AMBER: MM-PBSA questions

From: Miguel Ferreira <>
Date: Thu, 29 Jun 2006 01:26:14 +0000

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.


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Received on Sun Jul 02 2006 - 06:07:09 PDT
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