Hi,
One additional question - does this error occur when you run the
serial version of mmpbsa.py as well?
-Dan
On Sat, Jul 27, 2013 at 9:26 AM, Ryan Pavlovicz <pavlovicz.7.osu.edu> wrote:
> Hi Jason,
>
> Here are the additional details:
>
> Loading and checking parameter files for compatibility...
> sander found! Using /usr/local/amber/amber12/bin/sander
> cpptraj found! Using /usr/local/amber/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> 50 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning PB calculations with /usr/local/amber/amber12/bin/sander
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
> File "/usr/local/amber/amber12/bin/MMPBSA.py.MPI", line 100, in <module>
> app.write_final_outputs()
> File "/usr/local/amber/amber12/bin/MMPBSA_mods/main.py", line 643, in
> write_final_outputs
> self.normal_system, self.mutant_system, self.mut_str, self.pre)
> File "/usr/local/amber/amber12/bin/MMPBSA_mods/output_file.py", line 779,
> in write_decomp_binding_output
> for token in gb_com.allowed_tokens:
> UnboundLocalError: local variable 'gb_com' referenced before assignment
> Error occured on rank 0.
> Exiting. All files have been retained.
> [cli_0]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> mpiexec: Warning: task 0 exited with status 1.
> mpiexec: Warning: tasks 1-11 died with signal 15 (Terminated).
>
> Thanks for your help!
>
> -ryan
>
> On Fri, Jul 26, 2013 at 3:34 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Fri, Jul 26, 2013 at 11:29 AM, Ryan Pavlovicz <pavlovicz.7.osu.edu
>> >wrote:
>>
>> > Hi,
>> >
>> > I am experiencing a problem using the MMPBSA.py.MPI script when it comes
>> to
>> > calculating the DELTA energies for every frame of a decomposition (-deo)
>> > when only PB calculations are called for.
>> >
>> > Here is my input file:
>> >
>> > &general
>> > endframe=4000, verbose=2, keep_files=2,
>> > /
>> > &pb
>> > istrng=0.150, inp=1, cavity_offset=0.92, cavity_surften=0.00542,
>> > /
>> > &decomp
>> > idecomp=1, print_res="1-255"
>> > dec_verbose=1,
>> > /
>> >
>> > And the output:
>> >
>> > Loading and checking parameter files for compatibility...
>> > sander found! Using /usr/local/amber/amber12/bin/sander
>> > cpptraj found! Using /usr/local/amber/amber12/bin/cpptraj
>> > Preparing trajectories for simulation...
>> > 4000 frames were processed by cpptraj for use in calculation.
>> >
>> > Running calculations on normal system...
>> >
>> > Beginning PB calculations with /usr/local/amber/amber12/bin/sander
>> > calculating complex contribution...
>> > calculating receptor contribution...
>> > calculating ligand contribution...
>> > UnboundLocalError: local variable 'gb_com' referenced before assignment
>> > Error occured on rank 0.
>> > Exiting. All files have been retained.
>> > [cli_0]: aborting job:
>> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>> >
>> > This only occurs when I don't include the GB calculations. The -deo
>> output
>> > will print the PB complex, receptor, and ligand info, but fails when it
>> > gets to the 'DELTAS:' section.
>> >
>> > I am experiencing this problem with the AmberTools version 13.13.
>> >
>> > This seems like a possible bug, so i thought i'd bring it to someone's
>> > attention.
>> >
>>
>> It is. Can you change debug_printlevel to "2" in the _MMPBSA_info file and
>> then run:
>>
>> MMPBSA.py -rewrite-output
>>
>> ? That should print out a verbose traceback that will let me find where
>> the problem is.
>>
>> Thanks!
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sat Jul 27 2013 - 10:00:03 PDT
