Can you make me a tarball of the _MMPBSA_* files (please exclude the
trajectories to save on size). I will try to reproduce the problem.
Thanks,
Jason
On Wed, Jul 3, 2013 at 6:58 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> extremely sorry for the typo...it's
>
> mpirun -np 5 MMPBSA.py.MPI -O -i mmpbsa.in -o final_stats.out -sp
> pc.prmtop
> -cp pc_strip.prmtop -y ../../production/10.crd in previous mail...
>
>
> On Wed, Jul 3, 2013 at 4:26 PM, Asmita Gupta <asmita4des.gmail.com> wrote:
>
> > 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jul 03 2013 - 06:30:02 PDT
