Re: [AMBER] implicit solvent calculations with calcium ion

From: David A Case <>
Date: Thu, 6 Aug 2020 07:46:30 -0400

On Thu, Aug 06, 2020, Piotr Fajer wrote:
>I have a problem that was identified by Akansha Saxena in 2007, Ca ions
>escape an EF-hand protein in implicit solvent, to which question I cannot
>find the answer on the archives.
>It behaves correctly in the explicit solvent, where the two coordination
>sites are filled by water oxygens, but not in the implicit solvent.

This seems not unexected to me. Ca will really, really like to be in water in
implicit solvent, and the balance of forces between being bound partly to the
protein, and escaping into water will be highly dependent on the electrostatic
radius that is used for Ca.

There is an old paper about the problem of getting a good balance of forces in
binding of magnesium:

%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

The basic conclusion was that you can get any answer you want, depending
radius you choose for the divalent ion. So, you could see what happens if you
increase the Ca Born radius by small amounts.


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Received on Thu Aug 06 2020 - 05:00:03 PDT
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