AMBER Archive (2006)

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

From: Peng Tao (amberhelp_at_gmail.com)
Date: Tue Jan 10 2006 - 09:49:00 CST

Dr. Holger Gohlke ,

One more question about MM_PBSA calculations. In one of my decompose binding
energy to single residue calculations, I got the following message from log
file:\
...
    Processing GB TGBTOT
        Doing 1 GB TGBSOL
        Doing 1 MM TGAS
        Doing 1 GB TGBSOL
        Doing 1 MM TGAS
        Doing 1 GB TGBSOL
        Doing 1 MM TGAS
    Processing GB SGBTOT
        Doing 1 GB SGBSOL
    No values for GB_SGBSOL existing -> Skipping
    Processing GB BGBTOT
        Doing 1 GB BGBSOL
    No values for GB_BGBSOL existing -> Skipping
....

According to AMBER manual, SGBSOL is GBSUR (hydrophobic contribution to
solvation free energy for GB calculation) plus GB (reaction field energy
calculated by GB) for side chain (S)
BGBSOL is the same value for backbone (B). I don't know exactly what is
GB_SGBSOL or GB_BGBSOL for. But they seem to be some intermediate variables
for SGBTOT or BGBTOT calculations. I don't know what these two values are
missing, while the calculation for GB TGBTOT can go through. If I get these
messages, will the calculation results be significantly effected?

Thanks very much for help. 

--
Best regards,
Peng Tao

Graduate Student
Chemistry Department
The Ohio State University

....
=>> Treat special parameters
=>> Calc missing parameters
    Processing MM BGAS
        Doing 1 MM BINT
        Doing 1 MM BVDW
        Doing 1 MM BELE
        Doing 1 MM BINT
        Doing 1 MM BVDW
        Doing 1 MM BELE
        Doing 1 MM BINT
        Doing 1 MM BVDW
        Doing 1 MM BELE
    Processing MM TGAS
        Doing 1 MM TINT
        Doing 1 MM TVDW
        Doing 1 MM TELE
        Doing 1 MM TINT
        Doing 1 MM TVDW
        Doing 1 MM TELE
        Doing 1 MM TINT
        Doing 1 MM TVDW
        Doing 1 MM TELE
    Processing MM SGAS
        Doing 1 MM SINT
        Doing 1 MM SVDW
        Doing 1 MM SELE
        Doing 1 MM SINT
        Doing 1 MM SVDW
        Doing 1 MM SELE
        Doing 1 MM SINT
        Doing 1 MM SVDW
        Doing 1 MM SELE
    Processing GB TGBSOL
        Doing 1 GB TGB
        Doing 1 GB TGBSUR
        Doing 1 GB TGB
        Doing 1 GB TGBSUR
        Doing 1 GB TGB
        Doing 1 GB TGBSUR
    Processing GB TGBTOT
        Doing 1 GB TGBSOL
        Doing 1 MM TGAS
        Doing 1 GB TGBSOL
        Doing 1 MM TGAS
        Doing 1 GB TGBSOL
        Doing 1 MM TGAS
    Processing GB SGBTOT
        Doing 1 GB SGBSOL
    No values for GB_SGBSOL existing -> Skipping
    Processing GB BGBTOT
        Doing 1 GB BGBSOL
    No values for GB_BGBSOL existing -> Skipping
    Processing GB BGBSOL
        Doing 1 GB BGB
        Doing 1 GB BGBSUR
        Doing 1 GB BGB
        Doing 1 GB BGBSUR
        Doing 1 GB BGB
        Doing 1 GB BGBSUR
    Processing GB TGBELE
        Doing 1 GB TGB
        Doing 1 MM TELE
        Doing 1 GB TGB
        Doing 1 MM TELE
        Doing 1 GB TGB
        Doing 1 MM TELE
    Processing GB SGBELE
        Doing 1 GB SGB
        Doing 1 MM SELE
        Doing 1 GB SGB
        Doing 1 MM SELE
        Doing 1 GB SGB
        Doing 1 MM SELE
    Processing GB SGBSOL
        Doing 1 GB SGB
        Doing 1 GB SGBSUR
        Doing 1 GB SGB
        Doing 1 GB SGBSUR
        Doing 1 GB SGB
        Doing 1 GB SGBSUR
    Processing GB BGBELE
        Doing 1 GB BGB
        Doing 1 MM BELE
        Doing 1 GB BGB
        Doing 1 MM BELE
        Doing 1 GB BGB
        Doing 1 MM BELE
    Processing GB SGBTOT
        Doing 1 GB SGBSOL
        Doing 1 MM SGAS
        Doing 1 GB SGBSOL
        Doing 1 MM SGAS
        Doing 1 GB SGBSOL
        Doing 1 MM SGAS
    Processing GB BGBTOT
        Doing 1 GB BGBSOL
        Doing 1 MM BGAS
        Doing 1 GB BGBSOL
        Doing 1 MM BGAS
        Doing 1 GB BGBSOL
        Doing 1 MM BGAS
=>> Calc delta from raw data
=>> Calc average and stddev
=>> Print output (decomp) to fkbp12PrbPep_statistics.out

On 1/4/06, Holger Gohlke <gohlke_at_bioinformatik.uni-frankfurt.de> wrote:
>
> 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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