 29 18 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 27 29 30 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 27 29 18 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 27 29 30 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 10 11 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 12 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 13 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 6 3 10 11 3 ; CT-N-CT-HC # tert. amide + 6 3 10 12 3 ; CT-N-CT-HC # tert. amide + 6 3 10 13 3 ; CT-N-CT-HC # tert. amide + 2 3 6 7 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 8 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 9 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 10 3 6 7 3 ; CT-N-CT-HC # tert. amide + 10 3 6 8 3 ; CT-N-CT-HC # tert. amide + 10 3 6 9 3 ; CT-N-CT-HC # tert. amide + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 16 31 5 2 1 improper_Z_N_X_Y ; CU-H-N-SY + 14 19 16 5 1 improper_N2_X_N2_N2 ; CA-NB-CU-N + 20 18 17 14 1 improper_Z_CM_X_Y ; OS-CA-CW-CA + 29 21 18 17 1 improper_Z_CA_X_Y ; CA-CA-CA-CW + 23 22 21 18 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 25 24 23 21 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 27 26 25 23 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 29 28 27 25 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 27 30 29 18 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 17 15 14 16 1 improper_Z_CM_X_Y ; CW-HA-CA-CU + 2 6 3 10 1 improper_Z_N_X_Y ; SY-CT-N-CT + +[ pairs ] +; ai aj funct + 1 16 1 + 1 31 1 + 1 10 1 + 1 6 1 + 2 14 1 + 2 19 1 + 2 11 1 + 2 12 1 + 2 13 1 + 2 7 1 + 2 8 1 + 2 9 1 + 5 10 1 + 5 6 1 + 5 17 1 + 5 15 1 + 5 20 1 + 16 3 1 + 16 4 1 + 16 18 1 + 19 31 1 + 19 15 1 + 19 18 1 + 20 29 1 + 20 21 1 + 20 15 1 + 17 27 1 + 17 30 1 + 17 23 1 + 17 22 1 + 18 15 1 + 18 25 1 + 18 28 1 + 18 24 1 + 21 14 1 + 21 27 1 + 21 30 1 + 21 26 1 + 23 29 1 + 23 28 1 + 25 22 1 + 25 30 1 + 27 24 1 + 29 14 1 + 29 22 1 + 29 26 1 + 14 31 1 + 3 31 1 + 10 4 1 + 10 7 1 + 10 8 1 + 10 9 1 + 6 4 1 + 6 11 1 + 6 12 1 + 6 13 1 + 4 31 1 + 22 24 1 + 24 26 1 + 26 28 1 + 28 30 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 5 1 1000 1000 1000 + 16 1 1000 1000 1000 + 19 1 1000 1000 1000 + 20 1 1000 1000 1000 + 17 1 1000 1000 1000 + 18 1 1000 1000 1000 + 21 1 1000 1000 1000 + 23 1 1000 1000 1000 + 25 1 1000 1000 1000 + 27 1 1000 1000 1000 + 29 1 1000 1000 1000 + 14 1 1000 1000 1000 + 3 1 1000 1000 1000 + 10 1 1000 1000 1000 + 6 1 1000 1000 1000 + 4 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM43/SM43.mol2.1.pdb b/top/oplsaa/SM43/SM43.mol2.1.pdb new file mode 100644 index 0000000..8c0e2e0 --- /dev/null +++ b/top/oplsaa/SM43/SM43.mol2.1.pdb @@ -0,0 +1,32 @@ +HETATM 1 O1 UNK 1 -2.472 0.781 -0.017 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 N15 UNK 1 -1.565 2.605 -1.410 1.00 20.00 +HETATM 4 O18 UNK 1 -1.361 2.752 1.045 1.00 20.00 +HETATM 5 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 6 C17 UNK 1 -1.048 3.973 -1.503 1.00 20.00 +HETATM 7 H29 UNK 1 -0.002 3.946 -1.808 1.00 20.00 +HETATM 8 H30 UNK 1 -1.628 4.530 -2.239 1.00 20.00 +HETATM 9 H31 UNK 1 -1.131 4.459 -0.531 1.00 20.00 +HETATM 10 C16 UNK 1 -2.176 1.972 -2.581 1.00 20.00 +HETATM 11 H26 UNK 1 -3.246 2.180 -2.589 1.00 20.00 +HETATM 12 H27 UNK 1 -1.722 2.369 -3.488 1.00 20.00 +HETATM 13 H28 UNK 1 -2.016 0.894 -2.536 1.00 20.00 +HETATM 14 C14 UNK 1 2.495 1.137 -0.010 1.00 20.00 +HETATM 15 H25 UNK 1 2.786 0.098 -0.013 1.00 20.00 +HETATM 16 C4 UNK 1 1.184 1.678 -0.000 1.00 20.00 +HETATM 17 C7 UNK 1 3.303 2.239 -0.017 1.00 20.00 +HETATM 18 C8 UNK 1 4.781 2.254 -0.031 1.00 20.00 +HETATM 19 N5 UNK 1 1.322 2.979 0.006 1.00 20.00 +HETATM 20 O6 UNK 1 2.485 3.308 -0.003 1.00 20.00 +HETATM 21 C9 UNK 1 5.494 1.054 -0.038 1.00 20.00 +HETATM 22 H20 UNK 1 4.967 0.112 -0.034 1.00 20.00 +HETATM 23 C10 UNK 1 6.873 1.075 -0.055 1.00 20.00 +HETATM 24 H21 UNK 1 7.426 0.147 -0.065 1.00 20.00 +HETATM 25 C11 UNK 1 7.550 2.282 -0.056 1.00 20.00 +HETATM 26 H22 UNK 1 8.630 2.293 -0.065 1.00 20.00 +HETATM 27 C12 UNK 1 6.849 3.475 -0.043 1.00 20.00 +HETATM 28 H23 UNK 1 7.383 4.413 -0.044 1.00 20.00 +HETATM 29 C13 UNK 1 5.470 3.468 -0.031 1.00 20.00 +HETATM 30 H24 UNK 1 4.924 4.399 -0.022 1.00 20.00 +HETATM 31 H19 UNK 1 0.002 -0.004 0.002 1.00 20.00 +END diff --git a/top/oplsaa/SM43/SM43.pdb b/top/oplsaa/SM43/SM43.pdb new file mode 120000 index 0000000..668212f --- /dev/null +++ b/top/oplsaa/SM43/SM43.pdb @@ -0,0 +1 @@ +SM43.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM44/SM44.itp b/top/oplsaa/SM44/SM44.itp new file mode 120000 index 0000000..044343d --- /dev/null +++ b/top/oplsaa/SM44/SM44.itp @@ -0,0 +1 @@ +SM44.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM44/SM44.mol2 b/top/oplsaa/SM44/SM44.mol2 new file mode 100644 index 0000000..595043c --- /dev/null +++ b/top/oplsaa/SM44/SM44.mol2 @@ -0,0 +1,74 @@ +# Name: SM44 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 26 27 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -2.4342 0.7435 0.0434 O.2 + 2 S2 -1.4563 1.7742 0.0186 S.o2 + 3 N3 -0.0111 0.9658 0.0074 N.am + 4 C4 1.1952 1.6843 -0.0003 C.2 + 5 N5 1.3355 3.0174 0.0060 N.2 + 6 N6 2.5876 3.3093 -0.0046 N.2 + 7 C7 2.4511 1.1657 -0.0096 C.2 + 8 N8 3.2983 2.2362 -0.0177 N.pl3 + 9 C9 4.6992 2.1771 -0.0325 C.ar + 10 C10 5.3434 0.9473 -0.0405 C.ar + 11 C11 6.7233 0.8922 -0.0613 C.ar + 12 C12 7.4633 2.0604 -0.0616 C.ar + 13 C13 6.8246 3.2867 -0.0479 C.ar + 14 C14 5.4448 3.3481 -0.0333 C.ar + 15 C15 -1.4964 2.6518 -1.5685 C.3 + 16 O16 -1.3346 2.6947 1.0943 O.2 + 17 H17 0.0021 -0.0041 0.0020 H + 18 H18 2.7234 0.1206 -0.0120 H + 19 H19 4.7660 0.0346 -0.0350 H + 20 H20 7.2250 -0.0641 -0.0724 H + 21 H21 8.5423 2.0148 -0.0730 H + 22 H22 7.4052 4.1974 -0.0489 H + 23 H23 4.9465 4.3062 -0.0229 H + 24 H24 -1.4399 1.9306 -2.3839 H + 25 H25 -2.4248 3.2175 -1.6475 H + 26 H26 -0.6488 3.3344 -1.6278 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 1 + 4 2 16 2 + 5 3 4 1 + 6 3 17 1 + 7 4 5 1 + 8 4 7 2 + 9 5 6 2 + 10 6 8 1 + 11 7 8 1 + 12 7 18 1 + 13 8 9 1 + 14 9 14 ar + 15 9 10 ar + 16 10 11 ar + 17 10 19 1 + 18 11 12 ar + 19 11 20 1 + 20 12 13 ar + 21 12 21 1 + 22 13 14 ar + 23 13 22 1 + 24 14 23 1 + 25 15 24 1 + 26 15 25 1 + 27 15 26 1 + +# End of record + diff --git a/top/oplsaa/SM44/SM44.mol2.1.itp b/top/oplsaa/SM44/SM44.mol2.1.itp new file mode 100644 index 0000000..25c1f89 --- /dev/null +++ b/top/oplsaa/SM44/SM44.mol2.1.itp @@ -0,0 +1,267 @@ +; input pdb SMILES : O=[S](NC1=C[N](N=N1)C2=CC=CC=C2)(C)=O +; Script arguments : SM44.mol2 "5 opls_559 -0.290" "6 opls_559 -0.150" "18 opls_563 0.166" "7 opls_551 0.027" "8 opls_557 0.079" "9 opls_147" "4 opls_560 0.438" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 2 opls_474 1 UNK S2 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 3 opls_475 1 UNK O16 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 4 opls_476 1 UNK C15 3 -0.540 12.01100 ; CT # CH3 attached to S of sulfonamide + 5 opls_477 1 UNK H24 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 6 opls_477 1 UNK H25 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 7 opls_477 1 UNK H26 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 8 opls_480 1 UNK N3 15 -0.800 14.00670 ; N # N secondary amide of sulfonamide + 9 opls_560 1 UNK C4 15 0.438 12.01100 ; CV # C4 in imidazole ### user-defined OPLS atom type (opls_560) atom charge (0.438) + 10 opls_481 1 UNK H17 15 0.410 1.00800 ; H # H on N: secondary sulfonamide + 11 opls_145 1 UNK C10 23 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 12 opls_146 1 UNK H19 23 0.115 1.00800 ; HA # Benzene H - 12 site. + 13 opls_145 1 UNK C11 25 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 14 opls_146 1 UNK H20 25 0.115 1.00800 ; HA # Benzene H - 12 site. + 15 opls_145 1 UNK C12 27 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 16 opls_146 1 UNK H21 27 0.115 1.00800 ; HA # Benzene H - 12 site. + 17 opls_145 1 UNK C13 29 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 18 opls_146 1 UNK H22 29 0.115 1.00800 ; HA # Benzene H - 12 site. + 19 opls_145 1 UNK C14 31 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 20 opls_146 1 UNK H23 31 0.115 1.00800 ; HA # Benzene H - 12 site. + 21 opls_559 1 UNK N5 33 -0.290 14.00670 ; NB # N3 in imidazole ### user-defined OPLS atom type (opls_559) atom charge (-0.290) + 22 opls_559 1 UNK N6 33 -0.150 14.00670 ; NB # N3 in imidazole ### user-defined OPLS atom type (opls_559) atom charge (-0.150) + 23 opls_551 1 UNK C7 33 0.027 12.01100 ; CA # C4 in pyrazole ### user-defined OPLS atom type (opls_551) atom charge (0.027) + 24 opls_557 1 UNK N8 33 0.079 14.00670 ; NA # N1 in imidazole ### user-defined OPLS atom type (opls_557) atom charge (0.079) + 25 opls_147 1 UNK C9 33 0.000 12.01100 ; CA # Naphthalene fusion C (C9) ### user-defined OPLS atom type (opls_147) + 26 opls_563 1 UNK H18 33 0.166 1.00800 ; HA # H2 in imidazole ### user-defined OPLS atom type (opls_563) atom charge (0.166) +; Total charge : -0.000 ### Number of unassigned atoms : 0/26 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 8 1 ; SY-N # + 2 4 1 ; SY-CT # + 2 3 1 ; SY-OY # + 8 9 1 0.1381 357313.600 ; N-CV # LigParGen + 8 10 1 ; N-H # (H-N) + 9 21 1 ; CV-NB # ADE,GUA,HIS + 9 23 1 0.14000 392459.2 ; CV-CA # (CA-CV) by analogy from CA-CA : TRP,TYR,PHE + 21 22 1 0.1280 334720.000 ; NB-NB # LigParGen + 22 24 1 ; NB-NA # (NA-NB) -idem- + 23 24 1 ; CA-NA # GUA + 23 26 1 ; CA-HA # PHE, etc. + 24 25 1 ; NA-CA # (CA-NA) GUA + 25 19 1 ; CA-CA # TRP,TYR,PHE + 25 11 1 ; CA-CA # TRP,TYR,PHE + 11 13 1 ; CA-CA # TRP,TYR,PHE + 11 12 1 ; CA-HA # PHE, etc. + 13 15 1 ; CA-CA # TRP,TYR,PHE + 13 14 1 ; CA-HA # PHE, etc. + 15 17 1 ; CA-CA # TRP,TYR,PHE + 15 16 1 ; CA-HA # PHE, etc. + 17 19 1 ; CA-CA # TRP,TYR,PHE + 17 18 1 ; CA-HA # PHE, etc. + 19 20 1 ; CA-HA # PHE, etc. + 4 5 1 ; CT-HC # CHARMM 22 parameter file + 4 6 1 ; CT-HC # CHARMM 22 parameter file + 4 7 1 ; CT-HC # CHARMM 22 parameter file + +[ angles ] +; ai aj ak funct theta cth + 1 2 8 1 ; OY-SY-N # + 1 2 4 1 ; OY-SY-CT # + 1 2 3 1 ; OY-SY-OY # + 8 2 4 1 ; N-SY-CT # + 8 2 3 1 ; N-SY-OY # (OY-SY-N) + 4 2 3 1 ; CT-SY-OY # (OY-SY-CT) + 2 8 9 1 118.330 404.760 ; SY-N-CV # LigParGen + 2 8 10 1 ; SY-N-H # (H-N-SY) + 9 8 10 1 119.800 292.880 ; CV-N-H # LigParGen + 8 9 21 1 120.670 475.972 ; N-CV-NB # LigParGen + 8 9 23 1 120.000 585.760 ; N-CV-CA # LigParGen + 21 9 23 1 ; NB-CV-CA # (CA-CV-NB) wlj + 9 21 22 1 117.000 585.760 ; CV-NB-NB # LigParGen + 21 22 24 1 111.360 497.143 ; NB-NB-NA # LigParGen + 9 23 24 1 106.300 585.760 ; CV-CA-NA # LigParGen + 9 23 26 1 130.700 292.880 ; CV-CA-HA # LigParGen + 24 23 26 1 ; NA-CA-HA # (HA-CA-NA) + 22 24 23 1 ; NB-NA-CA # -idem- + 22 24 25 1 ; NB-NA-CA # -idem- + 23 24 25 1 ; CA-NA-CA # Added DSM (from C-NA-CA) + 24 25 19 1 ; NA-CA-CA # (CA-CA-NA) TRP(OL) + 24 25 11 1 ; NA-CA-CA # (CA-CA-NA) TRP(OL) + 11 25 19 1 ; CA-CA-CA # PHE(OL) + 25 11 13 1 ; CA-CA-CA # PHE(OL) + 25 11 12 1 ; CA-CA-HA # + 13 11 12 1 ; CA-CA-HA # + 11 13 15 1 ; CA-CA-CA # PHE(OL) + 11 13 14 1 ; CA-CA-HA # + 15 13 14 1 ; CA-CA-HA # + 13 15 17 1 ; CA-CA-CA # PHE(OL) + 13 15 16 1 ; CA-CA-HA # + 17 15 16 1 ; CA-CA-HA # + 15 17 19 1 ; CA-CA-CA # PHE(OL) + 15 17 18 1 ; CA-CA-HA # + 19 17 18 1 ; CA-CA-HA # + 25 19 17 1 ; CA-CA-CA # PHE(OL) + 25 19 20 1 ; CA-CA-HA # + 17 19 20 1 ; CA-CA-HA # + 2 4 5 1 ; SY-CT-HC # + 2 4 6 1 ; SY-CT-HC # + 2 4 7 1 ; SY-CT-HC # + 5 4 6 1 ; HC-CT-HC # CHARMM 22 parameter file + 5 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + 6 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 8 9 3 ; OY-SY-N-CV # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 8 10 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 8 9 3 -2.897 11.182 12.410 -20.694 -0.000 0.000 ; CT-SY-N-CV # LigParGen + 4 2 8 10 3 ; CT-SY-N-H # sulfonamide + 3 2 8 9 3 ; OY-SY-N-CV # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 8 10 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 4 5 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 1 2 4 6 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 1 2 4 7 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 8 2 4 5 3 ; N-SY-CT-HC # (HC-CT-SY-N) sulfonamide + 8 2 4 6 3 ; N-SY-CT-HC # (HC-CT-SY-N) sulfonamide + 8 2 4 7 3 ; N-SY-CT-HC # (HC-CT-SY-N) sulfonamide + 3 2 4 5 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 3 2 4 6 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 3 2 4 7 3 ; OY-SY-CT-HC # (OY-SY-CT-X generic proper dihedral) sulfonamide + 2 8 9 21 3 -2.935 -1.914 6.096 -1.247 -0.000 0.000 ; SY-N-CV-NB # LigParGen + 2 8 9 23 3 -3.431 -3.008 10.598 -4.159 -0.000 0.000 ; SY-N-CV-CA # LigParGen + 10 8 9 21 3 8.786 0.000 -8.786 -0.000 -0.000 0.000 ; H-N-CV-NB # LigParGen + 10 8 9 