Re: AMBER: Mg2+ issues of using MM-PB/GBSA

From: Ray Luo <rluo.uci.edu>
Date: Wed, 30 Nov 2005 08:46:56 -0800

>
> I wonder whether I can use MM-PB/GBSA method to calculate the binding
> free energy in the case of Mg2+ directly involving in the ligand
> binding. The initial tests showed that the energy difference
> calculated by different GB methods is up to ~80 kcal/mol, and the
> difference between GB and PB models is also quite large, over 50
> kcal/mol.

Were these differences observed with the same radii for Mg2+ and
everything else, i.e. using the radii in the same prmtop file (for pbsa,
this means using the radiopt=0)?

Best,
Ray 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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Received on Thu Dec 01 2005 - 19:53:00 PST
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