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.
Mark
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