Hello everyone,
After lengthy calculations to get an estimation of the entropic term by
the normal modes approximation via the MMPBSA.py.MPI script I get this
error:
AttributeError: 'list' object has no attribute 'stdev'
Error occured on rank 0.
Exiting. All files have been retained.
Re-running the script (serial version) with the -rewrite-output option
produces, possibly not surprisingly, the same error. Increasing the
debug level (up to 5) gives:
File "/a/progs/simu/amber/amber12/bin/MMPBSA.py", line 641, in <module>
[numframes, numframes_nmode], mut_str)
File "/a/progs/simu/amber/amber12/bin/MMPBSA_mods/output_file.py",
line 348, in write_binding_output
final_output.add_section(nm_sys_norm.print_summary())
File "/a/progs/simu/amber/amber12/bin/MMPBSA_mods/amber_outputs.py",
line 1118, in print_summary
stdev = self.data[key].stdev()
AttributeError: 'list' object has no attribute 'stdev'
Error occured on rank 0.
Exiting. All files have been retained.
That I am afraid is not enough to ring a bell...
I am using AmberTools 12 with Amber 11. Calculations using the same
input file for MMPBSA.py.MPI have worked on other production runs of the
same system. I thought therefore that perhaps the minimisation had not
converged for some snapshot, but a first inspection of the
_MMPBSA_*_nm.out.* files suggests that that is not the case. Before
going into deeper inspection of those files, I thought that perhaps
someone could suggest where to look.
Thank you!
Best,
--
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 Fri Nov 09 2012 - 07:00:03 PST
