Try upgrading to AmberTools 1.5. It has a new version of MMPBSA.py which
should be better.
The checkCoordinates() error messages leads me to believe that your prmtop
files aren't quite compatible with each other. Try visualizing the
intermediate trajectories to see if they look OK. I'm guessing you have
some extra water molecules or ions in your complex, receptor, or ligand
PRMTOP files that are stripped from the original trajectories.
HTH,
Jason
On Tue, Jul 19, 2011 at 5:54 PM, Rajesh Raju <rajesh.raju.mail.chem.tamu.edu
> wrote:
> 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
> >> ~
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 19 2011 - 16:00:02 PDT
