AMBER Archive (2008)

Subject: Re: AMBER: potassium ion

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu May 22 2008 - 13:27:21 CDT

> I'm doing a simulation of a protein with a potassium which is
> suggested by several experimental studies to be bound to certain
> residues in the active site. After equilibration, the potassium seems
> correctly located between to oxygen atoms of two amino acids. After
> starts flying around in the binding site, and eventually it jumps out
> in the solution.
>
> 1. Can I trust the potassium parameters that follows ff03?

The K+ parameters used to be and presumably still are derived from
simulations w/ water models like TIP3 in which the O vdw is large
enough to contain the H's (Aqvist). Thus the K+ vdw is likely smaller
than would be derived for K+ in contact with protein atoms. This may be
relevant to your situation. For a discussion see

        Ion-Induced Stabilization of the G-DNA Quadruplex: Free
        Energy Perturbation Studies. W.S. Ross and C.C. Hardin
        Journal of the American Chemical Society 116, 6070 (1994).

You may want to try again with K+ vdw parameters from this paper.

Bill
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