Re: AMBER: Solute-solvent boundary in pbsa

From: Ray Luo <>
Date: Wed, 25 May 2005 18:40:39 -0700


>I guess I'll have one last question about
>determination of solvent/solute boundary by pbsa,
>invoked by mm_pbsa.
>I know that mm_pbsa uses mosurf to compute SASA and
>G(non-electrostatic). I was wondering if pbsa uses the
>SASA information to determine solute-solvent boundary,
>or it has just its own codes to do that (any
>literature?) ?
pbsa computes SASA internally. This is done numerically, i.e. by using a
dot representation of SASA. First each atom's SASA is represented by
dots. Then the dots that are overlapped by other atoms' SASA are knocked
out. The remaining dots will be SASA of the solute.

Please cite the latest Amber paper for this procedure (/D.A. Case, T.
Cheatham, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C.
Simmerling, B. Wang, R. Woods, The Amber Biomolecular Simulation
Programs, J. Comp. Chem. In Press, 2005/).


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:
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Received on Thu May 26 2005 - 22:53:00 PDT
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