AMBER Archive (2006)

Subject: Re: AMBER: Simulating proteins with calcium ion

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Thu Dec 07 2006 - 19:56:02 CST

Maybe the Ca is bonded to the residue, otherwise why
the complex cannot be formed when mutate a bond
residue?

Sorrunding Ca there should be negative charges, thus
if the Ca change position too far away, then there
should be something wrong.

The other possibility is that the without explicit
solvent model is far away from the with water model.

I am looking forwrd to getting more discussion on it.

Best regards.

--- Qing Zhang <qingzhang_nyu_at_yahoo.com> wrote:

> Dear Amber users:
>
> I am trying to simulate a protein-protein complex
> with a calcium ion (Ca2+) at the binding interface.
> Energy minimizations on the initial crystal
> structure without explicit solvent lead to
> displacement of Ca2+, even though the ion is
> restrained. I searched the Amber achieve and found
> that the similar problems had been raised before and
> that two kinds of models had been used for solving
> the problem: bonded and non-bonded. The latter is
> preferred in my case because an experiment shows
> that the mutation of a particular residue that bonds
> to Ca2+ leads to ofpartial dissociation the
> complex.
>
> Although there have been clear demonstrations of
> non-bonded models for Zn2+ with Amber and Ca2+ with
> Charmm (indicating divalent ion coordination after
> MD simulations), I did not see such a clear
> demonstration of a nonbonded model for Ca2+ with
> Amber. Anyone knows?
>
> Thanks,
>
> Qing
>
> ======================================
> Qing Zhang, Ph.D.
> Research Associate
> Department of Molecular Biology, MB-5
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000
> Tel: (858) 784-2333
> Fax: (858) 784-2860
> Cell: (917) 509-3182
> Email: qzhang_at_scripps.edu
> Website: http://www.qingzhang.info
> ======================================
>
>
>
>
>
>
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