[gmx-users] topology database

Jochen Hub jhub at gwdg.de
Wed Apr 5 16:02:57 CEST 2006

Dhananjay wrote:

> Hello all,
> while pdb2gmx on my pdb I got following error
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3
> Source code file: resall.c, line: 438
> Fatal error:
> Residue 'MSE' not found in residue topology database
> Will it be possible to add MSE in topology database of Gromacs?
> If yes then how to add it ?

In your share/gromacs/top folder are the rtp files of the forcefield you 
want to use. There you can add your molecule. Additionally, you might 
have to add
a corresponding paragraph in the hydrogen database file (.hdb)

In the manual, the rtp and hdb files are explainded.

Good luck, jochen

>  if anyone have any other solution please tell me....
> -- Dhananjay
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Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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