AMBER Archive (2006)

Subject: Re: AMBER: How to run mm_pbsa_statistics.pl?

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Jan 04 2006 - 11:27:05 CST

Am Mittwoch, 4. Januar 2006 14:51 schrieb Peng Tao:
> Dear all,
>
> I am trying to use MM_PBSA to decompose interactions in a protein-peptide
> complex to residue pairs. For some reason, my calculation aborted
> unexpectedly. Probably the sizes of intermediate output files are too
> large.
>
> But I do have three intermediate files for final calculation:
> mysystem_com.all.out(1.5Gb) mysystem_lig.all.out(18Mb) and
> mysystem_rec.all.out(1.2Gb).
> I am thinking about running script mm_pbsa_statistics.pl to read these
> three files and generate final output, but don't know how.
> The parameter file (mysystem_statistics.in) for mm_pbsa_statistics.pl is
> very simple. There are only three lines:
> mysystem_com.all.out 1_120
> mysystem_rec.all.out 1_107
> mysystem_lig.all.out 108_120
> (Am I right about this?)
>
> But trying to run script mm_pbsa_statistics.pl by typing
> mm_pbsa_statistics.pl < mysystem_statistics.in
> simply didn't work.
> What I got is:
> USAGE: mm_pbsa_statistics.pl <calc delta ? 0..2> <calc decomp ? 0..2>
> <input file> <output file>
> [<snap_min> <snap_max>]

If you want to run mm_pbsa_statistics.pl for a single traj. version of
MM-PBSA, you need to set calc_delta to "1", for a three traj. version to "2".
If you want to calculate a decomposition per residue, you need to set
calc_decomp to "1", for a pairwise decomposition to "2", for no decomp. to
"0".

So the call for a 3-traj. version with decomp. per residue would be:

mm_pbsa_statistics.pl 2 1 mysystem_statistics.in mysystem_statistics.out

With snap_min, snap_max you can optionally restrict the number of snapshots to
consider in the analysis to the intervall of [snap_min, snap_max].

Let me know if it doesn't work!

Best regards

Holger

>
> Based on this information, I coulnd't figure out how to run
> mm_pbsa_statistics.pl correctly.
>
> Could you please help me about this?
>
> Many thanks in advance.
>
> My MM_PBSA input file:
> ###########################################################################
>##### @GENERAL
> PREFIX fkbp12PrbPep
> PATH ../01_GenerateSnapshots/
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ../fkbp12PepCom.top
> RECPT ../fkbp12.top
> LIGPT ../probe_peptide.top
> #
> GC 0
> AS 0
> DC 1
> #
> MM 1
> GB 1
> PB 0
> MS 0
> #
> NM 0
> #
> ###########################################################################
>##### @DECOMP
> DCTYPE 4
> #
> COMREC 1-107
> COMLIG 108-120
> COMPRI 1-120
> RECRES 1-107
> RECPRI 1-107
> RECMAP 1-107
> LIGRES 1-13
> LIGPRI 1-13
> LIGMAP 108-120
> @MM
> DIELC 1.0
> @GB
> IGB 2
> GBSA 2
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
>
>
>
> --
> Best regards,
> Peng Tao
>
> Graduate Student
> Chemistry Department
> The Ohio State University 

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessur fuer Molekulare Bioinformatik

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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