Hello Folks,
I am trying to calculate the binding energy of an analyte to to a "molecular micelle" system. I have tried to run the simulations more than once and it fails to run completely. Below is a copy of the command file used and the mmpbsa input file. Below that is the message I received at the end of the run.
command file to run MMPBSA
mpirun --oversubscribe -np 12 MMPBSA.py -O -i mmpbsa.in -o play2.out -sp RBNP_P4_water.prmtop -cp RBNP_P4.prmtop -rp ULV_228877.prmtop -lp R_BNP.prmtop -y RBNP_P4_water-new-final.traj
mmpbsa.in file
Input file for running PB and GB
&general
endframe=300000, verbose=1,
entropy=0,
/
&gb
igb=2, saltcon=0.100
/
#&pb
# istrng=0.100,
/
Message at "end of run"
Beginning GB calculations with /home/ebill/amber18/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating ligand contribution...
calculating ligand contribution...
File "/home/ebill/amber18/bin/MMPBSA.py", line 108, in <module>
app.parse_output_files()
File "/home/ebill/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 944, in parse_output_files
self.INPUT['verbose'], self.using_chamber)
File "/home/ebill/amber18/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 1007, in __init__
self.delta2()
File "/home/ebill/amber18/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 1236, in delta2
self.lig.fill_composite_terms()
File "/home/ebill/amber18/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 372, in fill_composite_terms
self.data[component] = self.data[key] + self.data[component]
File "/home/ebill/amber18/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 61, in __add__
raise LengthError('length mismatch in energy vectors')
LengthError: length mismatch in energy vectors
Exiting. All files have been retained.
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[3021,1],2]
Exit code: 1
--------------------------------------------------------------------------
./command_energy_new_test.in: line 3: : command not found
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Received on Sat Jan 18 2020 - 05:00:02 PST
