AMBER Archive (2006)

Subject: Re: AMBER: MM-PBSA questions

From: Ray Luo (rluo_at_uci.edu)
Date: Fri Jun 30 2006 - 00:56:42 CDT

Miguel,

I think these are all great scientific questions and can only be
answered after extensive literature studies on MMPBSA.

Best,
Ray

Miguel Ferreira wrote:

>
> Dear amber users,
>
> First, thanks for answering my last question. Now I would like to ask
> some advices about the best mm-pbsa protocol.
> - Is it better to use implicit or explicit solvent in the previous
> minimization and MD calculations?
>
> - In some articles, a sphere of water molecules is used. Is there some
> particular reason for the use of a sphere of waters instead of a box?
>
> - Does any one knows about the influence that the dielectric constant
> value chosen has in the mm-pbsa results, namely, in the ranking of
> similar ligands that bind to a protein?
> Most of the articles use dielectric constants of 1 (solute) and 80
> (solvent), and some justify this choice by saying that these values
> are considered to be a " reasonable estimate of the free energy of
> hydration for a given molecule" (J. Med. Chem., 2004, 47, 3065-3074).
> What this mean exactly? Is it better to use a dielectric constant of
> 1? Does anyone know about recent studies discussing the effect of
> dielectric constant values in the mm-pbsa results?
>
>
> Sorry if my questions are too basic.
> Thanks
>
> Miguel
>
> _________________________________________________________________
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>
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-- 
====================================================
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_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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