[gmx-users] request

[hadi behzadi]

Hi  all users 
  I constructed topology and gro (1.gro and 1.top) file for propane ( CH3CH2CH3) molecule from  PRODRG server as follow:
   
  1.go
   
  PRODRG COORDS
      3
      1DRG  CAB      1  -0.128   0.172   0.000
      1DRG  CAA      2  -0.128   0.019   0.000
      1DRG  CAC      3   0.017  -0.033   0.000
     0.35530   0.35530   0.35530
   
  1.top
  ;   
  ;       
  ;       This file was generated by PRODRG version 061128.0522
  ;       PRODRG written/copyrighted by Daan van Aalten
  ;       and Alexander Schuettelkopf
  ;       
  ;       Questions/comments to dava at davapc1.bioch.dundee.ac.uk
  ;       
  ;       When using this software in a publication, cite:
  ;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
  ;       PRODRG - a tool for high-throughput crystallography
  ;       of protein-ligand complexes.
  ;       Acta Crystallogr. D60, 1355--1363.
  ;       
  ;       
   
  [ moleculetype ]
  ; Name nrexcl
  DRG      3
   
  [ atoms ]
  ;   nr      type  resnr resid  atom  cgnr   charge     mass
       1       CH3     1  DRG     CAB     1   -0.012  15.0350   
       2       CH2     1  DRG     CAA     1    0.024  14.0270   
       3       CH3     1  DRG     CAC     1   -0.012  15.0350   
   
  [ bonds ]
  ; ai  aj  fu    c0, c1, ...
     1   2   1    0.153    334720.0    0.153    334720.0 ;   CAB  CAA   
     2   3   1    0.153    334720.0    0.153    334720.0 ;   CAA  CAC   
   
  [ pairs ]
  ; ai  aj  fu    c0, c1, ...
   
  [ angles ]
  ; ai  aj  ak  fu    c0, c1, ...
     1   2   3   1    111.0       460.2    111.0       460.2 ;   CAB  CAA  CAC   
   
  [ dihedrals ]
  ; ai  aj  ak  al  fu    c0, c1, m, ...
   
  Then, I construct 88 molecule of propane with editconf and genbox :
  editconf –f 1.gro -0  1.pdb –d   0.3
  genbox -cs 1.pdb -p 1.top -o 3.pdb -box 3 3 3
  then I chaned the  topology file  by adding the following phrase in the end of 1.top:  
   
   [ system ]
  ; Name     DRG
  [ molecules ]
  ; Compound      #mols
  DRG              88
   
  When  I want to performer the following commend   :
  grompp -v -f grompp.mdp -c b4em.pdb -p 1.top –o
  I encounter to this error :
   
  Program grompp, VERSION 3.3
  Source code file: topio.c, line: 385
  Fatal error:
  Invalid order for directive moleculetype, file ""1.top"", line 17
  The line 17 is [ moleculetype ].
   

I request you all to give suggestion for this.

 

I will be very thankful to you. 

 
   
   
   

 
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