W
hat is your input file?
On Mon, May 6, 2013 at 11:21 AM, Kshatresh Dutta Dubey
<kshatresh.gmail.com>wrote:
> Hi Chris
>
> I also tried that, and all topology files were generated by ante-MMPBSA.py
> but unfortunately I found same error.
>
>
> On Mon, May 6, 2013 at 8:48 PM, Chris Chris <alpharecept.yahoo.com> wrote:
>
> > Did you use ante-mmpbsa.py to make the topology files? If not I highly
> > recommend you do this. It could be that your topology files are not
> > compatible with each other MMPBSA.py is very sensitive to this issue.
> >
> >
> > ________________________________
> > From: Kshatresh Dutta Dubey <kshatresh.gmail.com>
> > To: AMBER Mailing List <amber.ambermd.org>
> > Sent: Monday, May 6, 2013 7:16 AM
> > Subject: [AMBER] MMPBSA.py error
> >
> >
> > Dear Users,
> >
> > I am running MMPBSA.py using Amber 12. I am getting an error like--
> >
> > *Reading command-line arguments and input files...
> > Loading and checking parameter files for compatibility...
> > mmpbsa_py_energy found! Using /usr/local/amber12/bin/mmpbsa_py_energy
> > cpptraj found! Using /usr/local/amber12/bin/cpptraj
> > ptraj found! Using /usr/local/amber12/bin/ptraj
> > Preparing trajectories for simulation...
> > 21 frames were processed by cpptraj for use in calculation.
> >
> > Beginning GB calculations with /usr/local/amber12/bin/mmpbsa_py_energy
> > calculating complex contribution...
> > calculating receptor contribution...
> > CalcError: /usr/local/amber12/bin/mmpbsa_py_energy failed with prmtop
> > receptor_ant.top!
> > Exiting. All files have been retained.
> > *
> >
> > I searched this problem and also followed suggestion by Jason to check
> for
> > -
> > mmpbsa_py_energy -O -i _MMPBSA_pb.mdin -p <complex_prmtop> -c
> > _MMPBSA_complex.pdb -y _MMPBSA_complex.mdcrd.0 -o output
> >
> > and found segmentation fault. I checked the intermediate files and
> noticed
> > that _MMPBSA_complex.pdb, _MMPBSA_receptor.pdb and _MMPBSA_ligand.pdb
> > files are same. It seems that MMPBSA.py does not seperate ligand and
> > receptor from complex.
> >
> > Does anyone suggest solution for it. I will deeply appreciate your
> support.
> >
> >
> >
> > With best regards
> >
> >
> *******************************************************************************************************************
> > Kshatresh Dutta Dubey, PhD
> > Post Doctoral Fellow
> > Indian Institute of Technology Kanpur
> > Kanpur, India
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> With best regards
>
> *******************************************************************************************************************
> Kshatresh Dutta Dubey, PhD
> Post Doctoral Fellow
> Indian Institute of Technology Kanpur
> Kanpur, India
> _______________________________________________
> 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
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Received on Mon May 06 2013 - 12:00:03 PDT