23 3 8.786 0.000 -8.786 -0.000 -0.000 0.000 ; H-N-CV-CA # LigParGen adapted + 8 9 21 22 3 ; N-CV-NB-NB # (X-CV-NB-X generic proper dihedral) + 23 9 21 22 3 ; CA-CV-NB-NB # (X-CV-NB-X generic proper dihedral) + 8 9 23 24 3 44.978 0.000 -44.978 -0.000 -0.000 0.000 ; N-CV-CA-NA # LigParGen + 8 9 23 26 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 ; N-CV-CA-HA # LigParGen + 21 9 23 24 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; NB-CV-CA-NA # LigParGen + 21 9 23 26 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; NB-CV-CA-HA # by analogy with X-CA-CA-X : aromatic ring (the same as LigParGen) + 9 21 22 24 3 41.840 0.000 -41.840 -0.000 -0.000 0.000 ; CV-NB-NB-NA # LigParGen + 21 22 24 23 3 ; NB-NB-NA-CA # (X-NA-NB-X generic proper dihedral) + 21 22 24 25 3 ; NB-NB-NA-CA # (X-NA-NB-X generic proper dihedral) + 9 23 24 22 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 ; CV-CA-NA-NB # LigParGen + 9 23 24 25 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 ; CV-CA-NA-CA # LigParGen + 26 23 24 22 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 ; HA-CA-NA-NB # LigParGen + 26 23 24 25 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 ; HA-CA-NA-CA # LigParGen + 22 24 25 19 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; NB-NA-CA-CA # LigParGen + 22 24 25 11 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; NB-NA-CA-CA # LigParGen + 23 24 25 19 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; CA-NA-CA-CA # LigParGen + 23 24 25 11 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; CA-NA-CA-CA # LigParGen + 24 25 19 17 3 ; NA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 25 19 20 3 ; NA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 25 19 17 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 25 19 20 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 25 11 13 3 ; NA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 25 11 12 3 ; NA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 25 11 13 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 25 11 12 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 11 13 15 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 11 13 14 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 12 11 13 15 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 12 11 13 14 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 13 15 17 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 13 15 16 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 13 15 17 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 13 15 16 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 13 15 17 19 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 13 15 17 18 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 15 17 19 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 15 17 18 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 17 19 25 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 17 19 20 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 17 19 25 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 17 19 20 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 9 10 8 2 1 improper_Z_N_X_Y ; CV-H-N-SY + 21 23 9 8 1 improper_N2_X_N2_N2 ; NB-CA-CV-N + 24 26 23 9 1 improper_Z_CM_X_Y ; NA-HA-CA-CV + 23 25 24 22 1 improper_Z_N_X_Y ; CA-CA-NA-NB + 19 11 25 24 1 improper_Z_CA_X_Y ; CA-CA-CA-NA + 13 12 11 25 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 15 14 13 11 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 17 16 15 13 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 19 18 17 15 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 17 20 19 25 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + +[ pairs ] +; ai aj funct + 1 9 1 + 1 10 1 + 1 5 1 + 1 6 1 + 1 7 1 + 2 21 1 + 2 23 1 + 8 5 1 + 8 6 1 + 8 7 1 + 8 22 1 + 8 24 1 + 8 26 1 + 9 4 1 + 9 3 1 + 9 25 1 + 21 10 1 + 21 26 1 + 21 25 1 + 22 26 1 + 22 19 1 + 22 11 1 + 23 10 1 + 23 19 1 + 23 11 1 + 24 17 1 + 24 20 1 + 24 13 1 + 24 12 1 + 25 26 1 + 25 15 1 + 25 18 1 + 25 14 1 + 11 17 1 + 11 20 1 + 11 16 1 + 13 19 1 + 13 18 1 + 15 12 1 + 15 20 1 + 17 14 1 + 19 12 1 + 19 16 1 + 4 10 1 + 3 10 1 + 3 5 1 + 3 6 1 + 3 7 1 + 12 14 1 + 14 16 1 + 16 18 1 + 18 20 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 8 1 1000 1000 1000 + 9 1 1000 1000 1000 + 21 1 1000 1000 1000 + 22 1 1000 1000 1000 + 23 1 1000 1000 1000 + 24 1 1000 1000 1000 + 25 1 1000 1000 1000 + 11 1 1000 1000 1000 + 13 1 1000 1000 1000 + 15 1 1000 1000 1000 + 17 1 1000 1000 1000 + 19 1 1000 1000 1000 + 4 1 1000 1000 1000 + 3 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM44/SM44.mol2.1.pdb b/top/oplsaa/SM44/SM44.mol2.1.pdb new file mode 100644 index 0000000..44aca1b --- /dev/null +++ b/top/oplsaa/SM44/SM44.mol2.1.pdb @@ -0,0 +1,27 @@ +HETATM 1 O1 UNK 1 -2.434 0.744 0.043 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 O16 UNK 1 -1.335 2.695 1.094 1.00 20.00 +HETATM 4 C15 UNK 1 -1.496 2.652 -1.569 1.00 20.00 +HETATM 5 H24 UNK 1 -1.440 1.931 -2.384 1.00 20.00 +HETATM 6 H25 UNK 1 -2.425 3.217 -1.647 1.00 20.00 +HETATM 7 H26 UNK 1 -0.649 3.334 -1.628 1.00 20.00 +HETATM 8 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 9 C4 UNK 1 1.195 1.684 -0.000 1.00 20.00 +HETATM 10 H17 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 11 C10 UNK 1 5.343 0.947 -0.041 1.00 20.00 +HETATM 12 H19 UNK 1 4.766 0.035 -0.035 1.00 20.00 +HETATM 13 C11 UNK 1 6.723 0.892 -0.061 1.00 20.00 +HETATM 14 H20 UNK 1 7.225 -0.064 -0.072 1.00 20.00 +HETATM 15 C12 UNK 1 7.463 2.060 -0.062 1.00 20.00 +HETATM 16 H21 UNK 1 8.542 2.015 -0.073 1.00 20.00 +HETATM 17 C13 UNK 1 6.825 3.287 -0.048 1.00 20.00 +HETATM 18 H22 UNK 1 7.405 4.197 -0.049 1.00 20.00 +HETATM 19 C14 UNK 1 5.445 3.348 -0.033 1.00 20.00 +HETATM 20 H23 UNK 1 4.947 4.306 -0.023 1.00 20.00 +HETATM 21 N5 UNK 1 1.335 3.017 0.006 1.00 20.00 +HETATM 22 N6 UNK 1 2.588 3.309 -0.005 1.00 20.00 +HETATM 23 C7 UNK 1 2.451 1.166 -0.010 1.00 20.00 +HETATM 24 N8 UNK 1 3.298 2.236 -0.018 1.00 20.00 +HETATM 25 C9 UNK 1 4.699 2.177 -0.033 1.00 20.00 +HETATM 26 H18 UNK 1 2.723 0.121 -0.012 1.00 20.00 +END diff --git a/top/oplsaa/SM44/SM44.pdb b/top/oplsaa/SM44/SM44.pdb new file mode 120000 index 0000000..bee97c2 --- /dev/null +++ b/top/oplsaa/SM44/SM44.pdb @@ -0,0 +1 @@ +SM44.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/SM45/SM45.mol2 b/top/oplsaa/SM45/SM45.mol2 deleted file mode 120000 index cdccb43..0000000 --- a/top/oplsaa/SM45/SM45.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/SM45/SM45.mol2 \ No newline at end of file diff --git a/top/oplsaa/SM45/SM45.mol2 b/top/oplsaa/SM45/SM45.mol2 new file mode 100644 index 0000000..62b30d3 --- /dev/null +++ b/top/oplsaa/SM45/SM45.mol2 @@ -0,0 +1,89 @@ +# Name: SM45 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 33 35 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 9.4313 -1.9481 -0.1315 O.2 + 2 S2 8.0779 -2.3787 -0.0863 S.o2 + 3 N3 7.1509 -1.0066 -0.0704 N.am + 4 C4 5.7504 -1.1056 -0.0577 C.2 + 5 N5 5.0254 -2.2331 -0.0571 N.2 + 6 N6 3.7758 -1.9304 -0.0440 N.2 + 7 C7 4.8620 -0.0774 -0.0499 C.2 + 8 N8 3.6239 -0.6523 -0.0357 N.pl3 + 9 C9 2.3994 0.0308 -0.0208 C.ar + 10 C10 1.2067 -0.6797 -0.0132 C.ar + 11 C11 0.0021 -0.0041 0.0020 C.ar + 12 C12 -0.0167 1.3786 0.0096 C.ar + 13 C13 1.1697 2.0889 0.0021 C.ar + 14 C14 2.3774 1.4188 -0.0131 C.ar + 15 C15 7.7661 -3.2012 -1.6130 C.ar + 16 C16 6.7532 -4.1379 -1.6992 C.ar + 17 C17 6.5054 -4.7797 -2.8982 C.ar + 18 C18 7.2773 -4.4923 -4.0084 C.ar + 19 C19 8.2936 -3.5593 -3.9208 C.ar + 20 C20 8.5380 -2.9138 -2.7232 C.ar + 21 O21 7.5643 -3.2218 0.9359 O.2 + 22 H22 7.5755 -0.1344 -0.0699 H + 23 H23 5.0890 0.9785 -0.0522 H + 24 H24 1.2207 -1.7596 -0.0195 H + 25 H25 -0.9261 -0.5562 0.0083 H + 26 H26 -0.9598 1.9047 0.0170 H + 27 H27 1.1519 3.1688 0.0078 H + 28 H28 3.3036 1.9742 -0.0194 H + 29 H29 6.1529 -4.3657 -0.8307 H + 30 H30 5.7117 -5.5088 -2.9665 H + 31 H31 7.0867 -4.9969 -4.9440 H + 32 H32 8.8970 -3.3350 -4.7881 H + 33 H33 9.3322 -2.1851 -2.6547 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 1 + 4 2 21 2 + 5 3 4 1 + 6 3 22 1 + 7 4 5 1 + 8 4 7 2 + 9 5 6 2 + 10 6 8 1 + 11 7 8 1 + 12 7 23 1 + 13 8 9 1 + 14 9 14 ar + 15 9 10 ar + 16 10 11 ar + 17 10 24 1 + 18 11 12 ar + 19 11 25 1 + 20 12 13 ar + 21 12 26 1 + 22 13 14 ar + 23 13 27 1 + 24 14 28 1 + 25 15 20 ar + 26 15 16 ar + 27 16 17 ar + 28 16 29 1 + 29 17 18 ar + 30 17 30 1 + 31 18 19 ar + 32 18 31 1 + 33 19 20 ar + 34 19 32 1 + 35 20 33 1 + +# End of record + diff --git a/top/oplsaa/SM46/SM46.itp b/top/oplsaa/SM46/SM46.itp new file mode 120000 index 0000000..daafb82 --- /dev/null +++ b/top/oplsaa/SM46/SM46.itp @@ -0,0 +1 @@ +SM46.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/SM46/SM46.mol2 b/top/oplsaa/SM46/SM46.mol2 new file mode 100644 index 0000000..87821bd --- /dev/null +++ b/top/oplsaa/SM46/SM46.mol2 @@ -0,0 +1,84 @@ +# Name: SM46 +# Creating user name: iorga +# Creation time: 09. 07. 2020 11:40 + +# Modifying user name: iorga +# Modification time: 09. 07. 2020 11:40 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 31 32 0 0 0 +UNK L +NO_CHARGES + + +@ATOM + 1 O1 -2.4719 0.7810 -0.0167 O.2 + 2 S2 -1.4563 1.7742 0.0186 S.o2 + 3 N3 -0.0111 0.9658 0.0074 N.am + 4 C4 1.1952 1.6843 -0.0003 C.2 + 5 N5 1.3355 3.0174 0.0060 N.2 + 6 N6 2.5876 3.3093 -0.0046 N.2 + 7 C7 2.4511 1.1657 -0.0096 C.2 + 8 N8 3.2983 2.2362 -0.0177 N.pl3 + 9 C9 4.6992 2.1771 -0.0325 C.ar + 10 C10 5.3434 0.9473 -0.0405 C.ar + 11 C11 6.7233 0.8922 -0.0613 C.ar + 12 C12 7.4633 2.0604 -0.0616 C.ar + 13 C13 6.8246 3.2867 -0.0479 C.ar + 14 C14 5.4448 3.3481 -0.0333 C.ar + 15 N15 -1.5645 2.6048 -1.4100 N.am + 16 C16 -2.1763 1.9715 -2.5809 C.3 + 17 C17 -1.0485 3.9727 -1.5029 C.3 + 18 O18 -1.3610 2.7523 1.0451 O.2 + 19 H19 0.0021 -0.0041 0.0020 H + 20 H20 2.7234 0.1206 -0.0120 H + 21 H21 4.7660 0.0346 -0.0350 H + 22 H22 7.2250 -0.0641 -0.0724 H + 23 H23 8.5423 2.0148 -0.0730 H + 24 H24 7.4052 4.1974 -0.0489 H + 25 H25 4.9465 4.3062 -0.0229 H + 26 H26 -3.2462 2.1800 -2.5892 H + 27 H27 -1.7216 2.3692 -3.4882 H + 28 H28 -2.0164 0.8942 -2.5364 H + 29 H29 -0.0024 3.9465 -1.8080 H + 30 H30 -1.6278 4.5303 -2.2389 H + 31 H31 -1.1314 4.4591 -0.5310 H +@BOND + 1 1 2 2 + 2 2 3 am + 3 2 15 am + 4 2 18 2 + 5 3 4 1 + 6 3 19 1 + 7 4 5 1 + 8 4 7 2 + 9 5 6 2 + 10 6 8 1 + 11 7 8 1 + 12 7 20 1 + 13 8 9 1 + 14 9 14 ar + 15 9 10 ar + 16 10 11 ar + 17 10 21 1 + 18 11 12 ar + 19 11 22 1 + 20 12 13 ar + 21 12 23 1 + 22 13 14 ar + 23 13 24 1 + 24 14 25 1 + 25 15 16 1 + 26 15 17 1 + 27 16 26 1 + 28 16 27 1 + 29 16 28 1 + 30 17 29 1 + 31 17 30 1 + 32 17 31 1 + +# End of record + diff --git a/top/oplsaa/SM46/SM46.mol2.1.itp b/top/oplsaa/SM46/SM46.mol2.1.itp new file mode 100644 index 0000000..d6c7f02 --- /dev/null +++ b/top/oplsaa/SM46/SM46.mol2.1.itp @@ -0,0 +1,307 @@ +; input pdb SMILES : O=[S](NC1=C[N](N=N1)C2=CC=CC=C2)(N(C)C)=O +; Script arguments : SM46.mol2 "5 opls_559 -0.290" "6 opls_559 -0.150" "20 opls_563 0.166" "7 opls_551 0.027" "8 opls_557 0.079" "9 opls_147" "4 opls_560 0.168" "19 opls_241 0.482" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_475 1 UNK O1 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 2 opls_474 1 UNK S2 1 0.852 32.06000 ; SY # S in sulfamide, S(=O)2(NR2) + 3 opls_480 1 UNK N15 1 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 4 opls_475 1 UNK O18 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 5 opls_480 1 UNK N3 3 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 6 opls_482 1 UNK C17 5 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 7 opls_483 1 UNK H29 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 8 opls_483 1 UNK H30 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 9 opls_483 1 UNK H31 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 10 opls_482 1 UNK C16 11 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 11 opls_483 1 UNK H26 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 12 opls_483 1 UNK H27 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 13 opls_483 1 UNK H28 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 14 opls_145 1 UNK C10 41 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 15 opls_146 1 UNK H21 41 0.115 1.00800 ; HA # Benzene H - 12 site. + 16 opls_145 1 UNK C11 43 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 17 opls_146 1 UNK H22 43 0.115 1.00800 ; HA # Benzene H - 12 site. + 18 opls_145 1 UNK C12 45 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 19 opls_146 1 UNK H23 45 0.115 1.00800 ; HA # Benzene H - 12 site. + 20 opls_145 1 UNK C13 47 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 21 opls_146 1 UNK H24 47 0.115 1.00800 ; HA # Benzene H - 12 site. + 22 opls_145 1 UNK C14 49 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 