MIND.itp

;;;;;; 3-METHYL-1H-INDOLE
;;;;; (amino acid TRyPtophan)
;
; Note(s):
;   For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;

[ moleculetype ]
; molname    nrexcl
  MIND         1 

[ atoms ]
; nr type resnr residue atom cgnr charge mass
   1  TC5   1    MIND    R1    1    0     45   
   2  TC5   1    MIND    R2    2    0     45   
   3  TC5   1    MIND    R3    3    0      0
   4  TC4   1    MIND    R4    4    0     45   
   5  TN6d  1    MIND    N5    5    0     45   

[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i  j  funct length
  1  2   1     0.293 1000000 ; cog
  1  4   1     0.404 1000000 ; cog
  1  5   1     0.470 1000000 ; cog
  2  5   1     0.412 1000000 ; cog
  4  5   1     0.335 1000000 ; cog

[ dihedrals ]
; improper
; i j k l  funct  ref.angle force_k
  1 2 4 5    2      180       200  ; default for fused bicyclic compounds 

[ virtual_sitesn ]
; site funct  constructing atom indices
   3     1     1 2 4 5

[ exclusions ]
 1 2 3 4 5
 2 3 4 5
 3 4 5
 4 5