[gmx-users] how can I get a topology?

[Yegor Isakov]

I need topology for this molecule -  SH-CH=O 
 I made a pdb file through pymol, opened PRODRG site (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html), generated an itp file over there:
 ;       
 ;       
 ;       This file was generated by PRODRG version 051202.0518
 ;       PRODRG written/copyrighted by Daan van Aalten
 ;       
 ;       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
 C=O      3
 
 [ atoms ]
 ;   nr      type  resnr resid  atom  cgnr   charge     mass
      1         O     1  C=O     O02     1   -0.367  15.9994   
      2         C     1  C=O     C01     1    0.252  12.0110   
      3         S     1  C=O     S01     1    0.096  32.0600   
      4        HS     1  C=O     HAA     1    0.019   1.0080   
 
 [ bonds ]
 ; ai  aj  fu    c0, c1, ...
    1   2   1    0.123    502080.0    0.123    502080.0 ;   O02  C01   
    2   3   1    0.175    261918.4    0.175    261918.4 ;   C01  S01   
    3   4   1    0.133    313800.0    0.133    313800.0 ;   S01  HAA   
 
 [ pairs ]
 ; ai  aj  fu    c0, c1, ...
    1   4   1                                           ;   O02  HAA   
 
 [ angles ]
 ; ai  aj  ak  fu    c0, c1, ...
    1   2   3   1    120.0       418.4    120.0       418.4 ;   O02  C01  S01   
    2   3   4   1     96.0       397.5     96.0       397.5 ;   C01  S01  HAA   
 
 [ dihedrals ]
 ; ai  aj  ak  al  fu    c0, c1, m, ...
    1   2   3   4   1      0.0    2.9 3      0.0    2.9 3 ; dih   O02  C01  S01  HAA   
 
 
 put this file in ~/share/top  directory, run pdb2gmx to convert this file to topology:
 
 HETATM    1  C01 C=O     1       0.000  -0.020   0.000  0.00  0.00           C
 HETATM    2  S01 C=O     1       1.475  -0.886   0.000  0.00  0.00           S
 HETATM    3  O02 C=O     1       0.000   1.188   0.000  0.00  0.00           O
 HETATM    4  H01 C=O     1       1.860  -1.113  -1.263  0.00  0.00           H
 HETATM    5  H03 C=O     1      -0.960  -0.584   0.000  0.00  0.00           H
 CONECT    1    2
 CONECT    1    3
 CONECT    1    3
 CONECT    1    5
 CONECT    2    1    4
 CONECT    3    1
 CONECT    3    1
 CONECT    4    2
 CONECT    5    1
 END
 
 and I have got this output:
 
 Select the Force Field:
  0: GROMOS96 43a1 Forcefield (official distribution)
  1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
  2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
  3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
  4: Gromacs Forcefield (see manual)
  5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
 0
 Looking whether force field file ffG43a1.rtp exists
 Opening library file /usr/local/gromacs/share/top/ffG43a1.rtp
 Opening library file /usr/local/gromacs/share/top/aminoacids.dat
 Reading drgnoh.pdb...
 Read 3 atoms
 Opening library file /usr/local/gromacs/share/top/xlateat.dat
 23 out of 23 lines of xlateat.dat converted succesfully
 Analyzing pdb file
 There are 1 chains and 0 blocks of water and 1 residues with 3 atoms
 
   chain  #res #atoms
   1 ' '     1      3  
 
 All occupancies are one
 Opening library file /usr/local/gromacs/share/top/ffG43a1.atp
 Atomtype 50
 Reading residue database... (ffG43a1)
 Opening library file /usr/local/gromacs/share/top/ffG43a1.rtp
 Residue 96
 Sorting it all out...
 Opening library file /usr/local/gromacs/share/top/ffG43a1.hdb
 Opening library file /usr/local/gromacs/share/top/ffG43a1-n.tdb
 Opening library file /usr/local/gromacs/share/top/ffG43a1-c.tdb
 
 Back Off! I just backed up topol.top to ./#topol.top.14#
 Processing chain 1 (3 atoms, 1 residues)
 Opening library file /usr/local/gromacs/share/top/specbond.dat
 5 out of 5 lines of specbond.dat converted succesfully
 There are 0 donors and 0 acceptors
 There are 0 hydrogen bonds
 Fatal error: Residue 'C=O' not found in residue topology database
 
 
 what is wrong? how can I generate a topology for this molecule?
 
 
 
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