23 opls_146 1 UNK H25 49 0.115 1.00800 ; HA # Benzene H - 12 site. + 24 opls_560 1 UNK C4 51 0.168 12.01100 ; CV # C4 in imidazole ### user-defined OPLS atom type (opls_560) atom charge (0.168) + 25 opls_559 1 UNK N5 51 -0.290 14.00670 ; NB # N3 in imidazole ### user-defined OPLS atom type (opls_559) atom charge (-0.290) + 26 opls_559 1 UNK N6 51 -0.150 14.00670 ; NB # N3 in imidazole ### user-defined OPLS atom type (opls_559) atom charge (-0.150) + 27 opls_551 1 UNK C7 51 0.027 12.01100 ; CA # C4 in pyrazole ### user-defined OPLS atom type (opls_551) atom charge (0.027) + 28 opls_557 1 UNK N8 51 0.079 14.00670 ; NA # N1 in imidazole ### user-defined OPLS atom type (opls_557) atom charge (0.079) + 29 opls_147 1 UNK C9 51 0.000 12.01100 ; CA # Naphthalene fusion C (C9) ### user-defined OPLS atom type (opls_147) + 30 opls_241 1 UNK H19 51 0.482 1.00800 ; H # H on N: secondary amide ### user-defined OPLS atom type (opls_241) atom charge (0.482) + 31 opls_563 1 UNK H20 51 0.166 1.00800 ; HA # H2 in imidazole ### user-defined OPLS atom type (opls_563) atom charge (0.166) +; Total charge : -0.000 ### Number of unassigned atoms : 0/31 + +[ bonds ] +; ai aj funct r k + 1 2 1 ; OY-SY # (SY-OY) + 2 5 1 ; SY-N # + 2 3 1 ; SY-N # + 2 4 1 ; SY-OY # + 5 24 1 0.1381 357313.600 ; N-CV # LigParGen + 5 30 1 ; N-H # (H-N) + 24 25 1 ; CV-NB # ADE,GUA,HIS + 24 27 1 0.14000 392459.2 ; CV-CA # (CA-CV) by analogy from CA-CA : TRP,TYR,PHE + 25 26 1 0.1280 334720.000 ; NB-NB # LigParGen + 26 28 1 ; NB-NA # (NA-NB) -idem- + 27 28 1 ; CA-NA # GUA + 27 31 1 ; CA-HA # PHE, etc. + 28 29 1 ; NA-CA # (CA-NA) GUA + 29 22 1 ; CA-CA # TRP,TYR,PHE + 29 14 1 ; CA-CA # TRP,TYR,PHE + 14 16 1 ; CA-CA # TRP,TYR,PHE + 14 15 1 ; CA-HA # PHE, etc. + 16 18 1 ; CA-CA # TRP,TYR,PHE + 16 17 1 ; CA-HA # PHE, etc. + 18 20 1 ; CA-CA # TRP,TYR,PHE + 18 19 1 ; CA-HA # PHE, etc. + 20 22 1 ; CA-CA # TRP,TYR,PHE + 20 21 1 ; CA-HA # PHE, etc. + 22 23 1 ; CA-HA # PHE, etc. + 3 10 1 ; N-CT # (CT-N) + 3 6 1 ; N-CT # (CT-N) + 10 11 1 ; CT-HC # CHARMM 22 parameter file + 10 12 1 ; CT-HC # CHARMM 22 parameter file + 10 13 1 ; CT-HC # CHARMM 22 parameter file + 6 7 1 ; CT-HC # CHARMM 22 parameter file + 6 8 1 ; CT-HC # CHARMM 22 parameter file + 6 9 1 ; CT-HC # CHARMM 22 parameter file + +[ angles ] +; ai aj ak funct theta cth + 1 2 5 1 ; OY-SY-N # + 1 2 3 1 ; OY-SY-N # + 1 2 4 1 ; OY-SY-OY # + 5 2 3 1 107.000 1004.160 ; N-SY-N # by analogy from OY-SY-N : + 5 2 4 1 ; N-SY-OY # (OY-SY-N) + 3 2 4 1 ; N-SY-OY # (OY-SY-N) + 2 5 24 1 118.330 404.760 ; SY-N-CV # LigParGen + 2 5 30 1 ; SY-N-H # (H-N-SY) + 24 5 30 1 119.800 292.880 ; CV-N-H # LigParGen + 5 24 25 1 120.670 475.972 ; N-CV-NB # LigParGen + 5 24 27 1 120.000 585.760 ; N-CV-CA # LigParGen + 25 24 27 1 ; NB-CV-CA # (CA-CV-NB) wlj + 24 25 26 1 117.000 585.760 ; CV-NB-NB # LigParGen + 25 26 28 1 111.360 497.143 ; NB-NB-NA # LigParGen + 24 27 28 1 106.300 585.760 ; CV-CA-NA # LigParGen + 24 27 31 1 130.700 292.880 ; CV-CA-HA # LigParGen + 28 27 31 1 ; NA-CA-HA # (HA-CA-NA) + 26 28 27 1 ; NB-NA-CA # -idem- + 26 28 29 1 ; NB-NA-CA # -idem- + 27 28 29 1 ; CA-NA-CA # Added DSM (from C-NA-CA) + 28 29 22 1 ; NA-CA-CA # (CA-CA-NA) TRP(OL) + 28 29 14 1 ; NA-CA-CA # (CA-CA-NA) TRP(OL) + 14 29 22 1 ; CA-CA-CA # PHE(OL) + 29 14 16 1 ; CA-CA-CA # PHE(OL) + 29 14 15 1 ; CA-CA-HA # + 16 14 15 1 ; CA-CA-HA # + 14 16 18 1 ; CA-CA-CA # PHE(OL) + 14 16 17 1 ; CA-CA-HA # + 18 16 17 1 ; CA-CA-HA # + 16 18 20 1 ; CA-CA-CA # PHE(OL) + 16 18 19 1 ; CA-CA-HA # + 20 18 19 1 ; CA-CA-HA # + 18 20 22 1 ; CA-CA-CA # PHE(OL) + 18 20 21 1 ; CA-CA-HA # + 22 20 21 1 ; CA-CA-HA # + 29 22 20 1 ; CA-CA-CA # PHE(OL) + 29 22 23 1 ; CA-CA-HA # + 20 22 23 1 ; CA-CA-HA # + 2 3 10 1 ; SY-N-CT # + 2 3 6 1 ; SY-N-CT # + 10 3 6 1 ; CT-N-CT # PRO(OL) DETAR JACS 99,1232 + 3 10 11 1 ; N-CT-HC # (HC-CT-N) + 3 10 12 1 ; N-CT-HC # (HC-CT-N) + 3 10 13 1 ; N-CT-HC # (HC-CT-N) + 11 10 12 1 ; HC-CT-HC # CHARMM 22 parameter file + 11 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 12 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 3 6 7 1 ; N-CT-HC # (HC-CT-N) + 3 6 8 1 ; N-CT-HC # (HC-CT-N) + 3 6 9 1 ; N-CT-HC # (HC-CT-N) + 7 6 8 1 ; HC-CT-HC # CHARMM 22 parameter file + 7 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + 8 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 1 2 5 24 3 ; OY-SY-N-CV # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 5 30 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 2 5 24 3 -2.897 11.182 12.410 -20.694 -0.000 0.000 ; N-SY-N-CV # LigParGen + 3 2 5 30 3 -15.611 0.703 20.506 -5.598 -0.000 0.000 ; N-SY-N-H # LigParGen + 4 2 5 24 3 ; OY-SY-N-CV # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 5 30 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 5 2 3 10 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 5 2 3 6 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; N-SY-N-CT # (CT-N-SY-N) adapted from CT-N-SY-CT : sulfonamide + 4 2 3 10 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 4 2 3 6 3 ; OY-SY-N-CT # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 5 24 25 3 -2.935 -1.914 6.096 -1.247 -0.000 0.000 ; SY-N-CV-NB # LigParGen + 2 5 24 27 3 -3.431 -3.008 10.598 -4.159 -0.000 0.000 ; SY-N-CV-CA # LigParGen + 30 5 24 25 3 8.786 0.000 -8.786 -0.000 -0.000 0.000 ; H-N-CV-NB # LigParGen + 30 5 24 27 3 8.786 0.000 -8.786 -0.000 -0.000 0.000 ; H-N-CV-CA # LigParGen adapted + 5 24 25 26 3 ; N-CV-NB-NB # (X-CV-NB-X generic proper dihedral) + 27 24 25 26 3 ; CA-CV-NB-NB # (X-CV-NB-X generic proper dihedral) + 5 24 27 28 3 44.978 0.000 -44.978 -0.000 -0.000 0.000 ; N-CV-CA-NA # LigParGen + 5 24 27 31 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 ; N-CV-CA-HA # LigParGen + 25 24 27 28 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; NB-CV-CA-NA # LigParGen + 25 24 27 31 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; NB-CV-CA-HA # by analogy with X-CA-CA-X : aromatic ring (the same as LigParGen) + 24 25 26 28 3 41.840 0.000 -41.840 -0.000 -0.000 0.000 ; CV-NB-NB-NA # LigParGen + 25 26 28 27 3 ; NB-NB-NA-CA # (X-NA-NB-X generic proper dihedral) + 25 26 28 29 3 ; NB-NB-NA-CA # (X-NA-NB-X generic proper dihedral) + 24 27 28 26 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 ; CV-CA-NA-NB # LigParGen + 24 27 28 29 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 ; CV-CA-NA-CA # LigParGen + 31 27 28 26 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 ; HA-CA-NA-NB # LigParGen + 31 27 28 29 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 ; HA-CA-NA-CA # LigParGen + 26 28 29 22 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; NB-NA-CA-CA # LigParGen + 26 28 29 14 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; NB-NA-CA-CA # LigParGen + 27 28 29 22 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; CA-NA-CA-CA # LigParGen + 27 28 29 14 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 ; CA-NA-CA-CA # LigParGen + 28 29 22 20 3 ; NA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 29 22 23 3 ; NA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 29 22 20 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 29 22 23 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 29 14 16 3 ; NA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 29 14 15 3 ; NA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 29 14 16 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 29 14 15 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 14 16 18 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 29 14 16 17 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 14 16 18 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 14 16 17 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 16 18 20 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 16 18 19 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 16 18 20 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 16 18 19 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 18 20 22 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 18 20 21 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 18 20 22 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 18 20 21 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 20 22 29 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 20 22 23 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 20 22 29 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 20 22 23 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 3 10 11 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 12 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 10 13 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 6 3 10 11 3 ; CT-N-CT-HC # tert. amide + 6 3 10 12 3 ; CT-N-CT-HC # tert. amide + 6 3 10 13 3 ; CT-N-CT-HC # tert. amide + 2 3 6 7 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 8 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 2 3 6 9 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 10 3 6 7 3 ; CT-N-CT-HC # tert. amide + 10 3 6 8 3 ; CT-N-CT-HC # tert. amide + 10 3 6 9 3 ; CT-N-CT-HC # tert. amide + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 24 30 5 2 1 improper_Z_N_X_Y ; CV-H-N-SY + 25 27 24 5 1 improper_N2_X_N2_N2 ; NB-CA-CV-N + 28 31 27 24 1 improper_Z_CM_X_Y ; NA-HA-CA-CV + 27 29 28 26 1 improper_Z_N_X_Y ; CA-CA-NA-NB + 22 14 29 28 1 improper_Z_CA_X_Y ; CA-CA-CA-NA + 16 15 14 29 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 18 17 16 14 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 20 19 18 16 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 22 21 20 18 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 20 23 22 29 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 2 6 3 10 1 improper_Z_N_X_Y ; SY-CT-N-CT + +[ pairs ] +; ai aj funct + 1 24 1 + 1 30 1 + 1 10 1 + 1 6 1 + 2 25 1 + 2 27 1 + 2 11 1 + 2 12 1 + 2 13 1 + 2 7 1 + 2 8 1 + 2 9 1 + 5 10 1 + 5 6 1 + 5 26 1 + 5 28 1 + 5 31 1 + 24 3 1 + 24 4 1 + 24 29 1 + 25 30 1 + 25 31 1 + 25 29 1 + 26 31 1 + 26 22 1 + 26 14 1 + 27 30 1 + 27 22 1 + 27 14 1 + 28 20 1 + 28 23 1 + 28 16 1 + 28 15 1 + 29 31 1 + 29 18 1 + 29 21 1 + 29 17 1 + 14 20 1 + 14 23 1 + 14 19 1 + 16 22 1 + 16 21 1 + 18 15 1 + 18 23 1 + 20 17 1 + 22 15 1 + 22 19 1 + 3 30 1 + 10 4 1 + 10 7 1 + 10 8 1 + 10 9 1 + 6 4 1 + 6 11 1 + 6 12 1 + 6 13 1 + 4 30 1 + 15 17 1 + 17 19 1 + 19 21 1 + 21 23 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 5 1 1000 1000 1000 + 24 1 1000 1000 1000 + 25 1 1000 1000 1000 + 26 1 1000 1000 1000 + 27 1 1000 1000 1000 + 28 1 1000 1000 1000 + 29 1 1000 1000 1000 + 14 1 1000 1000 1000 + 16 1 1000 1000 1000 + 18 1 1000 1000 1000 + 20 1 1000 1000 1000 + 22 1 1000 1000 1000 + 3 1 1000 1000 1000 + 10 1 1000 1000 1000 + 6 1 1000 1000 1000 + 4 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/SM46/SM46.mol2.1.pdb b/top/oplsaa/SM46/SM46.mol2.1.pdb new file mode 100644 index 0000000..a05e926 --- /dev/null +++ b/top/oplsaa/SM46/SM46.mol2.1.pdb @@ -0,0 +1,32 @@ +HETATM 1 O1 UNK 1 -2.472 0.781 -0.017 1.00 20.00 +HETATM 2 S2 UNK 1 -1.456 1.774 0.019 1.00 20.00 +HETATM 3 N15 UNK 1 -1.565 2.605 -1.410 1.00 20.00 +HETATM 4 O18 UNK 1 -1.361 2.752 1.045 1.00 20.00 +HETATM 5 N3 UNK 1 -0.011 0.966 0.007 1.00 20.00 +HETATM 6 C17 UNK 1 -1.048 3.973 -1.503 1.00 20.00 +HETATM 7 H29 UNK 1 -0.002 3.946 -1.808 1.00 20.00 +HETATM 8 H30 UNK 1 -1.628 4.530 -2.239 1.00 20.00 +HETATM 9 H31 UNK 1 -1.131 4.459 -0.531 1.00 20.00 +HETATM 10 C16 UNK 1 -2.176 1.972 -2.581 1.00 20.00 +HETATM 11 H26 UNK 1 -3.246 2.180 -2.589 1.00 20.00 +HETATM 12 H27 UNK 1 -1.722 2.369 -3.488 1.00 20.00 +HETATM 13 H28 UNK 1 -2.016 0.894 -2.536 1.00 20.00 +HETATM 14 C10 UNK 1 5.343 0.947 -0.041 1.00 20.00 +HETATM 15 H21 UNK 1 4.766 0.035 -0.035 1.00 20.00 +HETATM 16 C11 UNK 1 6.723 0.892 -0.061 1.00 20.00 +HETATM 17 H22 UNK 1 7.225 -0.064 -0.072 1.00 20.00 +HETATM 18 C12 UNK 1 7.463 2.060 -0.062 1.00 20.00 +HETATM 19 H23 UNK 1 8.542 2.015 -0.073 1.00 20.00 +HETATM 20 C13 UNK 1 6.825 3.287 -0.048 1.00 20.00 +HETATM 21 H24 UNK 1 7.405 4.197 -0.049 1.00 20.00 +HETATM 22 C14 UNK 1 5.445 3.348 -0.033 1.00 20.00 +HETATM 23 H25 UNK 1 4.947 4.306 -0.023 1.00 20.00 +HETATM 24 C4 UNK 1 1.195 1.684 -0.000 1.00 20.00 +HETATM 25 N5 UNK 1 1.335 3.017 0.006 1.00 20.00 +HETATM 26 N6 UNK 1 2.588 3.309 -0.005 1.00 20.00 +HETATM 27 C7 UNK 1 2.451 1.166 -0.010 1.00 20.00 +HETATM 28 N8 UNK 1 3.298 2.236 -0.018 1.00 20.00 +HETATM 29 C9 UNK 1 4.699 2.177 -0.033 1.00 20.00 +HETATM 30 H19 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 31 H20 UNK 1 2.723 0.121 -0.012 1.00 20.00 +END diff --git a/top/oplsaa/SM46/SM46.pdb b/top/oplsaa/SM46/SM46.pdb new file mode 120000 index 0000000..6c25663 --- /dev/null +++ b/top/oplsaa/SM46/SM46.pdb @@ -0,0 +1 @@ +SM46.