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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Received on Wed Jul 03 2013 - 04:00:03 PDT
