[gmx-users] Re: How I can create a gromacs input file from a gamess output

Ing. Vojtech Spiwok Vojtech.Spiwok at vscht.cz
Tue Jul 13 08:32:11 CEST 2004

> Please,
> I 'd like your help to create a input file (.pdb, .gro,etc..) from a
> gamess calculation result.
> I converted a xyz file from the z-matrix in gamess output to pdb with
> openbabel,
> but when I run pdb2gmx, the result is:
> "Fatal error: Residue 'UNK' not found in residue topology database"
> Thanks,
> Marcelo Lima using Gromacs 3.2.1 with debian woody-linux and only 1 cpu.
> P.S. I started in Gromacs a few weeks ago, I read the Gromacs manual,
> but I can't see any answer for me.

If your gamess output is a peptide you have change residue numbering,
atom types and residue types to fulfil PDB formating for proteins. For
ATOM    251  C   UNK     1      17.227  31.138  18.388
will turn to
ATOM    251  CA  ARG    33      17.227  31.138  18.388
if this is C-alpha atom of Arg33 etc.

If your gamess output is not peptide then use PRODRG.

Vojtech Spiwok
ICT Prague

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