Hi, Use genion -neutral and let gromacs do that hard work.
Regards, On Thu, Sep 4, 2014 at 9:03 AM, Ambarnil Ghosh <ambargrom...@gmail.com> wrote: > Dear users, > > My protein is a trimer and I want to run md : on binding of a peptide > (chain-D) to this trimer (chain-ABC). > > Therefore, I have four chains. So, when I create topol.top file using > pdb2gmx it automatically divide the topology in four *.itp files: > topol_Protein_chain_A.itp > topol_Protein_chain_B.itp > topol_Protein_chain_C.itp > topol_Protein_chain_D.itp > > so, in time of running "genion" command its required to mention the number > of ions to neutralize the protein. > Now, each of the protein monomer contains net charge of 2 (qtot) in chain > A, B and C. D-peptide have final qtot as 0. > > Now the question is : Where can I get final qtot for whole system? Is it > like that: I have to just sum up all three (2+2+2) and write "-nn 6" in > genion command ? Or the final qtot value is written in somewhere else in > some file, which I missed? > > I am new to multimeric simulation, any kind of help/lead is much > appreciated! > > Thanks much > Sincerely > Nil > -- > 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 gmx-users-requ...@gromacs.org. > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 gmx-users-requ...@gromacs.org.