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
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> AMBER.ambermd.org
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>
>
>
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Received on Sat Jul 27 2013 - 08:30:03 PDT
