Dear members,
Thanks for the responses.
As you suggested, I have included
.PROGRAMS
SANDER $AMBERHOME/exe/sander
It has an error like sander is not found than I have
included the full source of sander
.PROGRAMS
SANDER /usr/local/appl/Amber8/exe/sander
Still I have the same problem the job stops at the same
stage. Seems to be is not problem with my coordinates at all
I have checked out with coordinates taken from the worked
examples still got the same error.
=>> Calculating energy / entropy contributions
Calc contrib for
./01_GenerateSnapshots/ras_raf_II_wt_com.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for
./01_GenerateSnapshots/ras_raf_II_wt_com.crd.2
Calc MM/GB/SAS
without any error message the job stops here..no progress
------------------------------------------------------------------------------
Kindly some one suggests me how to solve it.
Thanks.
> Am Montag, 16. April 2007 20:26 schrieben Sie:
> > Dear Sir,
> > As you suggested I have modified my mm_pbsa.in script by
> > including
> > SANDER $AMBERHOME/exe/sander
>
> This line must go BELOW the .PROGRAMS line, i.e.:
>
> .PROGRAMS
> SANDER $AMBERHOME/exe/sander
>
> Best regards
>
> Holger
>
>
> > But binding energy calculations stops after reading the
> > first snapshot it never proceed after that step. Here
> > is part of binding_energy.log file
> >
> > =>> Calculating energy / entropy contributions
> > Calc contrib for ../EXTRA_COORDS/snapshot_com.crd.1
> > Calc MM/GB/SAS
> > Generate PDB
> > Center PDB
> > Calc PBSA
> > Generate PQR
> > Calc MS
> > Calc contrib for ../EXTRA_COORDS/snapshot_com.crd.2
> > Calc MM/GB/SAS
> > I cant understand what could be the error? Could you
> > please suggest me what could be the error and how to
> solve it? >
> > Here is my binding_energy_mmpbsa file
> > .GENERAL
> > PREFIX snapshot
> > PATH ../EXTRA_COORDS/
> > COMPLEX 1
> > RECEPTOR 1
> > LIGAND 1
> > COMPT ../4FVC_62_NCW.prmtop
> > RECPT ../4FVC_nCW.prmtop
> > LIGPT ../LIG.prmtop
> > GC 0
> > AS 0
> > DC 0
> > MM 1
> > GB 1
> > PB 1
> > MS 1
> > NM 0
> > .PB
> > PROC 2
> > REFE 0
> > INDI 1.0
> > EXDI 80.0
> > SCALE 2
> > LINIT 1000
> > PRBRAD 1.4
> > ISTRNG 0.0
> > RADIOPT 0
> > NPOPT 1
> > CAVITY_SURFTEN 0.0072
> > CAVITY_OFFSET 0.00
> > SURFTEN 0.0072
> > SURFOFF 0.00
> > .MM
> > DIELC 1.0
> > .GB
> > IGB 2
> > GBSA 1
> > SALTCON 0.00
> > EXTDIEL 80.0
> > INTDIEL 1.0
> > SURFTEN 0.0072
> > SURFOFF 0.00
> > .MS
> > PROBE 0.0
> > SANDER $AMBERHOME/exe/sander
> > .PROGRAMS
> >
> >
> > Thanks.
> >
> > Sincerely,
> > Odde
> > ---------------------------------
> >
> > > Am Freitag, 13. April 2007 17:34 schrieben Sie:
> > > > Dear Sir,
> > > > I have a problem in using binding energy calculation
> > > > script /usr/local/appl/Amber8/exe/mm_pbsa.pl
> > > >
> > > > When I use mm-pbsa.pl script to calculate free
> > > > energy in amber8, I got this error
> > > > "mpirun must be used to launch all MPI applications
> > > > /usr/local/etc/amber7/exe/sander -O -i
> > > > sander_rec.in -o sander_rec.1.out -c ../c1_rec.crd.1
> > > > -p ../x.top not successful"
> > >
> > > MM-PBSA requires the non-parallel version of sander to
> > > be used (see the -nopar flag when generating the
> > > config.h file before compiling the code). In case you
> > > do have a non-parallel version but with a different
> > > name, you can point the mm_pbsa script to this by
> > adding the line >
> > > SANDER <full path of the non-par version>
> > >
> > > to the end of the mm_pbsa.in file.
> > >
> > > Best regards
> > >
> > > Holger
> > >
> > > > Later, I have made a pbs file like this and
> > submitted >
> > > job >
> > >
> > > > #PBS -S /bin/bash
> > > > #PBS -l cput=1000:00:00
> > > > #PBS -l ncpus=2
> > > > #PBS -l mem=1597mb
> > > > #PBS -M odde
> > > > #PBS -m abe
> > > >
> > > > cd /ptmp/r1052/AMBER/
> > > >
> > > > mpirun -np 2 $AMBERHOME/exe/mm_pbsa.pl mm_pbsa.in >
> > > > binding_energy.log
> > > >
> > > >
> > > > here is the error in .log file
> > > >
> > > > MPI: redwood: 0x4fe8000043cdedbc: mm_pbsa.in not
> > > > opened MPI: could not run executable (case #4)
> > > > /var/spool/PBS/mom_priv/jobs/12735.redwood.SC: line
> > > > 10: 18335 Killed mpirun -np 2
> > > > $AMBERHOME/exe/mm_pbsa.pl mm_pbsa.in
> > > >binding_energy.log >
> > > > Could you please suggest me how to solve it..
> > > >
> > > > Thank you so much,
> > >
> > > --
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++
> > > 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.bioinformatik.uni-frankfurt.de
> > > URL: http://www.uni-frankfurt.de/~hgohlke
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > Dr. Srinivas Odde
> > University of Mississippi,
> > Department of Medicinal Chemistry,
> > 417 Faser Hall, University, MS 38677,
> > U. S. A
> > Mobile: 662-801-0772: Lab: 662-915-1853
> > Email: odde.olemiss.edu
>
> --
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> 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.bioinformatik.uni-frankfurt.de
> URL: http://www.uni-frankfurt.de/~hgohlke
> ++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
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Received on Wed Apr 18 2007 - 06:07:37 PDT
