AMBER Archive (2006)

Subject: AMBER: Simulating proteins with calcium ion

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Thu Dec 07 2006 - 18:15:42 CST

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 partial dissociation of 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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