AMBER Archive (2007)

Subject: Re: AMBER: calcium parameter for GB

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 16 2007 - 17:33:43 CST

On Tue, Jan 16, 2007, Wei Chen wrote:
>
> I try to simulate a metal protein having calcium ions with GB models. The
> name of calcium ion is defined as 'C0', which is in parm99.dat. When I
> checked the parmtop file, I found that 'RADII' and 'SCREEN' parameters of
> calcium ions are treated as the same as carbon atoms. So leap somehow
> recognized 'C0' as carbon atoms. I looked into the unitio.c file. But no
> parameters of calcium ions are in there. I am wondering if I can find
> 'RADII' and 'SCREEN' parameters of calcium ions somewhere.

As far as I know, no one has calibrated GB radii for calcium ions, at least in
the context of Amber potentials. There is a (somewhat old) paper that
discusses the problem and prospects for this for magnesium, and the same
principles presumably apply to calcium:

%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

Maybe others on the list can come up with more recent applications that give
guidance: this is (for sure) at pretty hard problem!

...dac

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