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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Received on Sat Jun 16 2012 - 21:00:03 PDT
