AMBER Archive (2004)

Subject: Re: AMBER: mm-pbsa:- atom charges and radii ?

From: Ray Luo (
Date: Tue May 11 2004 - 01:21:06 CDT

>There, to my knowledge, has not been an update of the continuum radii for
>use with the AMBER force field; there is nice work by Banavali and Roux
>how did extensive MD and FEP calculations to develop a more consistent set
>of continuum radii for use with the all-atom CHARMM27 force field.
If you can get a hold of the amber8 distribution, the PBSA utility
program has a set of radii definition for parm94/parm99 charges. They
are optimized with experimental solvation free energies as benchmark.
This is done for proteins only at the moment.

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:
Home page:

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