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

From: Jeffrey Dyason <>
Date: Tue, 11 May 2004 18:07:12 +1000

        I have been trying to get my head around the atomic charges and
radii used when performing a mm-pbsa calculation (I am using Amber7 at the
present time). From published articles, most people seem to have used
Amber charges, whether from the force field parameter file or fitted using
RESP and have combined this with PARSE radii. However, on reading the
article on the PARSE parameters (D.Sitkoff et al., J. Phys. Chem. 1994,
98, 1978-88) the following sentence seems to suggest this may not be a
good idea :- "The PARSE charges lie within the range of charges used in
the force field sets CVFF, CHARMM, and OPLS but differ significantly from
the AMBER and ab initio sets." Given that this paper was published in
1994, will this still pose problems with the latest version of the AMBER
force field ? Has there been any work published on how changes to charges
and radii affect the mm_pbsa calculation ?
        When the mm_pbsa script is preparing input files (.pqr) for
calculating the PB part of the calculation, it uses ambpdb. Looking at the
source code for ambpdb in Amber 7, it appears to use Bondi radii when
generating a .pqr file. Is it simply a matter of commenting out the Bondi
radii and un-commenting the PARSE radii and re-compiling to get it to
produce PARSE radii ?

Bye Jeff.
Jeff Dyason e-mail:
Institute for Glycomics
Griffith University (Gold Coast Campus)
PMB 50 Gold Coast Mail Centre Tel: +61 7 5552 7028
Queensland 9726 Australia Fax: +61 7 5552 8098
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Received on Tue May 11 2004 - 09:53:00 PDT
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