AMBER Archive (2006)

Subject: Re: AMBER: questions on mm_pbsa_statitistics.pl

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Oct 18 2006 - 13:19:20 CDT

Am Mittwoch, 18. Oktober 2006 17:12 schrieb Yongmei Pan:
> Hi, Holger
>
> Thank you very much! I checked my mm_pbsa3.in, I found that the two
> parameters, surften=0.00542, surfoff=0.092, are from the amber7 examples.
> But for default values in mm_pbsa_statistics.pm, they are 0.00542 and 0.92.
> I think the example and the mm_pbsa_statistics.pm are all from amber
> aothor, so why in the example it is 0.092, but in mm_pbsa_statistics.pm it
> is 0.92? So is there any reason to change from 0.92 to 0.092? I just
> curious. Thanks again, you did resolve my problem.

The surften=0.00542, surfoff=0.92 values are the ones that should be used
together with PARSE radii. The "0.92" is the correct value, "0.092" is a
typo.

Best regards

Holger

>
> Yongmei
>
> -----Original Message-----
> From: Holger Gohlke <gohlke_at_bioinformatik.uni-frankfurt.de>
> To: amber_at_scripps.edu
> Date: Wed, 18 Oct 2006 09:42:52 +0200
> Subject: Re: AMBER: questions on mm_pbsa_statitistics.pl
>
> Am Mittwoch, 18. Oktober 2006 00:57 schrieb Yongmei Pan:
> > Dear all:
> >
> > I have a question on the usage of mm_pbsa_statistics.pl. I found the
> > binding free energy from using this exe (use the file *statistics.in as
> > input file. it includes *_com.all.out, *_rec.all.out and *lig_all.out,
> > which are all output files from using mm_pbsa.pl) is about 0.5-1kcal/mol
> > different from the data derived directly from mm_pbsa.pl. The difference
> > reside in PBSUR item, all the other ones are same. Anyone knows why are
> > they different? thanks!
>
> If invoked directly from mm_pbsa.pl, the mm_pbsa_statistics modul uses the
> SURFTEN/SURFOFF values provided in the mm_pbsa.in file. If called from
> mm_pbsa_statistics.pl, default values are used instead that are hard-wired
> at the beginning of mm_pbsa_statistics.pm: gammaP/betaP for PB calc.,
> gammaG/betaG for GB calc.
> If you change those to the ones in your mm_pbsa.in file, the results will
> be identical.
>
> Best regards
>
> Holger
>
> > my command is: mm_pbsa_statistics.pl 1 0 *statistics.in *.out
> >
> > Yongmei pan
> > College of pharmacy, University of Kentucky
> >
> > -----------------------------------------------------------------------
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessor fuer Molekulare Bioinformatik

J.W. Goethe-Universitaet
Fachbereich Biowissenschaften
Institut für Zellbiologie und Neurowissenschaft
Max-von-Laue-Str. 9
60438 Frankfurt/Main
Germany

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29527
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
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