[gmx-users] charge neutralization in vacuum simulations

Vitaly V. Chaban vvchaban at gmail.com
Tue Sep 1 19:31:14 CEST 2015

To get a neutral protein, protonate all residues...

Another question is what's your simulation goal, since protonated and
deprotonated residues behave obviously in a different way.

On Tue, Sep 1, 2015 at 6:57 AM, tasneem kausar
<tasneemkausar12 at gmail.com> wrote:
> Dear Gromacs users
> I am trying to neutralized the protein having two chains with four negative
> charge.
> I ran the command line as : pdb2gmx -c prtn.pdb -p -o -glu -asp.
> I have  chosen one protonated glu and one protonated asp for each protein
> chain.
> The net charge is now zero.
> Am I going through the right step for the neutralization?
> If there is any other way to neutralize protein, please suggest.
> Thanks in advance
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