[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
> 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
> but when I run pdb2gmx, the result is:
> "Fatal error: Residue 'UNK' not found in residue topology database"
> 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.
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