Dear Amber Users,
I'm trying to run MMPBSA.py with residue decomposition, but the job keeps failing with the following output:
Loading and checking parameter files for compatibility...
sander found! Using /usr/local/apps/amber/amber14/bin/sander
cpptraj found! Using /usr/local/apps/amber/amber14/bin/cpptraj
Preparing trajectories for simulation...
1000 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /usr/local/apps/amber/amber14/bin/sander
calculating complex contribution...
calculating receptor contribution...
File "/usr/local/apps/amber/amber14/bin/MMPBSA.py.MPI", line 104, in <module>
app.run_mmpbsa()
File "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", line 431, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /usr/local/apps/amber/amber14/bin/sander failed with prmtop complex.prmtop!
Error occured on rank 127.
Exiting. All files have been retained.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 127 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.
--------------------------------------------------------------------------
File "/usr/local/apps/amber/amber14/bin/MMPBSA.py.MPI", line 104, in <module>
app.run_mmpbsa()
File "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", line 431, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /usr/local/apps/amber/amber14/bin/sander failed with prmtop complex.prmtop!
Error occured on rank 125.
Exiting. All files have been retained.
[cn0935:52965] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[cn0935:52965] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
My complex, receptor, and ligand files were generated with ante-MMPBSA.py and look fine as far as I can tell. I double checked the strip_mask and other likely problems. What other reasons could there be for this error message?
I tracked down this thread<
http://archive.ambermd.org/201412/0195.html> from 2014 that involves a similar error message, but it's not clear to me what was done to solve the problem in that case.
Sincerely,
Andrew Kalenkiewicz
Postbaccalaureate Technical IRTA
National Institutes of Health
andrew.kalenkiewicz.nih.gov
734-709-0355
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Received on Fri May 20 2016 - 15:30:04 PDT
