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
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