AMBER Archive (2004)

Subject: Re: AMBER: Calcium and GB

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 09 2004 - 21:10:26 CDT

On Tue, Jun 08, 2004, cailliez wrote:
>
> I would like to run a molecular dynamics simulation on a protein, which
> is complexed with calcium ions.

You should probably try some model compounds to see what happens. The
Amber GB parameterization has not been extended to calcium ions. A lot
depends on what the direct ligands to calcium are.

The following work on Mg2+ might help you get started, but note that this
is an "outer sphere" complex where the direct ligands to the metal are all
waters:

%A V. Tsui
%A D.A. Case
%T Calculations of the Absolute Free Energies of Binding between RNA and Metal
Ions Using Molecular Dynamics Simulations and Continuum Electrostatics
%J J. Phys. Chem. B
%V 105
%P 11314-11325
%D 2001

...good luck...dac

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