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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Received on Sun Jul 28 2013 - 06:30:03 PDT
