[gmx-users] adding ions in the genion for multimeric proteins

rajat desikan rajatdesikan at gmail.com
Thu Sep 4 06:25:17 CEST 2014


Use genion -neutral and let gromacs do that hard work.


On Thu, Sep 4, 2014 at 9:03 AM, Ambarnil Ghosh <ambargromacs at gmail.com>

> 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-request at gromacs.org.

Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

More information about the gromacs.org_gmx-users mailing list