AMBER Archive (2008)

Subject: Re: AMBER: potassium ion

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Thu Jun 12 2008 - 12:46:36 CDT

Thanks Bill for the quick response, and the tips about your paper.
However, I am slightly confused about which specific vdw radius I
should use. I think I want to try with r*=1.93 and e=0.1, but I want
to double check with you to get it right. Could you please just verify
that this is correct?

thus, my frcmod file would be like this:

MASS
K+ 39.10 1.060 potassium

NONBON
  K+ 1.93 0.1

Thanks in advance for any help in this issue. :-)

LS

On Thu, May 22, 2008 at 8:27 PM, Bill Ross <ross_at_cgl.ucsf.edu> wrote:
>> 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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