Dear users,
I am trying to run parallel MMPBSA.py.MPI on 1000 frames. this is my input
script:
===========================
&general
debug_printlevel=3,interval=10,full_traj=1,netcdf=1,verbose=2,strip_mask=:WAT:Na+:MG
/
&pb
indi=2.0,istrng=0.1
/
&decomp
idecomp=1
/
============================
i have submitted the script using following command
mpirun -np 5 MMPBSA.py -O -i mmpbsa.in -o final_stats.out -sp pc.prmtop -cp
pc_strip.prmtop -y ../../production/10.crd
but the job is getting killed with an error message
===========================================
File "/usr/soft/amber12/bin/MMPBSA.py", line 99, in <module>
app.parse_output_files()
File "/usr/soft/amber12/bin/MMPBSA_mods/main.py", line 926, in
parse_output_files
self.using_chamber)}
File "/usr/soft/amber12/bin/MMPBSA_mods/amber_outputs.py", line 725, in
__init__
AmberOutput._read(self)
File "/usr/soft/amber12/bin/MMPBSA_mods/amber_outputs.py", line 352, in
_read
self._get_energies(output_file)
File "/usr/soft/amber12/bin/MMPBSA_mods/amber_outputs.py", line 761, in
_get_energies
self.data['ENPOLAR'].append(float(words[2]))
IndexError: list index out of range
Exiting. All files have been retained.
============================================
What is happening here?
Thanks
Asmi
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Received on Wed Jul 03 2013 - 04:00:02 PDT
