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

[Camilo Andrés Jimenez Cruz]

I already found the problem, Thanks!

The point is that I was using a non standard forcefield, In this
forcefield, the protonated state is called ASH. the program tried to
find the ASPH and as it couldn't it didn't changed anything.

Thanks again!

On Wed, Jul 29, 2009 at 4:53 PM, Justin A. Lemkul<jalemkul at vt.edu> wrote:
>
>
> 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
>
> ========================================
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-- 
Camilo Andrés Jiménez Cruz