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 Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ > On 1 Sep 2015, at 10:57, tasneem kausar <[email protected]> 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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
