Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop

From: Jason Swails <>
Date: Thu, 31 Jul 2014 22:51:54 -0400

On Thu, Jul 31, 2014 at 9:23 PM, Vivek Shankar Bharadwaj <> 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

‚ÄčThis 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

What happens when you set "use_sander=1" in the &general section of your
input file?

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 31 2014 - 20:00:03 PDT
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