Dear AMBER user group
I have a problem with MMPBSA.py, when I run my calculation on our local
cluster.
Could some expert help me figure out where the problem is and how I should
address it?
Thank you very much for your help!
Here is the error message I received.
----------------------------------------------------------------------------
----------------
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /pdc/vol/amber/14/amber14/bin/mmpbsa_py_energy
cpptraj found! Using /pdc/vol/amber/14/amber14/bin/cpptraj
Preparing trajectories for simulation...
File "/pdc/vol/amber/14/amber14/bin/MMPBSA.py.MPI", line 103, in <module>
app.file_setup()
File
"/pdc/vol/amber/14/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py",
line 156, in file_setup
self.mpi_size, str(external_progs['cpptraj']), self.pre)
File
"/pdc/vol/amber/14/amber14/lib/python2.6/site-packages/MMPBSA_mods/make_traj
s.py", line 59, in make_trajectorie
s
traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
File
"/pdc/vol/amber/14/amber14/lib/python2.6/site-packages/MMPBSA_mods/make_traj
s.py", line 467, in __init__
self.Query()
File
"/pdc/vol/amber/14/amber14/lib/python2.6/site-packages/MMPBSA_mods/make_traj
s.py", line 611, in Query
raise RuntimeError('Unexpected output from cpptraj. Has format '
RuntimeError: Unexpected output from cpptraj. Has format changed?
Error occured on rank 0.
Exiting. All files have been retained.
Rank 0 [Mon Dec 14 21:58:14 2015] [c0-0c0s11n2] application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 0
_pmiu_daemon(SIGCHLD): [NID 00046] [c0-0c0s11n2] [Mon Dec 14 21:58:14 2015]
PE RANK 0 exit signal Aborted
----------------------------------------------------------------------------
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Received on Mon Dec 14 2015 - 13:30:04 PST
