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
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Received on Thu Jul 31 2014 - 20:00:03 PDT
