AMBER Archive (2005)

Subject: Re: AMBER: Protein with structural ions

From: Tim Meyer (tim_at_mmb.pcb.ub.es)
Date: Thu Apr 07 2005 - 09:05:15 CDT

> In my simulational system, there are three HIS coordinated with Zn2+. several MD simulation were performed with different ligands (the initial conformation of Ligands is from the result of autodock).
> I found that in one simulation three HIS residues keep a distance ~ 2A with Zn during 500 ps. But in some other trajectory, only two HIS keep this optimal coordinated distance, ~2A.

have you thought to use deprotonated HIS?
see

http://amber.scripps.edu/0Net/ions

tim
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