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

From: Vivek Shankar Bharadwaj <vbharadw.mymail.mines.edu>
Date: Thu, 31 Jul 2014 19:23:43 -0600

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

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

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

I am running this using amber12 and ambertools13

I would be thankful for any sort of help!

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 - 18:30:02 PDT
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