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/refCMC26/refCMC26.itp b/top/oplsaa/refCMC26/refCMC26.itp new file mode 120000 index 0000000..becdeeb --- /dev/null +++ b/top/oplsaa/refCMC26/refCMC26.itp @@ -0,0 +1 @@ +refCMC26.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/refCMC26/refCMC26.mol2 b/top/oplsaa/refCMC26/refCMC26.mol2 new file mode 100644 index 0000000..e976d4e --- /dev/null +++ b/top/oplsaa/refCMC26/refCMC26.mol2 @@ -0,0 +1,80 @@ +# Name: UNK +# Creating user name: iorga +# Creation time: 10. 07. 2020 09:50 + +# Modifying user name: iorga +# Modification time: 10. 07. 2020 09:50 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 29 30 0 0 0 +SMALL +NO_CHARGES + + +@ATOM + 1 O1 -2.3285 -0.1731 0.0243 O.2 + 2 C2 -1.2662 -0.7638 0.0105 C.2 + 3 C3 0.0021 -0.0041 0.0020 C.ar + 4 C4 -0.0169 1.3915 0.0097 C.ar + 5 C5 1.1702 2.0945 0.0021 C.ar + 6 C6 2.3776 1.4190 -0.0130 C.ar + 7 C7 2.4034 0.0357 -0.0207 C.ar + 8 C8 1.2235 -0.6793 -0.0133 C.ar + 9 N9 -1.2445 -2.1114 0.0031 N.am + 10 S10 -2.6651 -2.9624 0.0126 S.o2 + 11 C11 -3.4932 -2.6121 -1.5027 C.ar + 12 C12 -4.3747 -1.5501 -1.5791 C.ar + 13 C13 -5.0207 -1.2723 -2.7693 C.ar + 14 C14 -4.7930 -2.0629 -3.8802 C.ar + 15 C15 -3.9154 -3.1281 -3.8023 C.ar + 16 C16 -3.2655 -3.4027 -2.6136 C.ar + 17 O17 -2.3095 -4.3374 -0.0330 O.2 + 18 O18 -3.4629 -2.3999 1.0452 O.2 + 19 H19 -0.9587 1.9200 0.0170 H + 20 H20 1.1570 3.1744 0.0081 H + 21 H21 3.3041 1.9740 -0.0192 H + 22 H22 3.3492 -0.4856 -0.0329 H + 23 H23 1.2450 -1.7591 -0.0196 H + 24 H24 -0.3968 -2.5828 -0.0079 H + 25 H25 -4.5559 -0.9351 -0.7100 H + 26 H26 -5.7066 -0.4403 -2.8300 H + 27 H27 -5.3011 -1.8486 -4.8088 H + 28 H28 -3.7378 -3.7460 -4.6701 H + 29 H29 -2.5801 -4.2351 -2.5526 H +@BOND + 1 1 2 2 + 2 2 3 1 + 3 2 9 am + 4 3 8 ar + 5 3 4 ar + 6 4 5 ar + 7 4 19 1 + 8 5 6 ar + 9 5 20 1 + 10 6 7 ar + 11 6 21 1 + 12 7 8 ar + 13 7 22 1 + 14 8 23 1 + 15 9 10 am + 16 9 24 1 + 17 10 11 1 + 18 10 17 2 + 19 10 18 2 + 20 11 16 ar + 21 11 12 ar + 22 12 13 ar + 23 12 25 1 + 24 13 14 ar + 25 13 26 1 + 26 14 15 ar + 27 14 27 1 + 28 15 16 ar + 29 15 28 1 + 30 16 29 1 + +# End of record + diff --git a/top/oplsaa/refCMC26/refCMC26.mol2.1.itp b/top/oplsaa/refCMC26/refCMC26.mol2.1.itp new file mode 100644 index 0000000..4e93511 --- /dev/null +++ b/top/oplsaa/refCMC26/refCMC26.mol2.1.itp @@ -0,0 +1,301 @@ +; input pdb SMILES : O=C(C1=CC=CC=C1)N[S](C2=CC=CC=C2)(=O)=O +; Script arguments : refCMC26.mol2 "9 opls_251" "24 opls_254" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_474 1 UNK S10 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 2 opls_488 1 UNK C11 1 0.000 12.01100 ; CA # benzene C attached to S of sulfonamide + 3 opls_475 1 UNK O17 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 4 opls_475 1 UNK O18 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 5 opls_236 1 UNK O1 3 -0.500 15.99940 ; O # O: C=O in amide. Acyl R on C in amide is neutral - + 6 opls_234 1 UNK C2 3 0.615 12.01100 ; C # C: C=O in benzamide + 7 opls_145 1 UNK C3 3 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 8 opls_145 1 UNK C4 5 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 9 opls_146 1 UNK H19 5 0.115 1.00800 ; HA # Benzene H - 12 site. + 10 opls_145 1 UNK C5 7 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 11 opls_146 1 UNK H20 7 0.115 1.00800 ; HA # Benzene H - 12 site. + 12 opls_145 1 UNK C6 9 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 13 opls_146 1 UNK H21 9 0.115 1.00800 ; HA # Benzene H - 12 site. + 14 opls_145 1 UNK C7 11 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 15 opls_146 1 UNK H22 11 0.115 1.00800 ; HA # Benzene H - 12 site. + 16 opls_145 1 UNK C8 13 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 17 opls_146 1 UNK H23 13 0.115 1.00800 ; HA # Benzene H - 12 site. + 18 opls_145 1 UNK C12 15 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 19 opls_146 1 UNK H25 15 0.115 1.00800 ; HA # Benzene H - 12 site. + 20 opls_145 1 UNK C13 17 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 21 opls_146 1 UNK H26 17 0.115 1.00800 ; HA # Benzene H - 12 site. + 22 opls_145 1 UNK C14 19 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 23 opls_146 1 UNK H27 19 0.115 1.00800 ; HA # Benzene H - 12 site. + 24 opls_145 1 UNK C15 21 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 25 opls_146 1 UNK H28 21 0.115 1.00800 ; HA # Benzene H - 12 site. + 26 opls_145 1 UNK C16 23 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 27 opls_146 1 UNK H29 23 0.115 1.00800 ; HA # Benzene H - 12 site. + 28 opls_251 1 UNK N9 25 -0.490 14.00670 ; N # N in imide ### user-defined OPLS atom type (opls_251) + 29 opls_254 1 UNK H24 25 0.370 1.00800 ; H # H(N) in imide ### user-defined OPLS atom type (opls_254) +; Total charge : -0.000 ### Number of unassigned atoms : 0/29 + +[ bonds ] +; ai aj funct r k + 5 6 1 ; O-C # (C-O) URAGUA,CYT,AA + 6 7 1 ; C-CA # wlj 8/97 + 6 28 1 ; C-N # AA + 7 16 1 ; CA-CA # TRP,TYR,PHE + 7 8 1 ; CA-CA # TRP,TYR,PHE + 8 10 1 ; CA-CA # TRP,TYR,PHE + 8 9 1 ; CA-HA # PHE, etc. + 10 12 1 ; CA-CA # TRP,TYR,PHE + 10 11 1 ; CA-HA # PHE, etc. + 12 14 1 ; CA-CA # TRP,TYR,PHE + 12 13 1 ; CA-HA # PHE, etc. + 14 16 1 ; CA-CA # TRP,TYR,PHE + 14 15 1 ; CA-HA # PHE, etc. + 16 17 1 ; CA-HA # PHE, etc. + 28 1 1 ; N-SY # (SY-N) + 28 29 1 ; N-H # (H-N) + 1 2 1 ; SY-CA # + 1 3 1 ; SY-OY # + 1 4 1 ; SY-OY # + 2 26 1 ; CA-CA # TRP,TYR,PHE + 2 18 1 ; CA-CA # TRP,TYR,PHE + 18 20 1 ; CA-CA # TRP,TYR,PHE + 18 19 1 ; CA-HA # PHE, etc. + 20 22 1 ; CA-CA # TRP,TYR,PHE + 20 21 1 ; CA-HA # PHE, etc. + 22 24 1 ; CA-CA # TRP,TYR,PHE + 22 23 1 ; CA-HA # PHE, etc. + 24 26 1 ; CA-CA # TRP,TYR,PHE + 24 25 1 ; CA-HA # PHE, etc. + 26 27 1 ; CA-HA # PHE, etc. + +[ angles ] +; ai aj ak funct theta cth + 5 6 7 1 ; O-C-CA # (CA-C-O) wlj + 5 6 28 1 ; O-C-N # (N-C-O) AA(OL) + 7 6 28 1 ; CA-C-N # wlj 8/97 benzamide + 6 7 16 1 ; C-CA-CA # TYR(OL) + 6 7 8 1 ; C-CA-CA # TYR(OL) + 8 7 16 1 ; CA-CA-CA # PHE(OL) + 7 8 10 1 ; CA-CA-CA # PHE(OL) + 7 8 9 1 ; CA-CA-HA # + 10 8 9 1 ; CA-CA-HA # + 8 10 12 1 ; CA-CA-CA # PHE(OL) + 8 10 11 1 ; CA-CA-HA # + 12 10 11 1 ; CA-CA-HA # + 10 12 14 1 ; CA-CA-CA # PHE(OL) + 10 12 13 1 ; CA-CA-HA # + 14 12 13 1 ; CA-CA-HA # + 12 14 16 1 ; CA-CA-CA # PHE(OL) + 12 14 15 1 ; CA-CA-HA # + 16 14 15 1 ; CA-CA-HA # + 7 16 14 1 ; CA-CA-CA # PHE(OL) + 7 16 17 1 ; CA-CA-HA # + 14 16 17 1 ; CA-CA-HA # + 6 28 1 1 112.000 585.760 ; C-N-SY # LigParGen + 6 28 29 1 ; C-N-H # AA(OL) + 1 28 29 1 ; SY-N-H # (H-N-SY) + 28 1 2 1 ; N-SY-CA # + 28 1 3 1 ; N-SY-OY # (OY-SY-N) + 28 1 4 1 ; N-SY-OY # (OY-SY-N) + 2 1 3 1 ; CA-SY-OY # (OY-SY-CA) + 2 1 4 1 ; CA-SY-OY # (OY-SY-CA) + 3 1 4 1 ; OY-SY-OY # + 1 2 26 1 ; SY-CA-CA # + 1 2 18 1 ; SY-CA-CA # + 18 2 26 1 ; CA-CA-CA # PHE(OL) + 2 18 20 1 ; CA-CA-CA # PHE(OL) + 2 18 19 1 ; CA-CA-HA # + 20 18 19 1 ; CA-CA-HA # + 18 20 22 1 ; CA-CA-CA # PHE(OL) + 18 20 21 1 ; CA-CA-HA # + 22 20 21 1 ; CA-CA-HA # + 20 22 24 1 ; CA-CA-CA # PHE(OL) + 20 22 23 1 ; CA-CA-HA # + 24 22 23 1 ; CA-CA-HA # + 22 24 26 1 ; CA-CA-CA # PHE(OL) + 22 24 25 1 ; CA-CA-HA # + 26 24 25 1 ; CA-CA-HA # + 2 26 24 1 ; CA-CA-CA # PHE(OL) + 2 26 27 1 ; CA-CA-HA # + 24 26 27 1 ; CA-CA-HA # + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 5 6 7 16 3 ; O-C-CA-CA # (CA-CA-C-O) aryl acid, amide, ester + 5 6 7 8 3 ; O-C-CA-CA # (CA-CA-C-O) aryl acid, amide, ester + 28 6 7 16 3 ; N-C-CA-CA # (CA-CA-C-N) aryl amides, benzamides + 28 6 7 8 3 ; N-C-CA-CA # (CA-CA-C-N) aryl amides, benzamides + 5 6 28 1 3 25.476 0.000 -25.476 -0.000 -0.000 0.000 ; O-C-N-SY # LigParGen + 5 6 28 29 3 ; O-C-N-H # (H-N-C-O) amides wlj 6/20/97 + 7 6 28 1 3 20.502 0.000 -20.502 -0.000 -0.000 0.000 ; CA-C-N-SY # LigParGen + 7 6 28 29 3 20.502 0.000 -20.502 -0.000 -0.000 0.000 ; CA-C-N-H # LigParGen + 6 7 16 14 3 ; C-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 6 7 16 17 3 ; C-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 8 7 16 14 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 8 7 16 17 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 6 7 8 10 3 ; C-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 6 7 8 9 3 ; C-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 7 8 10 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 7 8 9 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 7 8 10 12 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 7 8 10 11 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 9 8 10 12 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 9 8 10 11 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 8 10 12 14 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 8 10 12 13 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 10 12 14 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 10 12 13 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 12 14 16 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 12 14 15 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 13 12 14 16 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 13 12 14 15 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 12 14 16 7 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 12 14 16 17 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 14 16 7 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 14 16 17 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 6 28 1 2 3 -2.897 11.182 12.410 -20.694 -0.000 0.000 ; C-N-SY-CA # LigParGen + 6 28 1 3 3 ; C-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 6 28 1 4 3 ; C-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 29 28 1 2 3 ; H-N-SY-CA # (CA-SY-N-H) sulfonamide + 29 28 1 3 3 ; H-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 29 28 1 4 3 ; H-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 28 1 2 26 3 ; N-SY-CA-CA # (CA-CA-SY-N) sulfonamide + 28 1 2 18 3 ; N-SY-CA-CA # (CA-CA-SY-N) sulfonamide + 3 1 2 26 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 3 1 2 18 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 4 1 2 26 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 4 1 2 18 3 ; OY-SY-CA-CA # (OY-SY-CA-X generic proper dihedral) sulfonamide + 1 2 26 24 3 ; SY-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 1 2 26 27 3 ; SY-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 2 26 24 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 2 26 27 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 1 2 18 20 3 ; SY-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 1 2 18 19 3 ; SY-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 2 18 20 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 2 18 19 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 18 20 22 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 2 18 20 21 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 18 20 22 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 18 20 21 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 20 22 24 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 20 22 23 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 20 22 24 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 20 22 23 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 20 22 24 26 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 20 22 24 25 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 22 24 26 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 22 24 25 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 24 26 2 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 24 26 27 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 24 26 2 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 24 26 27 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 7 28 6 5 1 improper_O_C_X_Y ; CA-N-C-O + 16 8 7 6 1 improper_Z_CA_X_Y ; CA-CA-CA-C + 10 9 8 7 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 12 11 10 8 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 14 13 12 10 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 16 15 14 12 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 14 17 16 7 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 1 29 28 6 1 improper_Z_N_X_Y ; SY-H-N-C + 26 18 2 1 1 improper_Z_CA_X_Y ; CA-CA-CA-SY + 20 19 18 2 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 22 21 20 18 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 24 23 22 20 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 26 25 24 22 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 24 27 26 2 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + +[ pairs ] +; ai aj funct + 5 16 1 + 5 8 1 + 5 1 1 + 5 29 1 + 6 14 1 + 6 17 1 + 6 10 1 + 6 9 1 + 6 2 1 + 6 3 1 + 6 4 1 + 7 1 1 + 7 29 1 + 7 12 1 + 7 15 1 + 7 11 1 + 8 28 1 + 8 14 1 + 8 17 1 + 8 13 1 + 10 16 1 + 