[AMBER] effect neutralizing ions on value of "saltcon" in generalized Born model

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Mon, 1 Oct 2012 16:36:09 -0400

Hi all,

I am running MD on a protein having about 3400 atoms. I am going to use
implicit solvation (igb=7). The protein has an unperturbed charge of (-10).
If I add 10 Na+ ions to neutralize will I have to consider that when
specifying the value of saltcon in generalized Bone model? This might
sound silly but the manual says that saltcon specifies the concentration(M)
of 1-1 mobile counterions in solution. So if I add 10 Na+ ions how should I
determine the value for saltcon?

Thank you

Sajeewa Dewage
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Received on Mon Oct 01 2012 - 14:00:01 PDT
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