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

[Justin A. Lemkul]

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 
compiled

-Jusitn

> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================