AMBER Archive (2006)

Subject: Re: AMBER: requirement of delphi for mm_pbsa

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Jan 04 2006 - 11:09:46 CST

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 mm_pbsa.in 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

Holger

>
> ...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
Germany

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29464
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.uni-frankfurt.de/~hgohlke
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