[gmx-users] about residues protonation

Cesar Lopez inmuno_cl at yahoo.com
Thu Sep 8 23:41:00 CEST 2005

Dear Gromacs users:

I wanto to know if the follow trick is correct. I need
the Cys residue without proton, and in the ffG43a1 ff
topology for residues, actually there is that residue,
but for any reason the pdb2gmx couldn't assume this
topoly, for that reason I changed the topology name of
Cys for cis (the same for the pdb) and then I ran the
pdb2gmx with -missing option, when I saw the topology
of my protein, the residue was in the protonation
state I wanted, and charges of atoms were ok. Is it
ok?????? Is there any way to demostrate that the
topology is ok?


Cesar Lopez Bautista
Research Assistant
Bioinformatics and Computational Biology Unit
Universidad Peruana Cayetano Heredia

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