You should examine the _MMPBSA_complex_pb.mdout files. There should be a
more helpful message in whichever mdout file the error occurred.
-Bill
On Sat, Jun 16, 2012 at 11:30 PM, Delwar Hossain <hossaind2004.yahoo.com>wrote:
> Hi Amber users,
> When I run MMPBSA.py.MPI script I got error message which is given below.
> Please note that I used mmpbsa.pl script for the same x.mdcrd output, and
> the calculation completed without any error message.
> I therefore, request you to help me solve the problem.
> progress.log
> Running MMPBSA.MPI on 32 processors
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /usr/local/amber12-gcc/bin/mmpbsa_py_energy
> cpptraj found! Using /usr/local/amber12-gcc/bin/cpptraj
> ptraj found! Using /usr/local/amber12-gcc/bin/ptraj
> Preparing trajectories for simulation...
> 50 frames were processed by cpptraj for use in calculation.
> Beginning GB calculations with /usr/local/amber12-gcc/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
> Beginning PB calculations with /usr/local/amber12-gcc/bin/mmpbsa_py_energy
> calculating complex contribution...
> CalcError: /usr/local/amber12-gcc/bin/mmpbsa_py_energy failed with prmtop
> M11-bec.gas.prmtop!
> Error occured on rank 1.
> Exiting. All files have been retained.
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 1.
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 1 with PID 25991 on
> node cluster3-126.chpc.ndsu.nodak.edu exiting without calling "finalize".
> This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Sat Jun 16 2012 - 21:00:03 PDT
