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

[Erik Marklund]

Hi,

In addition, if you only wish to alter the protonation states of, say, aspartates, you can use the -asp flag so that you don’t have to go through all possible titratable residues. See vmx pdb2gmx for more residue-specific options.

Erik

> On 28 Jun 2016, at 09:34, Marlon Sidore <marlon.sidore at gmail.com> wrote:
> 
> 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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