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Hi, I'm trying to preprocess PDBbind dataset. #6

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hcl14 opened this issue Jul 26, 2020 · 2 comments
Open

Hi, I'm trying to preprocess PDBbind dataset. #6

hcl14 opened this issue Jul 26, 2020 · 2 comments
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@hhassan1
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@hcl14
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hcl14 commented Jul 26, 2020 •
edited
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What I did to make preprocess running:

  1. Fixed rosetta path in constants.py as you suggested.
  2. Installed mgltools_x86_64Linux2_1.5.6 which was mentioned there and fixed path to it.
  3. Changed "python2" to "python3" in rosetta.py, as my rosetta was built for python3.
  4. Commented out #from htmd.builder.preparation import proteinPrepare in make_complex_pdb.py as it is unused (the call was commented out in the source code) and looks like library does not work anymore (it fails to run binary when imported): https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
  5. Installed a LOT of other packages to fix upcoming import issues.
  6. Made proper labels file and placed it along with PDBbind v2019 into test_dataset.

Running python3 -m RosENet -- preprocess test_dataset

Now I have the following lines printed:

protocols.ligand_docking.ligand_options.MinimizeBackbone: [ WARNING ] for backbone minimization to work properly, a stretch of at least 4 residues needs to be allowed to move. Stretch between 101 and 102 is too short.  This should never happen after extending the interface

And the following files created:

(rosenet) egbeliaev@egor-big:/data/RosENet/test_dataset/3zdv$ ls -l
total 4072
-rw-r--r-- 1 egbeliaev egbeliaev 518428 Jul 26 20:43 3zdv_complex.pdb
-rw-r--r-- 1 egbeliaev egbeliaev 594351 Jul 26 20:44 3zdv_complex_0001.pdb
-rw-r--r-- 1 egbeliaev egbeliaev 594312 Jul 26 20:44 3zdv_complex_0010.pdb
-rw-r--r-- 1 egbeliaev egbeliaev 594323 Jul 26 20:45 3zdv_complex_0011.pdb
-rw-r--r-- 1 egbeliaev egbeliaev 594405 Jul 26 20:45 3zdv_complex_0014.pdb
-rw-r--r-- 1 egbeliaev egbeliaev 594354 Jul 26 20:46 3zdv_complex_0021.pdb
-rw-r--r-- 1 egbeliaev egbeliaev   5182 Jul 26 13:25 3zdv_ligand.mol2
-rw-r--r-- 1 egbeliaev egbeliaev   6736 Jul 26 20:43 3zdv_ligand.params
-rw-r--r-- 1 egbeliaev egbeliaev   4131 Jul 26 20:43 3zdv_ligand.pdb
-rw-r--r-- 1 egbeliaev egbeliaev   3751 Jul 26 13:25 3zdv_ligand.sdf
-rw-r--r-- 1 egbeliaev egbeliaev  23885 Jul 26 13:25 3zdv_pocket.pdb
-rw-r--r-- 1 egbeliaev egbeliaev 553535 Jul 26 13:25 3zdv_protein.pdb
-rw-r--r-- 1 egbeliaev egbeliaev  30572 Jul 26 20:45 ROSETTA_CRASH.log
-rw-r--r-- 1 egbeliaev egbeliaev     43 Jul 26 20:43 constraints
-rw-r--r-- 1 egbeliaev egbeliaev    561 Jul 26 20:43 flags_relax.txt
-rw-r--r-- 1 egbeliaev egbeliaev     62 Jul 26 20:43 metadata.json
-rw-r--r-- 1 egbeliaev egbeliaev   2250 Jul 26 20:46 score.sc

I see here some crash log from Rosetta. In contains the following things:

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
 -in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd4d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_lower without the variant type CUTPOINT_LOWER



[END_MESSAGE]
[END_CRASH_REPORT]

It seems to me to be related to the data. But some files are generated, I don't know if it is a problem at all. Can you please help me on this?

Full crash log 
##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd4d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_lower without the variant type CUTPOINT_LOWER



[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd5d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_upper:protein_cutpoint_lower without the variant type CUTPOINT_UPPER



[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd4d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_lower without the variant type CUTPOINT_LOWER



[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd5d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_upper without the variant type CUTPOINT_UPPER



[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd5d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_upper without the variant type CUTPOINT_UPPER



[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd5d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_upper:protein_cutpoint_lower without the variant type CUTPOINT_UPPER



[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd4d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_lower without the variant type CUTPOINT_LOWER



[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd4d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_lower without the variant type CUTPOINT_LOWER



[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd4d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_lower without the variant type CUTPOINT_LOWER



[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd5d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_upper:protein_cutpoint_lower without the variant type CUTPOINT_UPPER



[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd4d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_lower without the variant type CUTPOINT_LOWER



[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in -in:ignore_waters=false -in:auto_setup_metals -in:metals_distance_constraint_multiplier=3 -in:metals_angle_constraint_multiplier=3 -in:path:database=/data/rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file -in:file:s=./3zdv_complex.pdb -in:file:extra_res_fa=./3zdv_ligand.params -out:overwrite -out:nstruct=50 -out:mute=core.util.prof core.io.database -run:ignore_zero_occupancy=false -parser:protocol=/data/RosENet/RosENet/static/dock_relax.xml -score:set_weights=atom_pair_constraint 1.0 -packing -packing:ex1 -packing:ex2 -packing:ex1aro -constraints:cst_fa_file=./constraints -pH:keep_input_protonation_state

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x3a91d6f]
[0x5fe5ef3]
[0x608c3d6]
[0x5ae08b0]
[0x4674316]
[0x1c6fd5d]
[0x1c1455f]
[0x38a7bb1]
[0x38a87ab]
[0x38a8f06]
[0x393cf94]
[0x393ebc1]
[0x39d8148]
[0x411fcb]
[0x65816d4]
[0x630dfd]

[END_BACKTRACE]

[FILE]: src/core/chemical/ResidueTypeSet.cc
[LINE]: 1039
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find a version of ASP:MP-OD1-connect:MP-OD1-pruneH:MP-OD2-connect:MP-OD2-pruneH:MP-OD1-connect:MP-OD1-pruneH:protein_cutpoint_upper without the variant type CUTPOINT_UPPER



[END_MESSAGE]
[END_CRASH_REPORT]
@wanyueli321
Copy link

About the 4th step, you did in preprocessing, I used" from moleculekit.tools.preparation import proteinPrepare" instead, and it can works.
And a question I want to ask is that how did you make the labels file for the PDBbind dataset? Only write the PDB folder name and the binding affinity into it? Did you do some transform operation about the bind affinity value?

@BCornelsen
Copy link

About step 4 and 5: It looks like the install.sh-script didn't install the pip dependencies correctly. After I executed pip install -r pip-requirements.txt many dependencies have been installed, including htmd-pdb2pqr.

@hhassan1 hhassan1 added the bug Something isn't working label Sep 7, 2020
@hhassan1 hhassan1 self-assigned this Sep 7, 2020
@BCornelsen BCornelsen mentioned this issue Oct 6, 2020
Open
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@hhassan1 hhassan1

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@hcl14 @BCornelsen @hhassan1 @wanyueli321