[gmx-users] Advices needed!

Triguero, Luciano O ltriguero at miami.edu
Sat Feb 24 00:47:29 CET 2007

Hi David,

I don't see the source of error in the pdb format of the file. I can visualize it with any program and the oxygen is there. 
The problem appears when I want to create the .gro file form the pdb2gms program. I am trying to bind a oxygen atom to the sulfur atom 
of the MET residue. The pdb2gmx complains, although I have tried several different options. The oxygen atom is not a part of the MET residue 
database. Is these any way to overcome that or I just need to redifine a new residue type, like METO, in the residue database?

Thank for your answer,



Dr. Luciano Triguero
College of Art and Science
Department of Chemistry
Cox Science Building
1301 Memorial Drive, Room 146
P.O Box 249118
Coral Gables, FL 33124-0431
Cellular: 305-904-2419
Office: 305-284-3938

-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Fri 2/23/2007 4:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Advices needed!
Triguero, Luciano O wrote:
> Hi Everyone,
> I need your help in the following matter. How do I generate a .gro file from a pdb file where I added an oxygen atom to 
> one of the residue? 
> I get the following error message when I run pdb2gmx:
> =======================================
> Program pdb2gmx, VERSION 3.3.1
> Source code file: resall.c, line: 438
> Fatal error:
> Residue '' not found in residue topology database
> ========================================

you probably have made an error in the format of the file.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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