10 15 1 + 12 9 1 + 12 17 1 + 14 11 1 + 16 28 1 + 16 9 1 + 16 13 1 + 28 26 1 + 28 18 1 + 1 24 1 + 1 27 1 + 1 20 1 + 1 19 1 + 2 29 1 + 2 22 1 + 2 25 1 + 2 21 1 + 18 3 1 + 18 4 1 + 18 24 1 + 18 27 1 + 18 23 1 + 20 26 1 + 20 25 1 + 22 19 1 + 22 27 1 + 24 21 1 + 26 3 1 + 26 4 1 + 26 19 1 + 26 23 1 + 3 29 1 + 4 29 1 + 9 11 1 + 11 13 1 + 13 15 1 + 15 17 1 + 19 21 1 + 21 23 1 + 23 25 1 + 25 27 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 5 1 1000 1000 1000 + 6 1 1000 1000 1000 + 7 1 1000 1000 1000 + 8 1 1000 1000 1000 + 10 1 1000 1000 1000 + 12 1 1000 1000 1000 + 14 1 1000 1000 1000 + 16 1 1000 1000 1000 + 28 1 1000 1000 1000 + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 18 1 1000 1000 1000 + 20 1 1000 1000 1000 + 22 1 1000 1000 1000 + 24 1 1000 1000 1000 + 26 1 1000 1000 1000 + 3 1 1000 1000 1000 + 4 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/refCMC26/refCMC26.mol2.1.pdb b/top/oplsaa/refCMC26/refCMC26.mol2.1.pdb new file mode 100644 index 0000000..37eebfe --- /dev/null +++ b/top/oplsaa/refCMC26/refCMC26.mol2.1.pdb @@ -0,0 +1,30 @@ +HETATM 1 S10 UNK 1 -2.665 -2.962 0.013 1.00 20.00 +HETATM 2 C11 UNK 1 -3.493 -2.612 -1.503 1.00 20.00 +HETATM 3 O17 UNK 1 -2.309 -4.337 -0.033 1.00 20.00 +HETATM 4 O18 UNK 1 -3.463 -2.400 1.045 1.00 20.00 +HETATM 5 O1 UNK 1 -2.329 -0.173 0.024 1.00 20.00 +HETATM 6 C2 UNK 1 -1.266 -0.764 0.011 1.00 20.00 +HETATM 7 C3 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 8 C4 UNK 1 -0.017 1.391 0.010 1.00 20.00 +HETATM 9 H19 UNK 1 -0.959 1.920 0.017 1.00 20.00 +HETATM 10 C5 UNK 1 1.170 2.095 0.002 1.00 20.00 +HETATM 11 H20 UNK 1 1.157 3.174 0.008 1.00 20.00 +HETATM 12 C6 UNK 1 2.378 1.419 -0.013 1.00 20.00 +HETATM 13 H21 UNK 1 3.304 1.974 -0.019 1.00 20.00 +HETATM 14 C7 UNK 1 2.403 0.036 -0.021 1.00 20.00 +HETATM 15 H22 UNK 1 3.349 -0.486 -0.033 1.00 20.00 +HETATM 16 C8 UNK 1 1.224 -0.679 -0.013 1.00 20.00 +HETATM 17 H23 UNK 1 1.245 -1.759 -0.020 1.00 20.00 +HETATM 18 C12 UNK 1 -4.375 -1.550 -1.579 1.00 20.00 +HETATM 19 H25 UNK 1 -4.556 -0.935 -0.710 1.00 20.00 +HETATM 20 C13 UNK 1 -5.021 -1.272 -2.769 1.00 20.00 +HETATM 21 H26 UNK 1 -5.707 -0.440 -2.830 1.00 20.00 +HETATM 22 C14 UNK 1 -4.793 -2.063 -3.880 1.00 20.00 +HETATM 23 H27 UNK 1 -5.301 -1.849 -4.809 1.00 20.00 +HETATM 24 C15 UNK 1 -3.915 -3.128 -3.802 1.00 20.00 +HETATM 25 H28 UNK 1 -3.738 -3.746 -4.670 1.00 20.00 +HETATM 26 C16 UNK 1 -3.265 -3.403 -2.614 1.00 20.00 +HETATM 27 H29 UNK 1 -2.580 -4.235 -2.553 1.00 20.00 +HETATM 28 N9 UNK 1 -1.244 -2.111 0.003 1.00 20.00 +HETATM 29 H24 UNK 1 -0.397 -2.583 -0.008 1.00 20.00 +END diff --git a/top/oplsaa/refCMC26/refCMC26.pdb b/top/oplsaa/refCMC26/refCMC26.pdb new file mode 120000 index 0000000..91c744a --- /dev/null +++ b/top/oplsaa/refCMC26/refCMC26.pdb @@ -0,0 +1 @@ +refCMC26.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/refJMC11/refJMC11.mol2 b/top/oplsaa/refJMC11/refJMC11.mol2 deleted file mode 120000 index 6642f23..0000000 --- a/top/oplsaa/refJMC11/refJMC11.mol2 +++ /dev/null @@ -1 +0,0 @@ -../../../../01_struct3D/refJMC11/refJMC11.mol2 \ No newline at end of file diff --git a/top/oplsaa/refJMC11/refJMC11.mol2 b/top/oplsaa/refJMC11/refJMC11.mol2 new file mode 100644 index 0000000..846c4b7 --- /dev/null +++ b/top/oplsaa/refJMC11/refJMC11.mol2 @@ -0,0 +1,79 @@ +# Name: UNK +# Creating user name: iorga +# Creation time: 10. 07. 2020 09:43 + +# Modifying user name: iorga +# Modification time: 10. 07. 2020 09:43 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 29 29 0 0 0 +SMALL +NO_CHARGES + + +@ATOM + 1 C1 0.8091 10.4291 -2.3116 C.3 + 2 S2 -0.5250 9.4710 -3.0816 S.o2 + 3 O3 -0.4641 9.5797 -4.4971 O.2 + 4 O4 -1.7471 9.6677 -2.3837 O.2 + 5 N5 -0.1296 7.8923 -2.7758 N.am + 6 C6 -0.1109 7.3956 -1.3976 C.3 + 7 C7 -0.0901 5.8658 -1.4071 C.3 + 8 C8 -0.0705 5.3471 0.0321 C.3 + 9 C9 -0.0501 3.8402 0.0228 C.ar + 10 C10 1.1563 3.1654 0.0081 C.ar + 11 C11 1.1750 1.7832 0.0004 C.ar + 12 C12 -0.0126 1.0758 0.0080 C.ar + 13 C13 -1.2190 1.7506 0.0173 C.ar + 14 C14 -1.2377 3.1328 0.0294 C.ar + 15 H15 1.7619 10.1533 -2.7635 H + 16 H16 0.6282 11.4928 -2.4658 H + 17 H17 0.8388 10.2167 -1.2429 H + 18 H18 0.0895 7.2964 -3.5091 H + 19 H19 -1.0011 7.7436 -0.8738 H + 20 H20 0.7786 7.7679 -0.8894 H + 21 H21 0.8001 5.5177 -1.9309 H + 22 H22 -0.9796 5.4935 -1.9154 H + 23 H23 -0.9608 5.6951 0.5560 H + 24 H24 0.8190 5.7193 0.5404 H + 25 H25 2.0842 3.7181 0.0029 H + 26 H26 2.1175 1.2560 -0.0111 H + 27 H27 0.0021 -0.0041 0.0020 H + 28 H28 -2.1469 1.1980 0.0188 H + 29 H29 -2.1802 3.6600 0.0413 H +@BOND + 1 1 2 1 + 2 1 15 1 + 3 1 16 1 + 4 1 17 1 + 5 2 3 2 + 6 2 4 2 + 7 2 5 am + 8 5 6 1 + 9 5 18 1 + 10 6 7 1 + 11 6 19 1 + 12 6 20 1 + 13 7 8 1 + 14 7 21 1 + 15 7 22 1 + 16 8 9 1 + 17 8 23 1 + 18 8 24 1 + 19 9 14 ar + 20 9 10 ar + 21 10 11 ar + 22 10 25 1 + 23 11 12 ar + 24 11 26 1 + 25 12 13 ar + 26 12 27 1 + 27 13 14 ar + 28 13 28 1 + 29 14 29 1 + +# End of record + diff --git a/top/oplsaa/refJMC12/refJMC12.itp b/top/oplsaa/refJMC12/refJMC12.itp new file mode 120000 index 0000000..c21eb3c --- /dev/null +++ b/top/oplsaa/refJMC12/refJMC12.itp @@ -0,0 +1 @@ +refJMC12.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/refJMC12/refJMC12.mol2 b/top/oplsaa/refJMC12/refJMC12.mol2 new file mode 100644 index 0000000..b35aa8f --- /dev/null +++ b/top/oplsaa/refJMC12/refJMC12.mol2 @@ -0,0 +1,77 @@ +# Name: UNK +# Creating user name: iorga +# Creation time: 10. 07. 2020 09:44 + +# Modifying user name: iorga +# Modification time: 10. 07. 2020 09:44 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 28 28 0 0 0 +SMALL +NO_CHARGES + + +@ATOM + 1 C1 1.4398 10.1791 -1.8192 C.3 + 2 S2 -0.1524 9.7093 -2.5505 S.o2 + 3 O3 -0.1950 10.0677 -3.9249 O.2 + 4 O4 -1.2207 10.0399 -1.6737 O.2 + 5 N5 -0.1300 8.0535 -2.5607 N.am + 6 C6 -0.1105 7.3726 -1.3978 C.2 + 7 O7 -0.1095 7.9725 -0.3438 O.2 + 8 C8 -0.0901 5.8658 -1.4071 C.3 + 9 C9 -0.0705 5.3471 0.0321 C.3 + 10 C10 -0.0501 3.8402 0.0228 C.ar + 11 C11 1.1563 3.1654 0.0081 C.ar + 12 C12 1.1750 1.7832 0.0004 C.ar + 13 C13 -0.0126 1.0758 0.0080 C.ar + 14 C14 -1.2190 1.7506 0.0173 C.ar + 15 C15 -1.2377 3.1328 0.0294 C.ar + 16 H16 2.2511 9.7869 -2.4325 H + 17 H17 1.5119 11.2657 -1.7729 H + 18 H18 1.5132 9.7668 -0.8128 H + 19 H19 -0.1308 7.5737 -3.4037 H + 20 H20 0.8001 5.5177 -1.9309 H + 21 H21 -0.9796 5.4935 -1.9154 H + 22 H22 -0.9608 5.6951 0.5560 H + 23 H23 0.8190 5.7193 0.5404 H + 24 H24 2.0842 3.7181 0.0029 H + 25 H25 2.1175 1.2560 -0.0111 H + 26 H26 0.0021 -0.0041 0.0020 H + 27 H27 -2.1469 1.1980 0.0188 H + 28 H28 -2.1802 3.6600 0.0413 H +@BOND + 1 1 2 1 + 2 1 16 1 + 3 1 17 1 + 4 1 18 1 + 5 2 3 2 + 6 2 4 2 + 7 2 5 am + 8 5 6 am + 9 5 19 1 + 10 6 7 2 + 11 6 8 1 + 12 8 9 1 + 13 8 20 1 + 14 8 21 1 + 15 9 10 1 + 16 9 22 1 + 17 9 23 1 + 18 10 15 ar + 19 10 11 ar + 20 11 12 ar + 21 11 24 1 + 22 12 13 ar + 23 12 25 1 + 24 13 14 ar + 25 13 26 1 + 26 14 15 ar + 27 14 27 1 + 28 15 28 1 + +# End of record + diff --git a/top/oplsaa/refJMC12/refJMC12.mol2.1.itp b/top/oplsaa/refJMC12/refJMC12.mol2.1.itp new file mode 100644 index 0000000..cba4de6 --- /dev/null +++ b/top/oplsaa/refJMC12/refJMC12.mol2.1.itp @@ -0,0 +1,284 @@ +; input pdb SMILES : C[S](=O)(=O)NC(=O)CCC1=CC=CC=C1 +; Script arguments : refJMC12.mol2 "5 opls_251" "19 opls_254" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_474 1 UNK S2 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 2 opls_475 1 UNK O3 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 3 opls_475 1 UNK O4 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 4 opls_476 1 UNK C1 3 -0.540 12.01100 ; CT # CH3 attached to S of sulfonamide + 5 opls_477 1 UNK H16 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 6 opls_477 1 UNK H17 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 7 opls_477 1 UNK H18 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 8 opls_235 1 UNK C6 15 0.500 12.01100 ; C # C=O in amide, dmf, peptide bond + 9 opls_236 1 UNK O7 15 -0.500 15.99940 ; O # O: C=O in amide. Acyl R on C in amide is neutral - + 10 opls_149 1 UNK C9 16 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 11 opls_145 1 UNK C10 16 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 12 opls_140 1 UNK H22 16 0.060 1.00800 ; HC # alkane H. + 13 opls_140 1 UNK H23 16 0.060 1.00800 ; HC # alkane H. + 14 opls_136 1 UNK C8 26 -0.120 12.01100 ; CT # alkane CH2 + 15 opls_140 1 UNK H20 26 0.060 1.00800 ; HC # alkane H. + 16 opls_140 1 UNK H21 26 0.060 1.00800 ; HC # alkane H. + 17 opls_145 1 UNK C11 30 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 18 opls_146 1 UNK H24 30 0.115 1.00800 ; HA # Benzene H - 12 site. + 19 opls_145 1 UNK C12 32 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 20 opls_146 1 UNK H25 32 0.115 1.00800 ; HA # Benzene H - 12 site. + 21 opls_145 1 UNK C13 34 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 22 opls_146 1 UNK H26 34 0.115 1.00800 ; HA # Benzene H - 12 site. + 23 opls_145 1 UNK C14 36 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 24 opls_146 1 UNK H27 36 0.115 1.00800 ; HA # Benzene H - 12 site. + 25 opls_145 1 UNK C15 38 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 26 opls_146 1 UNK H28 38 0.115 1.00800 ; HA # Benzene H - 12 site. + 27 opls_251 1 UNK N5 40 -0.490 14.00670 ; N # N in imide ### user-defined OPLS atom type (opls_251) + 28 opls_254 1 UNK H19 40 0.370 1.00800 ; H # H(N) in imide ### user-defined OPLS atom type (opls_254) +; Total charge : -0.000 ### Number of unassigned atoms : 0/28 + +[ bonds ] +; ai aj funct r k + 4 1 1 ; CT-SY # (SY-CT) + 4 5 1 ; CT-HC # CHARMM 22 parameter file + 4 6 1 ; CT-HC # CHARMM 22 parameter file + 4 7 1 ; CT-HC # CHARMM 22 parameter file + 1 2 1 ; SY-OY # + 1 3 1 ; SY-OY # + 1 27 1 ; SY-N # + 27 8 1 ; N-C # (C-N) AA + 27 28 1 ; N-H # (H-N) + 8 9 1 ; C-O # URAGUA,CYT,AA + 8 14 1 ; C-CT # + 14 10 1 ; CT-CT # CHARMM 22 parameter file + 14 15 1 ; CT-HC # CHARMM 22 parameter file + 14 16 1 ; CT-HC # CHARMM 22 parameter file + 10 11 1 ; CT-CA # (CA-CT) PHE,TYR + 10 12 1 ; CT-HC # CHARMM 22 parameter file + 10 13 1 ; CT-HC # CHARMM 22 parameter file + 11 25 1 ; CA-CA # TRP,TYR,PHE + 11 17 1 ; CA-CA # TRP,TYR,PHE + 17 19 1 ; CA-CA # TRP,TYR,PHE + 17 18 1 ; CA-HA # PHE, etc. + 19 21 1 ; CA-CA # TRP,TYR,PHE + 19 20 1 ; CA-HA # PHE, etc. + 21 23 1 ; CA-CA # TRP,TYR,PHE + 21 22 1 ; CA-HA # PHE, etc. + 23 25 1 ; CA-CA # TRP,TYR,PHE + 23 24 1 ; CA-HA # PHE, etc. + 25 26 1 ; CA-HA # PHE, etc. + +[ angles ] +; ai aj ak funct theta cth + 1 4 5 1 ; SY-CT-HC # + 1 4 6 1 ; SY-CT-HC # + 1 4 7 1 ; SY-CT-HC # + 5 4 6 1 ; HC-CT-HC # CHARMM 22 parameter file + 5 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + 6 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + 4 1 2 1 ; CT-SY-OY # (OY-SY-CT) + 4 1 3 1 ; CT-SY-OY # (OY-SY-CT) + 4 1 27 1 ; CT-SY-N # (N-SY-CT) + 2 1 3 1 ; OY-SY-OY # + 2 1 27 1 ; OY-SY-N # + 3 1 27 1 ; OY-SY-N # + 1 27 8 1 112.000 585.760 ; SY-N-C # LigParGen + 1 27 28 1 ; SY-N-H # (H-N-SY) + 8 27 28 1 ; C-N-H # AA(OL) + 27 8 9 1 ; N-C-O # AA(OL) + 27 8 14 1 ; N-C-CT # (CT-C-N) + 9 8 14 1 ; O-C-CT # (CT-C-O) + 8 14 10 1 ; C-CT-CT # AA + 8 14 15 1 ; C-CT-HC # + 8 14 16 1 ; C-CT-HC # + 10 14 15 1 ; CT-CT-HC # CHARMM 22 parameter file + 10 14 16 1 ; CT-CT-HC # CHARMM 22 parameter file + 15 14 16 1 ; HC-CT-HC # CHARMM 22 parameter file + 14 10 11 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 14 10 12 1 ; CT-CT-HC # CHARMM 22 parameter file + 14 10 13 1 ; CT-CT-HC # CHARMM 22 parameter file + 11 10 12 1 ; CA-CT-HC # + 11 10 13 1 ; CA-CT-HC # + 12 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 10 11 25 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 10 11 17 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 17 11 25 1 ; CA-CA-CA # PHE(OL) + 11 17 19 1 ; CA-CA-CA # PHE(OL) + 11 17 18 1 ; CA-CA-HA # + 19 17 18 1 ; CA-CA-HA # + 17 19 21 1 ; CA-CA-CA # PHE(OL) + 17 19 20 1 ; CA-CA-HA # + 21 19 20 1 ; CA-CA-HA # + 19 21 23 1 ; CA-CA-CA # PHE(OL) + 19 21 22 1 ; CA-CA-HA # + 23 21 22 1 ; CA-CA-HA # + 21 23 25 1 ; CA-CA-CA # PHE(OL) + 21 23 24 1 ; CA-CA-HA # + 25 23 24 1 ; CA-CA-HA # + 11 25 23 1 ; CA-CA-CA # PHE(OL) + 11 25 26 1 ; CA-CA-HA # + 23 25 26 1 ; CA-CA-HA # + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 5 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 5 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 5 4 1 27 3 ; HC-CT-SY-N # sulfonamide + 6 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 6 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 6 4 1 27 3 ; HC-CT-SY-N # sulfonamide + 7 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 7 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 7 4 1 27 3 ; HC-CT-SY-N # sulfonamide + 4 1 27 8 3 -2.897 11.182 12.410 -20.694 -0.000 0.000 ; CT-SY-N-C # LigParGen + 4 1 27 28 3 ; CT-SY-N-H # sulfonamide + 2 1 27 8 3 ; OY-SY-N-C # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 1 27 28 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 1 27 8 3 ; OY-SY-N-C # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 1 27 28 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 27 8 9 3 25.476 0.000 -25.476 -0.000 -0.000 0.000 ; SY-N-C-O # LigParGen + 1 27 8 14 3 -3.431 -3.008 10.598 -4.159 -0.000 0.000 ; SY-N-C-CT # LigParGen + 28 27 8 9 3 ; H-N-C-O # amides wlj 6/20/97 + 28 27 8 14 3 ; H-N-C-CT # (CT-C-N-H) amides C-C(O)-N-H + 27 8 14 10 3 ; N-C-CT-CT # (CT-CT-C-N) propanamide + 27 8 14 15 3 ; N-C-CT-HC # (HC-CT-C-N) acetamide + 27 8 14 16 3 ; N-C-CT-HC # (HC-CT-C-N) acetamide + 9 8 14 10 3 ; O-C-CT-CT # (CT-CT-C-O) propanamide + 9 8 14 15 3 ; O-C-CT-HC # (HC-CT-C-O) all carbonyls + 9 8 14 16 3 ; O-C-CT-HC # (HC-CT-C-O) all carbonyls + 8 14 10 11 3 ; C-CT-CT-CA # aldehyde & ketone & acyl halide + 8 14 10 12 3 ; C-CT-CT-HC # + 8 14 10 13 3 ; C-CT-CT-HC # + 15 14 10 11 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 15 14 10 12 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 15 14 10 13 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 16 14 10 11 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 16 14 10 12 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 16 14 10 13 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 14 10 11 25 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 14 10 11 17 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 12 10 11 25 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 12 10 11 17 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 13 10 11 25 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 13 10 11 17 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 10 11 25 23 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 11 25 26 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 11 25 23 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 11 25 26 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 11 17 19 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 11 17 18 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 11 17 19 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 11 17 18 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 17 19 21 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 17 19 20 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 17 19 21 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 17 19 20 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 19 21 23 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 19 21 22 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 20 19 21 23 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 20 19 21 22 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 21 23 25 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 21 23 24 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 21 23 25 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 21 23 24 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 23 25 11 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 23 25 26 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 11 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 26 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 8 28 27 1 1 improper_Z_N_X_Y ; C-H-N-SY + 27 14 8 9 1 improper_O_C_X_Y ; N-CT-C-O + 25 17 11 10 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 19 18 17 11 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 21 20 19 17 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 23 22 21 19 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 25 24 23 21 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 23 26 25 11 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + +[ pairs ] +; ai aj funct + 4 8 1 + 4 28 1 + 1 9 1 + 1 14 1 + 2 5 1 + 2 6 1 + 2 7 1 + 2 8 1 + 2 28 1 + 3 5 1 + 3 6 1 + 3 7 1 + 3 8 1 + 3 28 1 + 27 5 1 + 27 6 1 + 27 7 1 + 27 10 1 + 27 15 1 + 27 16 1 + 8 11 1 + 8 12 1 + 8 13 1 + 9 28 1 + 9 10 1 + 9 15 1 + 9 16 1 + 14 28 1 + 14 25 1 + 14 17 1 + 10 23 1 + 10 26 1 + 10 19 1 + 10 18 1 + 11 15 1 + 11 16 1 + 11 21 1 + 11 24 1 + 11 20 1 + 17 12 1 + 17 13 1 + 17 23 1 + 17 26 1 + 17 22 1 + 19 25 1 + 19 24 1 + 21 18 1 + 21 26 1 + 23 20 1 + 25 12 1 + 25 13 1 + 25 18 1 + 25 22 1 + 15 12 1 + 15 13 1 + 16 12 1 + 16 13 1 + 18 20 1 + 20 22 1 + 22 24 1 + 24 26 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 4 1 1000 1000 1000 + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 3 1 1000 1000 1000 + 27 1 1000 1000 1000 + 8 1 1000 1000 1000 + 9 1 1000 1000 1000 + 14 1 1000 1000 1000 + 10 1 1000 1000 1000 + 11 1 1000 1000 1000 + 17 1 1000 1000 1000 + 19 1 1000 1000 1000 + 21 1 1000 1000 1000 + 23 1 1000 1000 1000 + 25 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/refJMC12/refJMC12.mol2.1.pdb b/top/oplsaa/refJMC12/refJMC12.mol2.1.pdb new file mode 100644 index 0000000..6f59233 --- /dev/null +++ b/top/oplsaa/refJMC12/refJMC12.mol2.1.pdb @@ -0,0 +1,29 @@ +HETATM 1 S2 UNK 1 -0.152 9.709 -2.550 1.00 20.00 +HETATM 2 O3 UNK 1 -0.195 10.068 -3.925 1.00 20.00 +HETATM 3 O4 UNK 1 -1.221 10.040 -1.674 1.00 20.00 +HETATM 4 C1 UNK 1 1.440 10.179 -1.819 1.00 20.00 +HETATM 5 H16 UNK 1 2.251 9.787 -2.433 1.00 20.00 +HETATM 6 H17 UNK 1 1.512 11.266 -1.773 1.00 20.00 +HETATM 7 H18 UNK 1 1.513 9.767 -0.813 1.00 20.00 +HETATM 8 C6 UNK 1 -0.111 7.373 -1.398 1.00 20.00 +HETATM 9 O7 UNK 1 -0.110 7.973 -0.344 1.00 20.00 +HETATM 10 C9 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 11 C10 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 12 H22 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 13 H23 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 14 C8 UNK 1 -0.090 5.866 -1.407 1.00 20.00 +HETATM 15 H20 UNK 1 0.800 5.518 -1.931 1.00 20.00 +HETATM 16 H21 UNK 1 -0.980 5.494 -1.915 1.00 20.00 +HETATM 17 C11 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 18 H24 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 19 C12 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 20 H25 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 21 C13 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 22 H26 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 23 C14 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 24 H27 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 25 C15 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 26 H28 UNK 1 -2.180 3.660 0.041 1.00 20.00 +HETATM 27 N5 UNK 1 -0.130 8.053 -2.561 1.00 20.00 +HETATM 28 H19 UNK 1 -0.131 7.574 -3.404 1.00 20.00 +END diff --git a/top/oplsaa/refJMC12/refJMC12.pdb b/top/oplsaa/refJMC12/refJMC12.pdb new file mode 120000 index 0000000..5dc47af --- /dev/null +++ b/top/oplsaa/refJMC12/refJMC12.pdb @@ -0,0 +1 @@ +refJMC12.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/refJMC13/refJMC13.itp b/top/oplsaa/refJMC13/refJMC13.itp new file mode 120000 index 0000000..66ac018 --- /dev/null +++ b/top/oplsaa/refJMC13/refJMC13.itp @@ -0,0 +1 @@ +refJMC13.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/refJMC13/refJMC13.mol2 b/top/oplsaa/refJMC13/refJMC13.mol2 new file mode 100644 index 0000000..58481ca --- /dev/null +++ b/top/oplsaa/refJMC13/refJMC13.mol2 @@ -0,0 +1,87 @@ +# Name: UNK +# Creating user name: iorga +# Creation time: 10. 07. 2020 09:45 + +# Modifying user name: iorga +# Modification time: 10. 07. 2020 09:45 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 33 33 0 0 0 +SMALL +NO_CHARGES + + +@ATOM + 1 C1 2.4399 10.4528 -2.7545 C.3 + 2 N2 1.2802 10.2149 -1.8915 N.am + 3 C3 1.3880 10.4242 -0.4455 C.3 + 4 S4 -0.1524 9.7093 -2.5505 S.o2 + 5 O5 -0.1351 10.1193 -3.9109 O.2 + 6 O6 -1.1713 10.0911 -1.6366 O.2 + 7 N7 -0.1300 8.0535 -2.5607 N.am + 8 C8 -0.1105 7.3726 -1.3978 C.2 + 9 O9 -0.1095 7.9725 -0.3438 O.2 + 10 C10 -0.0901 5.8658 -1.4071 C.3 + 11 C11 -0.0705 5.3471 0.0321 C.3 + 12 C12 -0.0501 3.8402 0.0228 C.ar + 13 C13 1.1563 3.1654 0.0081 C.ar + 14 C14 1.1750 1.7832 0.0004 C.ar + 15 C15 -0.0126 1.0758 0.0080 C.ar + 16 C16 -1.2190 1.7506 0.0173 C.ar + 17 C17 -1.2377 3.1328 0.0294 C.ar + 18 H18 2.4374 11.4903 -3.0886 H + 19 H19 3.3549 10.2529 -2.1969 H + 20 H20 2.3903 9.7923 -3.6201 H + 21 H21 0.4317 10.1987 0.0265 H + 22 H22 2.1574 9.7675 -0.0397 H + 23 H23 1.6549 11.4623 -0.2476 H + 24 H24 -0.1308 7.5737 -3.4037 H + 25 H25 0.8001 5.5177 -1.9309 H + 26 H26 -0.9796 5.4935 -1.9154 H + 27 H27 -0.9608 5.6951 0.5560 H + 28 H28 0.8190 5.7193 0.5404 H + 29 H29 2.0842 3.7181 0.0029 H + 30 H30 2.1175 1.2560 -0.0111 H + 31 H31 0.0021 -0.0041 0.0020 H + 32 H32 -2.1469 1.1980 0.0188 H + 33 H33 -2.1802 3.6600 0.0413 H +@BOND + 1 1 2 1 + 2 1 18 1 + 3 1 19 1 + 4 1 20 1 + 5 2 3 1 + 6 2 4 am + 7 3 21 1 + 8 3 22 1 + 9 3 23 1 + 10 4 5 2 + 11 4 6 2 + 12 4 7 am + 13 7 8 am + 14 7 24 1 + 15 8 9 2 + 16 8 10 1 + 17 10 11 1 + 18 10 25 1 + 19 10 26 1 + 20 11 12 1 + 21 11 27 1 + 22 11 28 1 + 23 12 17 ar + 24 12 13 ar + 25 13 14 ar + 26 13 29 1 + 27 14 15 ar + 28 14 30 1 + 29 15 16 ar + 30 15 31 1 + 31 16 17 ar + 32 16 32 1 + 33 17 33 1 + +# End of record + diff --git a/top/oplsaa/refJMC13/refJMC13.mol2.1.itp b/top/oplsaa/refJMC13/refJMC13.mol2.1.itp new file mode 100644 index 0000000..e7a8a90 --- /dev/null +++ b/top/oplsaa/refJMC13/refJMC13.mol2.1.itp @@ -0,0 +1,324 @@ +; input pdb SMILES : CN(C)[S](=O)(=O)NC(=O)CCC1=CC=CC=C1 +; Script arguments : refJMC13.mol2 "7 opls_251 -0.352" "24 opls_254" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_474 1 UNK S4 1 0.852 32.06000 ; SY # S in sulfamide, S(=O)2(NR2) + 2 opls_475 1 UNK O5 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 3 opls_475 1 UNK O6 1 -0.444 15.99940 ; OY # O in sulfamide, S(=O)2(NR2) + 4 opls_251 1 UNK N7 1 -0.352 14.00670 ; N # N in imide ### user-defined OPLS atom type (opls_251) atom charge (-0.352) + 5 opls_480 1 UNK N2 3 -0.464 14.00670 ; N # N tertiary amide of sulfamide + 6 opls_482 1 UNK C3 5 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 7 opls_483 1 UNK H21 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 8 opls_483 1 UNK H22 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 9 opls_483 1 UNK H23 5 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 10 opls_482 1 UNK C1 11 -0.155 12.01100 ; CT # alpha CH3-N of sulfamide + 11 opls_483 1 UNK H18 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 12 opls_483 1 UNK H19 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 13 opls_483 1 UNK H20 11 0.132 1.00800 ; HC # H of alpha CH3-N of sulfamide + 14 opls_235 1 UNK C8 29 0.500 12.01100 ; C # C=O in amide, dmf, peptide bond + 15 opls_236 1 UNK O9 29 -0.500 15.99940 ; O # O: C=O in amide. Acyl R on C in amide is neutral - + 16 opls_149 1 UNK C11 30 -0.005 12.01100 ; CT # C: CH2, ethyl benzene + 17 opls_145 1 UNK C12 30 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 18 opls_140 1 UNK H27 30 0.060 1.00800 ; HC # alkane H. + 19 opls_140 1 UNK H28 30 0.060 1.00800 ; HC # alkane H. + 20 opls_136 1 UNK C10 46 -0.120 12.01100 ; CT # alkane CH2 + 21 opls_140 1 UNK H25 46 0.060 1.00800 ; HC # alkane H. + 22 opls_140 1 UNK H26 46 0.060 1.00800 ; HC # alkane H. + 23 opls_145 1 UNK C13 50 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 24 opls_146 1 UNK H29 50 0.115 1.00800 ; HA # Benzene H - 12 site. + 25 opls_145 1 UNK C14 52 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 26 opls_146 1 UNK H30 52 0.115 1.00800 ; HA # Benzene H - 12 site. + 27 opls_145 1 UNK C15 54 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 28 opls_146 1 UNK H31 54 0.115 1.00800 ; HA # Benzene H - 12 site. + 29 opls_145 1 UNK C16 56 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 30 opls_146 1 UNK H32 56 0.115 1.00800 ; HA # Benzene H - 12 site. + 31 opls_145 1 UNK C17 58 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 32 opls_146 1 UNK H33 58 0.115 1.00800 ; HA # Benzene H - 12 site. + 33 opls_254 1 UNK H24 60 0.370 1.00800 ; H # H(N) in imide ### user-defined OPLS atom type (opls_254) +; Total charge : 0.000 ### Number of unassigned atoms : 0/33 + +[ bonds ] +; ai aj funct r k + 10 5 1 ; CT-N # + 10 11 1 ; CT-HC # CHARMM 22 parameter file + 10 12 1 ; CT-HC # CHARMM 22 parameter file + 10 13 1 ; CT-HC # CHARMM 22 parameter file + 5 6 1 ; N-CT # (CT-N) + 5 1 1 ; N-SY # (SY-N) + 6 7 1 ; CT-HC # CHARMM 22 parameter file + 6 8 1 ; CT-HC # CHARMM 22 parameter file + 6 9 1 ; CT-HC # CHARMM 22 parameter file + 1 2 1 ; SY-OY # + 1 3 1 ; SY-OY # + 1 4 1 ; SY-N # + 4 14 1 ; N-C # (C-N) AA + 4 33 1 ; N-H # (H-N) + 14 15 1 ; C-O # URAGUA,CYT,AA + 14 20 1 ; C-CT # + 20 16 1 ; CT-CT # CHARMM 22 parameter file + 20 21 1 ; CT-HC # CHARMM 22 parameter file + 20 22 1 ; CT-HC # CHARMM 22 parameter file + 16 17 1 ; CT-CA # (CA-CT) PHE,TYR + 