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
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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 23 2012 - 05:00:02 PDT
