[gmx-users] How to change the protonation state of an aminoacid in a peptide

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 29 22:53:15 CEST 2009

Camilo Andrés Jimenez Cruz wrote:
> Hi.
> I have the gro file for a peptide in vacuum, in the peptide, there is
> only one ASP, and I want to change it to ASPH.
> If I run pdb2gmx -asp and select the protonated state, the only change
> is in the name of the residue (it doesn't add the needed hydrogen).
> Is there any automatic way changing the protonated state for this residue?

Well, the command that you entered should have worked (it always has for me). 
As for getting any extra advice, you will have to provide a much more complete 
description, including the following:

1. Which force field you are trying to use
2. Relevant output (from screen and from the structure/topology)
3. Which Gromacs version you are using
4. Any relevant details on compiler types, computer system, and how Gromacs was 


> Thanks in advance


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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