I just checked, and the serial version has the same issue:
calculating ligand contribution...
File "/usr/local/amber/amber12/bin/MMPBSA.py", 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
Exiting. All files have been retained.
-ryan
On Sat, Jul 27, 2013 at 12:31 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> >>
> >>
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Sat Jul 27 2013 - 15:30:02 PDT
