Dear Amber users
I am looking for your kind suggestions in restarting MMPBSA job. The
problem is as mentioned below:-
I submitted a MMPBSA job with following input:-
&general
startframe=1, endframe=10000, interval=20
strip_mask= :WAT,Na+,
/
&gb
igb=5, saltcon=0.150,
/
&pb
istrng=0.150, inp=2, radiopt=0, prbrad=1.4,
/
The job had completed the following steps before kill due to some
administrative problem:-
mpbsa_py_energy found! Using
/usr/shared_apps/packages/amber-18-build5/amber18/bin/mmpbsa_py_energy
cpptraj found! Using
/usr/shared_apps/packages/amber-18-build5/amber18/bin/cpptraj
Preparing trajectories for simulation...
500 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with
/usr/shared_apps/packages/amber-18-build5/amber18/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with
/usr/shared_apps/packages/amber-18-build5/amber18/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution.
My question is how should I restart the job?
I tried to rerun the PB calculations by commenting out GB section in the
input but I got the following error:-
File
"/usr/shared_apps/packages/amber-18-build5/amber18/bin/MMPBSA.py.MPI", line
100, in <module>
app.run_mmpbsa()
File
"/usr/shared_apps/packages/amber-18-build5/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/usr/shared_apps/packages/amber-18-build5/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/usr/shared_apps/packages/amber-18-build5/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 433, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError:
/usr/shared_apps/packages/amber-18-build5/amber18/bin/mmpbsa_py_energy
failed with prmtop com.prmtop!
Exiting. All files have been retained.
--------------------------------------------------------------------------
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.
--------------------------------------------------------------------------
I would be thankful for your kind suggestions.
Thanks in advance.
Sadaf
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Received on Thu Dec 16 2021 - 13:30:02 PST