16 18 1 ; CT-HC # CHARMM 22 parameter file + 16 19 1 ; CT-HC # CHARMM 22 parameter file + 17 31 1 ; CA-CA # TRP,TYR,PHE + 17 23 1 ; CA-CA # TRP,TYR,PHE + 23 25 1 ; CA-CA # TRP,TYR,PHE + 23 24 1 ; CA-HA # PHE, etc. + 25 27 1 ; CA-CA # TRP,TYR,PHE + 25 26 1 ; CA-HA # PHE, etc. + 27 29 1 ; CA-CA # TRP,TYR,PHE + 27 28 1 ; CA-HA # PHE, etc. + 29 31 1 ; CA-CA # TRP,TYR,PHE + 29 30 1 ; CA-HA # PHE, etc. + 31 32 1 ; CA-HA # PHE, etc. + +[ angles ] +; ai aj ak funct theta cth + 5 10 11 1 ; N-CT-HC # (HC-CT-N) + 5 10 12 1 ; N-CT-HC # (HC-CT-N) + 5 10 13 1 ; N-CT-HC # (HC-CT-N) + 11 10 12 1 ; HC-CT-HC # CHARMM 22 parameter file + 11 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 12 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 10 5 6 1 ; CT-N-CT # PRO(OL) DETAR JACS 99,1232 + 10 5 1 1 ; CT-N-SY # (SY-N-CT) + 6 5 1 1 ; CT-N-SY # (SY-N-CT) + 5 6 7 1 ; N-CT-HC # (HC-CT-N) + 5 6 8 1 ; N-CT-HC # (HC-CT-N) + 5 6 9 1 ; N-CT-HC # (HC-CT-N) + 7 6 8 1 ; HC-CT-HC # CHARMM 22 parameter file + 7 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + 8 6 9 1 ; HC-CT-HC # CHARMM 22 parameter file + 5 1 2 1 ; N-SY-OY # (OY-SY-N) + 5 1 3 1 ; N-SY-OY # (OY-SY-N) + 5 1 4 1 107.000 1004.160 ; N-SY-N # by analogy from OY-SY-N : + 2 1 3 1 ; OY-SY-OY # + 2 1 4 1 ; OY-SY-N # + 3 1 4 1 ; OY-SY-N # + 1 4 14 1 112.000 585.760 ; SY-N-C # LigParGen + 1 4 33 1 ; SY-N-H # (H-N-SY) + 14 4 33 1 ; C-N-H # AA(OL) + 4 14 15 1 ; N-C-O # AA(OL) + 4 14 20 1 ; N-C-CT # (CT-C-N) + 15 14 20 1 ; O-C-CT # (CT-C-O) + 14 20 16 1 ; C-CT-CT # AA + 14 20 21 1 ; C-CT-HC # + 14 20 22 1 ; C-CT-HC # + 16 20 21 1 ; CT-CT-HC # CHARMM 22 parameter file + 16 20 22 1 ; CT-CT-HC # CHARMM 22 parameter file + 21 20 22 1 ; HC-CT-HC # CHARMM 22 parameter file + 20 16 17 1 ; CT-CT-CA # (CA-CT-CT) PHE(OL) SCH JPC 79,2379 + 20 16 18 1 ; CT-CT-HC # CHARMM 22 parameter file + 20 16 19 1 ; CT-CT-HC # CHARMM 22 parameter file + 17 16 18 1 ; CA-CT-HC # + 17 16 19 1 ; CA-CT-HC # + 18 16 19 1 ; HC-CT-HC # CHARMM 22 parameter file + 16 17 31 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 16 17 23 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 23 17 31 1 ; CA-CA-CA # PHE(OL) + 17 23 25 1 ; CA-CA-CA # PHE(OL) + 17 23 24 1 ; CA-CA-HA # + 25 23 24 1 ; CA-CA-HA # + 23 25 27 1 ; CA-CA-CA # PHE(OL) + 23 25 26 1 ; CA-CA-HA # + 27 25 26 1 ; CA-CA-HA # + 25 27 29 1 ; CA-CA-CA # PHE(OL) + 25 27 28 1 ; CA-CA-HA # + 29 27 28 1 ; CA-CA-HA # + 27 29 31 1 ; CA-CA-CA # PHE(OL) + 27 29 30 1 ; CA-CA-HA # + 31 29 30 1 ; CA-CA-HA # + 17 31 29 1 ; CA-CA-CA # PHE(OL) + 17 31 32 1 ; CA-CA-HA # + 29 31 32 1 ; CA-CA-HA # + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 11 10 5 6 3 ; HC-CT-N-CT # (CT-N-CT-HC) tert. amide + 11 10 5 1 3 ; HC-CT-N-SY # sulfonamide + 12 10 5 6 3 ; HC-CT-N-CT # (CT-N-CT-HC) tert. amide + 12 10 5 1 3 ; HC-CT-N-SY # sulfonamide + 13 10 5 6 3 ; HC-CT-N-CT # (CT-N-CT-HC) tert. amide + 13 10 5 1 3 ; HC-CT-N-SY # sulfonamide + 10 5 6 7 3 ; CT-N-CT-HC # tert. amide + 10 5 6 8 3 ; CT-N-CT-HC # tert. amide + 10 5 6 9 3 ; CT-N-CT-HC # tert. amide + 1 5 6 7 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 1 5 6 8 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 1 5 6 9 3 ; SY-N-CT-HC # (HC-CT-N-SY) sulfonamide + 10 5 1 2 3 ; CT-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 10 5 1 3 3 ; CT-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 10 5 1 4 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; CT-N-SY-N # adapted from CT-N-SY-CT : sulfonamide + 6 5 1 2 3 ; CT-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 6 5 1 3 3 ; CT-N-SY-OY # (OY-SY-N-X generic proper dihedral) sulfonamide + 6 5 1 4 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; CT-N-SY-N # adapted from CT-N-SY-CT : sulfonamide + 5 1 4 14 3 -2.897 11.182 12.410 -20.694 -0.000 0.000 ; N-SY-N-C # LigParGen + 5 1 4 33 3 -15.611 0.703 20.506 -5.598 -0.000 0.000 ; N-SY-N-H # LigParGen + 2 1 4 14 3 ; OY-SY-N-C # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 1 4 33 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 1 4 14 3 ; OY-SY-N-C # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 1 4 33 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 4 14 15 3 25.476 0.000 -25.476 -0.000 -0.000 0.000 ; SY-N-C-O # LigParGen + 1 4 14 20 3 -3.431 -3.008 10.598 -4.159 -0.000 0.000 ; SY-N-C-CT # LigParGen + 33 4 14 15 3 ; H-N-C-O # amides wlj 6/20/97 + 33 4 14 20 3 ; H-N-C-CT # (CT-C-N-H) amides C-C(O)-N-H + 4 14 20 16 3 ; N-C-CT-CT # (CT-CT-C-N) propanamide + 4 14 20 21 3 ; N-C-CT-HC # (HC-CT-C-N) acetamide + 4 14 20 22 3 ; N-C-CT-HC # (HC-CT-C-N) acetamide + 15 14 20 16 3 ; O-C-CT-CT # (CT-CT-C-O) propanamide + 15 14 20 21 3 ; O-C-CT-HC # (HC-CT-C-O) all carbonyls + 15 14 20 22 3 ; O-C-CT-HC # (HC-CT-C-O) all carbonyls + 14 20 16 17 3 ; C-CT-CT-CA # aldehyde & ketone & acyl halide + 14 20 16 18 3 ; C-CT-CT-HC # + 14 20 16 19 3 ; C-CT-CT-HC # + 21 20 16 17 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 21 20 16 18 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 21 20 16 19 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 22 20 16 17 3 ; HC-CT-CT-CA # (CA-CT-CT-HC) ethyl benzene + 22 20 16 18 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 22 20 16 19 3 ; HC-CT-CT-HC # hydrocarbon *new* 11/99 + 20 16 17 31 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 20 16 17 23 3 ; CT-CT-CA-CA # (CA-CA-CT-CT) ethyl benzene + 18 16 17 31 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 18 16 17 23 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 19 16 17 31 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 19 16 17 23 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 16 17 31 29 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 17 31 32 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 17 31 29 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 17 31 32 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 17 23 25 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 17 23 24 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 17 23 25 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 31 17 23 24 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 23 25 27 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 23 25 26 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 27 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 24 23 25 26 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 25 27 29 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 23 25 27 28 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 25 27 29 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 26 25 27 28 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 27 29 31 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 25 27 29 30 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 27 29 31 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 28 27 29 30 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 29 31 17 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 27 29 31 32 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 29 31 17 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 30 29 31 32 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 1 6 5 10 1 improper_Z_N_X_Y ; SY-CT-N-CT + 14 33 4 1 1 improper_Z_N_X_Y ; C-H-N-SY + 4 20 14 15 1 improper_O_C_X_Y ; N-CT-C-O + 31 23 17 16 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 25 24 23 17 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 27 26 25 23 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 29 28 27 25 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 31 30 29 27 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 29 32 31 17 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + +[ pairs ] +; ai aj funct + 10 7 1 + 10 8 1 + 10 9 1 + 10 2 1 + 10 3 1 + 10 4 1 + 5 14 1 + 5 33 1 + 6 11 1 + 6 12 1 + 6 13 1 + 6 2 1 + 6 3 1 + 6 4 1 + 1 11 1 + 1 12 1 + 1 13 1 + 1 7 1 + 1 8 1 + 1 9 1 + 1 15 1 + 1 20 1 + 2 14 1 + 2 33 1 + 3 14 1 + 3 33 1 + 4 16 1 + 4 21 1 + 4 22 1 + 14 17 1 + 14 18 1 + 14 19 1 + 15 33 1 + 15 16 1 + 15 21 1 + 15 22 1 + 20 33 1 + 20 31 1 + 20 23 1 + 16 29 1 + 16 32 1 + 16 25 1 + 16 24 1 + 17 21 1 + 17 22 1 + 17 27 1 + 17 30 1 + 17 26 1 + 23 18 1 + 23 19 1 + 23 29 1 + 23 32 1 + 23 28 1 + 25 31 1 + 25 30 1 + 27 24 1 + 27 32 1 + 29 26 1 + 31 18 1 + 31 19 1 + 31 24 1 + 31 28 1 + 21 18 1 + 21 19 1 + 22 18 1 + 22 19 1 + 24 26 1 + 26 28 1 + 28 30 1 + 30 32 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 10 1 1000 1000 1000 + 5 1 1000 1000 1000 + 6 1 1000 1000 1000 + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 3 1 1000 1000 1000 + 4 1 1000 1000 1000 + 14 1 1000 1000 1000 + 15 1 1000 1000 1000 + 20 1 1000 1000 1000 + 16 1 1000 1000 1000 + 17 1 1000 1000 1000 + 23 1 1000 1000 1000 + 25 1 1000 1000 1000 + 27 1 1000 1000 1000 + 29 1 1000 1000 1000 + 31 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/refJMC13/refJMC13.mol2.1.pdb b/top/oplsaa/refJMC13/refJMC13.mol2.1.pdb new file mode 100644 index 0000000..3a9fa35 --- /dev/null +++ b/top/oplsaa/refJMC13/refJMC13.mol2.1.pdb @@ -0,0 +1,34 @@ +HETATM 1 S4 UNK 1 -0.152 9.709 -2.550 1.00 20.00 +HETATM 2 O5 UNK 1 -0.135 10.119 -3.911 1.00 20.00 +HETATM 3 O6 UNK 1 -1.171 10.091 -1.637 1.00 20.00 +HETATM 4 N7 UNK 1 -0.130 8.053 -2.561 1.00 20.00 +HETATM 5 N2 UNK 1 1.280 10.215 -1.891 1.00 20.00 +HETATM 6 C3 UNK 1 1.388 10.424 -0.446 1.00 20.00 +HETATM 7 H21 UNK 1 0.432 10.199 0.026 1.00 20.00 +HETATM 8 H22 UNK 1 2.157 9.768 -0.040 1.00 20.00 +HETATM 9 H23 UNK 1 1.655 11.462 -0.248 1.00 20.00 +HETATM 10 C1 UNK 1 2.440 10.453 -2.755 1.00 20.00 +HETATM 11 H18 UNK 1 2.437 11.490 -3.089 1.00 20.00 +HETATM 12 H19 UNK 1 3.355 10.253 -2.197 1.00 20.00 +HETATM 13 H20 UNK 1 2.390 9.792 -3.620 1.00 20.00 +HETATM 14 C8 UNK 1 -0.111 7.373 -1.398 1.00 20.00 +HETATM 15 O9 UNK 1 -0.110 7.973 -0.344 1.00 20.00 +HETATM 16 C11 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 17 C12 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 18 H27 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 19 H28 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 20 C10 UNK 1 -0.090 5.866 -1.407 1.00 20.00 +HETATM 21 H25 UNK 1 0.800 5.518 -1.931 1.00 20.00 +HETATM 22 H26 UNK 1 -0.980 5.494 -1.915 1.00 20.00 +HETATM 23 C13 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 24 H29 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 25 C14 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 26 H30 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 27 C15 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 28 H31 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 29 C16 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 30 H32 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 31 C17 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 32 H33 UNK 1 -2.180 3.660 0.041 1.00 20.00 +HETATM 33 H24 UNK 1 -0.131 7.574 -3.404 1.00 20.00 +END diff --git a/top/oplsaa/refJMC13/refJMC13.pdb b/top/oplsaa/refJMC13/refJMC13.pdb new file mode 120000 index 0000000..1a476ef --- /dev/null +++ b/top/oplsaa/refJMC13/refJMC13.pdb @@ -0,0 +1 @@ +refJMC13.mol2.1.pdb \ No newline at end of file diff --git a/top/oplsaa/refJMC14/refJMC14.itp b/top/oplsaa/refJMC14/refJMC14.itp new file mode 120000 index 0000000..da9c917 --- /dev/null +++ b/top/oplsaa/refJMC14/refJMC14.itp @@ -0,0 +1 @@ +refJMC14.mol2.1.itp \ No newline at end of file diff --git a/top/oplsaa/refJMC14/refJMC14.mol2 b/top/oplsaa/refJMC14/refJMC14.mol2 new file mode 100644 index 0000000..c97b808 --- /dev/null +++ b/top/oplsaa/refJMC14/refJMC14.mol2 @@ -0,0 +1,75 @@ +# Name: UNK +# Creating user name: iorga +# Creation time: 10. 07. 2020 09:46 + +# Modifying user name: iorga +# Modification time: 10. 07. 