AMBER Archive (2006)

Subject: AMBER: How to run mm_pbsa_statistics.pl?

From: Peng Tao (amberhelp_at_gmail.com)
Date: Wed Jan 04 2006 - 07:51:55 CST

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>]

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

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