Hi Bill,
Thanks for ur reply
My mdcrd file contains 5000 frames. Iam using ambertools 1.4
Thanks
On Tue, 19 Jul 2011 17:48:16 -0400
Bill Miller III <brmilleriii.gmail.com> wrote:
> 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 - 15:00:04 PDT
