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

From: Holger Gohlke <>
Date: Wed, 12 May 2004 08:40:52 +0200

Jeffrey Dyason schrieb:
> Hi,
> 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.

In Amber7, mm_pbsa prepares a pdb file for coordinate input only to
delphi. Radii are then read directly by delphi via e.g. the
my_parse_delphi.siz file provided in the Example directory of the
mm_pbsa source tree. So to input Bondi radii, it is only necessary to
provide a new .siz file (and inform mm_pbsa by changing the SIZE entry

Best regards


> 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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Dr. Holger Gohlke
J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29826
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Received on Wed May 12 2004 - 07:53:00 PDT
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