The last line says a lot here.
=>> PBS: job killed: mem job total 27153656 kb exceeded limit 8388608 kb
So you ran out of memory trying to run MMPBSA.py. Can you ask for more?
Also, how many frames are in your original mdcrd file that was read in by
MMPBSA.py? And finally, are you using AmberTools 1.5?
You also might want to try running it in serial to test if the same problem
exists, or if it is an MPI problem.
-Bill
On Tue, Jul 19, 2011 at 4:53 PM, Rajesh Raju <rajesh.raju.mail.chem.tamu.edu
> wrote:
> Dear Amber Users,
>
> I am using MMGBSA.py script to calculate the binding free energy
> between a DNA-protein system. I am getting the following error. Ligand
> (DNA) contains 2 residues and receptor (protein) contains 435
> resiues.. I have included 500 snapshots for analysis...
>
> I cannot understand the error,. I beleive my topology files are
> correct
>
>
> Activated Environment for using: Intel MKL v10.2.6.038.
> Activated environment for using: Intel Compilers, version 11.1 (073)
> Activated environment for using: OpenMPI, version 1.4.3
> Activated Environment for using: Intel MKL v10.2.6.038.
> Activated environment for using: Intel Compilers, version 11.1 (073)
> Activated environment for using: OpenMPI, version 1.4.3
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> sh: line 1: 11050 Segmentation fault
> /g/software/lms/amber11/exe/ptraj com.prmtop
> _MMPBSA_ptrajentropy.in > _MMPBSA_ptraj_entropy.out
> Error! Ptraj failed. Check coordinate and topology files for the
> complex.
> Error! Ptraj failed. Check coordinate and topology files for the
> complex.
> Error! Ptraj failed. Check coordinate and topology files for the
> complex.
> Error! Ptraj failed. Check coordinate and topology files for the
> complex.
> Error! Ptraj failed. Check coordinate and topology files for the
> complex.
> Error! Ptraj failed. Check coordinate and topology files for the
> complex.
> Error! Ptraj failed. Check coordinate and topology files for the
> complex.
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_receptor.mdcrd
> If this is not a compressed file then there is a problem
> =>> PBS: job killed: mem job total 27153656 kb exceeded limit 8388608
> kb
> mpirun: killing job...
>
> --------------------------------------------------------------------------
> mpirun was unable to cleanly terminate the daemons on the nodes shown
> below. Additional manual cleanup may be required - please refer to
> the "orte-clean" tool for assistance.
> --------------------------------------------------------------------------
> node307
> node308
> ~
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Jul 19 2011 - 15:00:03 PDT
