Re: AMBER: requirement of delphi for mm_pbsa

From: Holger Gohlke <>
Date: Wed, 4 Jan 2006 18:09:46 +0100

Am Mittwoch, 4. Januar 2006 17:22 schrieb David A. Case:
> On Wed, Jan 04, 2006, Manish Datt wrote:
> > i`m trying to do binding energy calculations using mm_pbsa in amber8 on
> > red hat 9. the program seems to run correctly but the strange part is
> > that i don`t have delphi installed on my system. in the in put file the
> > path for delphi executable is same as given in example input file.
> >
> > is it necessary to have delphi to run mm_pbsa? if yes then why am i not
> > encountering any error if no then what is the significance of giving path
> > for delphi in the input file.
> I think the default for Amber 8 is to use "pbsa", Amber's Poisson-Boltzmann
> solver. So you should not need delphi.

That is correct.

> But it should probably not print
> out the directory if it is not being used....maybe someone will look into
> fixing that (hint, hint).

It just prints out that it has found a DELPHI line in the .PROGRAMS section
upon reading the file.
Which method it actually uses for calculation is determined by the PROC
variable in the .PB section. Thus, if you set PROC=2, Amber's pbsa is used
(and you could even comment the DELPHI line).

Best regards


> ...dac
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Dr. Holger Gohlke
J.W. Goethe-Universitaet
Fachbereich Biowissenschaften
Institut für Zellbiologie und Neurowissenschaft
Marie-Curie-Str. 9
60439 Frankfurt/Main
Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29464
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Received on Wed Jan 04 2006 - 18:17:18 PST
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