[gmx-users] charge neutralization in vacuum simulations

[Johnny Lu]

was that for mass spectrometry?

On Tue, Sep 1, 2015 at 1:30 PM, Vitaly V. Chaban <vvchaban at gmail.com> wrote:

> 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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