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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Received on Mon May 06 2013 - 08:30:05 PDT
