Hi Jason,
The change fixes the problem. Thanks for looking into it!
-ryan
On Sun, Jul 28, 2013 at 9:16 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sun, Jul 28, 2013 at 9:15 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> >
> >
> >
> > On Sat, Jul 27, 2013 at 6:19 PM, Ryan Pavlovicz <pavlovicz.7.osu.edu
> >wrote:
> >
> >> 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.
> >>
> >
> > Ugh. It was a simple fix. If you go to line 779 of output_file.py
> > ($AMBERHOME/AmberTools/src/mmpbsa_py/MMPBSA_mods/output_file.py) and
> change
> > "gb_com.allowed_tokens" to "pb_com.allowed_tokens", does it fix your
> > problem?
> >
>
> Sorry, a little extra info. You need to run "make install" in
> $AMBERHOME/AmberTools/src/mmpbsa_py/ after making the change to have it
> take effect.
>
> Also, you can use the command: [[MMPBSA.py -rewrite-output]] to avoid
> having to rerun the calculation.
>
> Thanks again for the report,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Mon Jul 29 2013 - 21:00:03 PDT