2020 09:46 + +# Program: corina 4.2.0 0026 27.09.2018 + +@MOLECULE +UNK + 27 27 0 0 0 +SMALL +NO_CHARGES + + +@ATOM + 1 C1 1.4382 9.8552 -2.5075 C.3 + 2 S2 -0.1514 9.2568 -3.1443 S.o2 + 3 O3 -0.1909 9.3580 -4.5612 O.2 + 4 O4 -1.2225 9.7401 -2.3452 O.2 + 5 N5 -0.1267 7.6271 -2.8519 N.am + 6 C6 -0.1094 7.1701 -1.5840 C.2 + 7 O7 -0.1120 7.9545 -0.6550 O.2 + 8 N8 -0.0893 5.8437 -1.3460 N.am + 9 C9 -0.0705 5.3471 0.0321 C.3 + 10 C10 -0.0501 3.8402 0.0228 C.ar + 11 C11 1.1563 3.1654 0.0081 C.ar + 12 C12 1.1750 1.7832 0.0004 C.ar + 13 C13 -0.0126 1.0758 0.0080 C.ar + 14 C14 -1.2190 1.7506 0.0173 C.ar + 15 C15 -1.2377 3.1328 0.0294 C.ar + 16 H16 2.2517 9.3591 -3.0369 H + 17 H17 1.5087 10.9321 -2.6604 H + 18 H18 1.5095 9.6339 -1.4426 H + 19 H19 -0.1246 7.0013 -3.5930 H + 20 H20 -0.0872 5.2179 -2.0871 H + 21 H21 -0.9608 5.6951 0.5560 H + 22 H22 0.8190 5.7193 0.5404 H + 23 H23 2.0842 3.7181 0.0029 H + 24 H24 2.1175 1.2560 -0.0111 H + 25 H25 0.0021 -0.0041 0.0020 H + 26 H26 -2.1469 1.1980 0.0188 H + 27 H27 -2.1802 3.6600 0.0413 H +@BOND + 1 1 2 1 + 2 1 16 1 + 3 1 17 1 + 4 1 18 1 + 5 2 3 2 + 6 2 4 2 + 7 2 5 am + 8 5 6 am + 9 5 19 1 + 10 6 7 2 + 11 6 8 am + 12 8 9 1 + 13 8 20 1 + 14 9 10 1 + 15 9 21 1 + 16 9 22 1 + 17 10 15 ar + 18 10 11 ar + 19 11 12 ar + 20 11 23 1 + 21 12 13 ar + 22 12 24 1 + 23 13 14 ar + 24 13 25 1 + 25 14 15 ar + 26 14 26 1 + 27 15 27 1 + +# End of record + diff --git a/top/oplsaa/refJMC14/refJMC14.mol2.1.itp b/top/oplsaa/refJMC14/refJMC14.mol2.1.itp new file mode 100644 index 0000000..1130fe6 --- /dev/null +++ b/top/oplsaa/refJMC14/refJMC14.mol2.1.itp @@ -0,0 +1,270 @@ +; input pdb SMILES : C[S](=O)(=O)NC(=O)NCC1=CC=CC=C1 +; Script arguments : refJMC14.mol2 "5 opls_251" "19 opls_254" "8 opls_238" "20 opls_241" "9 0.195" + +[ moleculetype ] +; Name nrexcl +UNK 3 + +[ atoms ] +; atomnr atomtype resnr resname atomname chargegrp charge mass + 1 opls_474 1 UNK S2 1 1.480 32.06000 ; SY # S in sulfonamide, S(=O)2(OR) + 2 opls_475 1 UNK O3 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 3 opls_475 1 UNK O4 1 -0.680 15.99940 ; OY # O in sulfonamide, S(=O)2(OR) + 4 opls_476 1 UNK C1 3 -0.540 12.01100 ; CT # CH3 attached to S of sulfonamide + 5 opls_477 1 UNK H16 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 6 opls_477 1 UNK H17 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 7 opls_477 1 UNK H18 3 0.180 1.00800 ; HC # H of Me attached to S of sulfonamide + 8 opls_235 1 UNK C6 15 0.500 12.01100 ; C # C=O in amide, dmf, peptide bond + 9 opls_236 1 UNK O7 15 -0.500 15.99940 ; O # O: C=O in amide. Acyl R on C in amide is neutral - + 10 opls_149 1 UNK C9 17 0.195 12.01100 ; CT # C: CH2, ethyl benzene ### user-defined atom charge (0.195) + 11 opls_145 1 UNK C10 17 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 12 opls_140 1 UNK H21 17 0.060 1.00800 ; HC # alkane H. + 13 opls_140 1 UNK H22 17 0.060 1.00800 ; HC # alkane H. + 14 opls_145 1 UNK C11 27 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 15 opls_146 1 UNK H23 27 0.115 1.00800 ; HA # Benzene H - 12 site. + 16 opls_145 1 UNK C12 29 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 17 opls_146 1 UNK H24 29 0.115 1.00800 ; HA # Benzene H - 12 site. + 18 opls_145 1 UNK C13 31 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 19 opls_146 1 UNK H25 31 0.115 1.00800 ; HA # Benzene H - 12 site. + 20 opls_145 1 UNK C14 33 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 21 opls_146 1 UNK H26 33 0.115 1.00800 ; HA # Benzene H - 12 site. + 22 opls_145 1 UNK C15 35 -0.115 12.01100 ; CA # Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl + 23 opls_146 1 UNK H27 35 0.115 1.00800 ; HA # Benzene H - 12 site. + 24 opls_251 1 UNK N5 37 -0.490 14.00670 ; N # N in imide ### user-defined OPLS atom type (opls_251) + 25 opls_238 1 UNK N8 37 -0.500 14.00670 ; N # N: secondary amide, peptide bond (see #279 for formyl H) ### user-defined OPLS atom type (opls_238) + 26 opls_254 1 UNK H19 37 0.370 1.00800 ; H # H(N) in imide ### user-defined OPLS atom type (opls_254) + 27 opls_241 1 UNK H20 37 0.300 1.00800 ; H # H on N: secondary amide ### user-defined OPLS atom type (opls_241) +; Total charge : -0.000 ### Number of unassigned atoms : 0/27 + +[ bonds ] +; ai aj funct r k + 4 1 1 ; CT-SY # (SY-CT) + 4 5 1 ; CT-HC # CHARMM 22 parameter file + 4 6 1 ; CT-HC # CHARMM 22 parameter file + 4 7 1 ; CT-HC # CHARMM 22 parameter file + 1 2 1 ; SY-OY # + 1 3 1 ; SY-OY # + 1 24 1 ; SY-N # + 24 8 1 ; N-C # (C-N) AA + 24 26 1 ; N-H # (H-N) + 8 9 1 ; C-O # URAGUA,CYT,AA + 8 25 1 ; C-N # AA + 25 10 1 ; N-CT # (CT-N) + 25 27 1 ; N-H # (H-N) + 10 11 1 ; CT-CA # (CA-CT) PHE,TYR + 10 12 1 ; CT-HC # CHARMM 22 parameter file + 10 13 1 ; CT-HC # CHARMM 22 parameter file + 11 22 1 ; CA-CA # TRP,TYR,PHE + 11 14 1 ; CA-CA # TRP,TYR,PHE + 14 16 1 ; CA-CA # TRP,TYR,PHE + 14 15 1 ; CA-HA # PHE, etc. + 16 18 1 ; CA-CA # TRP,TYR,PHE + 16 17 1 ; CA-HA # PHE, etc. + 18 20 1 ; CA-CA # TRP,TYR,PHE + 18 19 1 ; CA-HA # PHE, etc. + 20 22 1 ; CA-CA # TRP,TYR,PHE + 20 21 1 ; CA-HA # PHE, etc. + 22 23 1 ; CA-HA # PHE, etc. + +[ angles ] +; ai aj ak funct theta cth + 1 4 5 1 ; SY-CT-HC # + 1 4 6 1 ; SY-CT-HC # + 1 4 7 1 ; SY-CT-HC # + 5 4 6 1 ; HC-CT-HC # CHARMM 22 parameter file + 5 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + 6 4 7 1 ; HC-CT-HC # CHARMM 22 parameter file + 4 1 2 1 ; CT-SY-OY # (OY-SY-CT) + 4 1 3 1 ; CT-SY-OY # (OY-SY-CT) + 4 1 24 1 ; CT-SY-N # (N-SY-CT) + 2 1 3 1 ; OY-SY-OY # + 2 1 24 1 ; OY-SY-N # + 3 1 24 1 ; OY-SY-N # + 1 24 8 1 112.000 585.760 ; SY-N-C # LigParGen + 1 24 26 1 ; SY-N-H # (H-N-SY) + 8 24 26 1 ; C-N-H # AA(OL) + 24 8 9 1 ; N-C-O # AA(OL) + 24 8 25 1 ; N-C-N # copy from above for Urea (jtr 5-14-91) + 9 8 25 1 ; O-C-N # (N-C-O) AA(OL) + 8 25 10 1 ; C-N-CT # + 8 25 27 1 ; C-N-H # AA(OL) + 10 25 27 1 ; CT-N-H # + 25 10 11 1 ; N-CT-CA # (CA-CT-N) + 25 10 12 1 ; N-CT-HC # (HC-CT-N) + 25 10 13 1 ; N-CT-HC # (HC-CT-N) + 11 10 12 1 ; CA-CT-HC # + 11 10 13 1 ; CA-CT-HC # + 12 10 13 1 ; HC-CT-HC # CHARMM 22 parameter file + 10 11 22 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 10 11 14 1 ; CT-CA-CA # (CA-CA-CT) PHE(OL) + 14 11 22 1 ; CA-CA-CA # PHE(OL) + 11 14 16 1 ; CA-CA-CA # PHE(OL) + 11 14 15 1 ; CA-CA-HA # + 16 14 15 1 ; CA-CA-HA # + 14 16 18 1 ; CA-CA-CA # PHE(OL) + 14 16 17 1 ; CA-CA-HA # + 18 16 17 1 ; CA-CA-HA # + 16 18 20 1 ; CA-CA-CA # PHE(OL) + 16 18 19 1 ; CA-CA-HA # + 20 18 19 1 ; CA-CA-HA # + 18 20 22 1 ; CA-CA-CA # PHE(OL) + 18 20 21 1 ; CA-CA-HA # + 22 20 21 1 ; CA-CA-HA # + 11 22 20 1 ; CA-CA-CA # PHE(OL) + 11 22 23 1 ; CA-CA-HA # + 20 22 23 1 ; CA-CA-HA # + +[ dihedrals ] +; ai aj ak al funct C0 ... C5 + 5 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 5 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 5 4 1 24 3 ; HC-CT-SY-N # sulfonamide + 6 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 6 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 6 4 1 24 3 ; HC-CT-SY-N # sulfonamide + 7 4 1 2 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 7 4 1 3 3 ; HC-CT-SY-OY # (OY-SY-CT-X generic proper dihedral) sulfonamide + 7 4 1 24 3 ; HC-CT-SY-N # sulfonamide + 4 1 24 8 3 -2.897 11.182 12.410 -20.694 -0.000 0.000 ; CT-SY-N-C # LigParGen + 4 1 24 26 3 ; CT-SY-N-H # sulfonamide + 2 1 24 8 3 ; OY-SY-N-C # (OY-SY-N-X generic proper dihedral) sulfonamide + 2 1 24 26 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 1 24 8 3 ; OY-SY-N-C # (OY-SY-N-X generic proper dihedral) sulfonamide + 3 1 24 26 3 ; OY-SY-N-H # (OY-SY-N-X generic proper dihedral) sulfonamide + 1 24 8 9 3 25.476 0.000 -25.476 -0.000 -0.000 0.000 ; SY-N-C-O # LigParGen + 1 24 8 25 3 20.502 0.000 -20.502 -0.000 -0.000 0.000 ; SY-N-C-N # LigParGen + 26 24 8 9 3 ; H-N-C-O # amides wlj 6/20/97 + 26 24 8 25 3 ; H-N-C-N # imides + 24 8 25 10 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; N-C-N-CT # (CT-N-C-N) adapted from C-N-C-N : imides + 24 8 25 27 3 ; N-C-N-H # (H-N-C-N) imides + 9 8 25 10 3 ; O-C-N-CT # (CT-N-C-O) amides O-C(O)-N-C + 9 8 25 27 3 ; O-C-N-H # (H-N-C-O) amides wlj 6/20/97 + 8 25 10 11 3 ; C-N-CT-CA # from N-ethylformamide + 8 25 10 12 3 ; C-N-CT-HC # N-methylformamide + 8 25 10 13 3 ; C-N-CT-HC # N-methylformamide + 27 25 10 11 3 ; H-N-CT-CA # (H-N-CT-X generic proper dihedral) peptides + 27 25 10 12 3 ; H-N-CT-HC # N-methylformamide + 27 25 10 13 3 ; H-N-CT-HC # N-methylformamide + 25 10 11 22 3 ; N-CT-CA-CA # (CA-CA-CT-N) (From wildcard) aromatics + 25 10 11 14 3 ; N-CT-CA-CA # (CA-CA-CT-N) (From wildcard) aromatics + 12 10 11 22 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 12 10 11 14 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 13 10 11 22 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 13 10 11 14 3 ; HC-CT-CA-CA # (CA-CA-CT-HC) ethyl benzene + 10 11 22 20 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 11 22 23 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 11 22 20 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 11 22 23 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 11 14 16 3 ; CT-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 10 11 14 15 3 ; CT-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 11 14 16 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 22 11 14 15 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 14 16 18 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 11 14 16 17 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 14 16 18 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 15 14 16 17 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 16 18 20 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 14 16 18 19 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 16 18 20 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 17 16 18 19 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 18 20 22 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 16 18 20 21 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 18 20 22 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 19 18 20 21 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 20 22 11 3 ; CA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 18 20 22 23 3 ; CA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 20 22 11 3 ; HA-CA-CA-CA # (X-CA-CA-X generic proper dihedral) aromatic ring + 21 20 22 23 3 ; HA-CA-CA-HA # (X-CA-CA-X generic proper dihedral) aromatic ring + +[ dihedrals ] +; impropers +; ai aj ak al funct improper + 8 26 24 1 1 improper_Z_N_X_Y ; C-H-N-SY + 24 25 8 9 1 improper_O_C_X_Y ; N-N-C-O + 8 27 25 10 1 improper_Z_N_X_Y ; C-H-N-CT + 22 14 11 10 1 improper_Z_CA_X_Y ; CA-CA-CA-CT + 16 15 14 11 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 18 17 16 14 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 20 19 18 16 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 22 21 20 18 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + 20 23 22 11 1 improper_Z_CA_X_Y ; CA-HA-CA-CA + +[ pairs ] +; ai aj funct + 4 8 1 + 4 26 1 + 1 9 1 + 1 25 1 + 2 5 1 + 2 6 1 + 2 7 1 + 2 8 1 + 2 26 1 + 3 5 1 + 3 6 1 + 3 7 1 + 3 8 1 + 3 26 1 + 24 5 1 + 24 6 1 + 24 7 1 + 24 10 1 + 24 27 1 + 8 11 1 + 8 12 1 + 8 13 1 + 9 26 1 + 9 10 1 + 9 27 1 + 25 26 1 + 25 22 1 + 25 14 1 + 10 20 1 + 10 23 1 + 10 16 1 + 10 15 1 + 11 27 1 + 11 18 1 + 11 21 1 + 11 17 1 + 14 12 1 + 14 13 1 + 14 20 1 + 14 23 1 + 14 19 1 + 16 22 1 + 16 21 1 + 18 15 1 + 18 23 1 + 20 17 1 + 22 12 1 + 22 13 1 + 22 15 1 + 22 19 1 + 27 12 1 + 27 13 1 + 15 17 1 + 17 19 1 + 19 21 1 + 21 23 1 + +#ifdef POSRES +[ position_restraints ] +; atom type fx fy fz + 4 1 1000 1000 1000 + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 3 1 1000 1000 1000 + 24 1 1000 1000 1000 + 8 1 1000 1000 1000 + 9 1 1000 1000 1000 + 25 1 1000 1000 1000 + 10 1 1000 1000 1000 + 11 1 1000 1000 1000 + 14 1 1000 1000 1000 + 16 1 1000 1000 1000 + 18 1 1000 1000 1000 + 20 1 1000 1000 1000 + 22 1 1000 1000 1000 +#endif + diff --git a/top/oplsaa/refJMC14/refJMC14.mol2.1.pdb b/top/oplsaa/refJMC14/refJMC14.mol2.1.pdb new file mode 100644 index 0000000..f501e60 --- /dev/null +++ b/top/oplsaa/refJMC14/refJMC14.mol2.1.pdb @@ -0,0 +1,28 @@ +HETATM 1 S2 UNK 1 -0.151 9.257 -3.144 1.00 20.00 +HETATM 2 O3 UNK 1 -0.191 9.358 -4.561 1.00 20.00 +HETATM 3 O4 UNK 1 -1.222 9.740 -2.345 1.00 20.00 +HETATM 4 C1 UNK 1 1.438 9.855 -2.507 1.00 20.00 +HETATM 5 H16 UNK 1 2.252 9.359 -3.037 1.00 20.00 +HETATM 6 H17 UNK 1 1.509 10.932 -2.660 1.00 20.00 +HETATM 7 H18 UNK 1 1.510 9.634 -1.443 1.00 20.00 +HETATM 8 C6 UNK 1 -0.109 7.170 -1.584 1.00 20.00 +HETATM 9 O7 UNK 1 -0.112 7.955 -0.655 1.00 20.00 +HETATM 10 C9 UNK 1 -0.070 5.347 0.032 1.00 20.00 +HETATM 11 C10 UNK 1 -0.050 3.840 0.023 1.00 20.00 +HETATM 12 H21 UNK 1 -0.961 5.695 0.556 1.00 20.00 +HETATM 13 H22 UNK 1 0.819 5.719 0.540 1.00 20.00 +HETATM 14 C11 UNK 1 1.156 3.165 0.008 1.00 20.00 +HETATM 15 H23 UNK 1 2.084 3.718 0.003 1.00 20.00 +HETATM 16 C12 UNK 1 1.175 1.783 0.000 1.00 20.00 +HETATM 17 H24 UNK 1 2.118 1.256 -0.011 1.00 20.00 +HETATM 18 C13 UNK 1 -0.013 1.076 0.008 1.00 20.00 +HETATM 19 H25 UNK 1 0.002 -0.004 0.002 1.00 20.00 +HETATM 20 C14 UNK 1 -1.219 1.751 0.017 1.00 20.00 +HETATM 21 H26 UNK 1 -2.147 1.198 0.019 1.00 20.00 +HETATM 22 C15 UNK 1 -1.238 3.133 0.029 1.00 20.00 +HETATM 23 H27 UNK 1 -2.180 3.660 0.041 1.00 20.00 +HETATM 24 N5 UNK 1 -0.127 7.627 -2.852 1.00 20.00 +HETATM 25 N8 UNK 1 -0.089 5.844 -1.346 1.00 20.00 +HETATM 26 H19 UNK 1 -0.125 7.001 -3.593 1.00 20.00 +HETATM 27 H20 UNK 1 -0.087 5.218 -2.087 1.00 20.00 +END diff --git a/top/oplsaa/refJMC14/refJMC14.pdb b/top/oplsaa/refJMC14/refJMC14.pdb new file mode 120000 index 0000000..4120733 --- /dev/null +++ b/top/oplsaa/refJMC14/refJMC14.pdb @@ -0,0 +1 @@ +refJMC14.mol2.1.pdb \ No newline at end of file