[gmx-users] charge neutralization in vacuum simulations

Erik Marklund erik.marklund at chem.ox.ac.uk
Tue Sep 1 12:30:29 CEST 2015

Dear Tasneem,

It first of all depends on the purpose of your simulation. Note that charge neutrality is not required like it is in solution; in mass spectrometry, for example, proteins are necessarily charged.

Secondly, knowing which sites get (de)protonated is not entirely straightforward. If you have good reason to believe that those Glu and Asp are neutral then your approach appear sound.

Kind regards,

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road

> On 1 Sep 2015, at 10:57, 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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