Le 23/07/12 13:41, Jason Swails a écrit :
> Hmm... A combo that seems not to have been tried before. Can you add
> "debug_printlevel=2" to the &general section and re-run using
> "-rewrite-output"?
>
> That should tell me where the error is occurring so it can be fixed.
> (Note, since all of the output files are intact, you will not have to
> re-run any of the calculations, you can continue to use -rewrite-output).
>
> Thanks!
> Jason
>
Thank you, Jason.
Sorry, I (wrongly?) thought from some messages in the list that using
AmberTools 12 was a good thing to do if one had Amber 11.
This is what I get with debug_printlevel=2:
(A)> MMPBSA.py.MPI -rewrite-output
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
File "/a/progs/simu/amber/amber12/bin/MMPBSA.py.MPI", line 650, in
<module>
[numframes, numframes_nmode], mut_str)
File "/a/progs/simu/amber/amber12/bin/MMPBSA_mods/output_file.py",
line 438, in write_binding_output
'DELTA TOTAL', 'Total')
File "/a/progs/simu/amber/amber12/bin/MMPBSA_mods/amber_outputs.py",
line 1155, in diff
return (self.data[key1].avg() - self.data[key2].avg(),
KeyError: 'Total'
Error occured on rank 0.
Exiting. All files have been retained.
I hope it helps.
Best,
-- Miguel
> On Mon, Jul 23, 2012 at 4:01 AM, Miguel Ortiz Lombardía <
> miguel.ortiz-lombardia.afmb.univ-mrs.fr> wrote:
>
>> Hi again,
>>
>> I've found yet another problem with the MMPBSA.py script.
>> This time I'm using:
>>
>> Amber 11
>> AmberTools 12
>>
>> all patched and installed from scratch following directions from the
>> excellent Jason's web page.
>>
>> After (rather lengthy) calculations using MMBPSA.py.MPI to get MMPBSA
>> data (GB, PB and entropy from NM) I consistently get this error message:
>>
>> KeyError: 'Total'
>> Error occured on rank 0.
>> Exiting. All files have been retained.
>>
>> Trying the -rewrite-output option (with either the serial or the
>> parallel versions of the script) does not help, I get the same error. I
>> used keep_files=1 and verbose=1, hoping it would be enough.
>>
>> The output files seem all (from GB, PB and NM) correct in the sense that
>> they end as expected and bear no error messages. The final results file
>> contains the entropy (NM) and the GB results but stops right before the
>> expected line:
>>
>> Using Normal Mode Entropy Approximation: DELTA G binding = (...)
>>
>> No PB results parsed.
>>
>> Any ideas?
>>
>> Best regards,
>>
>>
>> --
>> Miguel
>>
>> Architecture et Fonction des Macromolécules Biologiques (UMR7257)
>> CNRS, Aix-Marseille Université
>> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
>> Tel: +33(0) 491 82 55 93
>> Fax: +33(0) 491 26 67 20
>> mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
>> http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
--
Miguel
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
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Received on Mon Jul 23 2012 - 06:00:03 PDT
