Hi Jason,
I was able to get the mdout files to output the error.
It says there is 'NATOM mismatch on coord and topology files'.
Vivek
On Thu, Jul 31, 2014 at 8:51 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Jul 31, 2014 at 9:23 PM, Vivek Shankar Bharadwaj <
> vbharadw.mymail.mines.edu> wrote:
>
> > Hi there,
> >
> > I am trying to calculate binding energies using MMGBSA for a carbohydrate
> > molecule (built using Glycam06 FF) in an enzyme. I keep running into the
> > error,
> >
> > CalcError: /home/common/packages/amber12/bin/mmpbsa_py_energy failed with
> > prmtop complex.prmtop!
> >
> > I looked for an error in the _MMPBSA_complex_gb.mdout.0 file but it is
> > empty.
> >
> > I tried to run mmpbsa_py_energy alone using the following command and I
> get
> > a segmentation fault.
> >
> > -- mmpbsa_py_energy -i _MMPBSA_gb.mdin -p complex.prmtop -c
> > _MMPBSA_complex.pdb -y _MMPBSA_complex.mdcrd.0
> >
>
> This is strange. There may be an error in your files of some sort that
> mmpbsa_py_energy just doesn't pick up. It's possible that sander may
> produce a more helpful error message if, indeed, there is some sort of
> problem.
>
> What happens when you set "use_sander=1" in the &general section of your
> input file?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Vivek S. Bharadwaj
Graduate Student
Department of Chemical and Biological Engg.
Colorado School of Mines
Golden Colorado
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Received on Thu Jul 31 2014 - 20:30:03 PDT
