[gmx-users] charge of aminoacids in an special pH

[Marlon Sidore]

You can change the protonation state of amino acids with pdb2gmx -inter
option.
It will ask you the protonation state of every AA. You could also start
with a tool like propka in order to know which ones are protonated.

Best regards,

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-06-28 9:18 GMT+02:00 Atila Petrosian <atila.petrosian at gmail.com>:

> Dear Gromacs users,
>
> I want to study MD simulation of my protein in an special pH (2).
>
> I want to investigate partially unfolding in this protein.
>
> How to set charge of aminoacids in pdb file, prior to start MD?
>
> Any help will highly appreciated.
>
> Best
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