Also, what version of MMPBSA.py are using?
MMPBSA.py.MPI --version
should give the information I need (as well as [$AMBERHOME/update_amber
--version])
On Wed, Jul 3, 2013 at 9:26 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 03 2013 - 06:30:02 PDT
