Re: [AMBER] protein-ligand-metal complex simulation

From: David A Case <>
Date: Fri, 22 Jul 2011 08:24:57 -0400

On Fri, Jul 22, 2011, Sangeetha B wrote:
> I want to study the metal coordinated interaction of a protein-ligand
> complex. The ligand interacts with my protein through two Mg2+ ions.
> I do not have any idea of how to setup a simulation with metals.

You are not alone. Attempts to model divalent ions with a simple fixed charge
force field generally yield results that have lots of problems. If you know
that the Mg2+ is "structural" and always stays in one place (without changing
its coordination environment) you could model this metal-ligand bonds,
as in Tutorial "A1-old" on the Amber web site.

....good luck....dac

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Received on Fri Jul 22 2011 - 05:30:05 PDT
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