Please guess something to resolve from this problem
I am using the following command to rum MMPBSA analysis:
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
complex_sol.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop
-y prodn.mdcrd
*
Following is the output I am getting:*
ptraj found! Using /home/ppilab/AMBER10/exe/ptraj
sander found! Using /home/ppilab/AMBER10/exe/sander
Assuming /home/ppilab/AMBER10/exe/sander is part of
amber9 or amber10. Using old PB input file.
Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified
Bondi radii (mbondi)
Preparing trajectories with ptraj...
50 frames were read in and processed by ptraj for use in calculation.
Starting calculations...
Starting gb calculation...
calculating ligand contribution...
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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.
--------------------------------------------------------------------------
calculating receptor contribution...
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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.
--------------------------------------------------------------------------
calculating complex contribution...
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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.
--------------------------------------------------------------------------
Starting pb calculation...
calculating ligand contribution...
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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.
--------------------------------------------------------------------------
calculating receptor contribution...
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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.
--------------------------------------------------------------------------
calculating complex contribution...
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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.
--------------------------------------------------------------------------
Calculations complete. Writing output file(s)...
Error: No potential terms in sander output! Check output files.
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
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Received on Mon Mar 07 2011 - 06:00:05 PST
