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

[Yang Ye]

After generating the molecule from PRODRG, it is not neede to run pdb2gmx.

Yang Ye

Yegor Isakov wrote:
> 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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