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

Ambarnil Ghosh ambargromacs at gmail.com
Thu Sep 4 05:51:24 CEST 2014

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:

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

Thanks much

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