[gmx-users] Advices needed!

Mark Abraham Mark.Abraham at anu.edu.au
Sat Feb 24 04:11:19 CET 2007

Triguero, Luciano O wrote:
> 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?

You will certainly need a new residue type in the .rtp file. See chapter 
5. Also you will need to consider whether there are any parameters in 
the force field suitable for this S-O bond, and what you are going to do 
to satisfy valency.


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