Hey,
everything went fine during a run of MMPBSA.py.MPI analyzing ~100 MD
frames. Then, I decreased the frame interval by a factor of 10, leading
to ~1000 frames to analyze. Nothing else changed. I've re-run MMPBSA
with the -O option and then encountered the following Python traceback
(at the end of this second MMPBSA.py.MPI run):
Beginning GB calculations with sander...
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Traceback (most recent call last):
File
"/home/bioinfp/jang/apps/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI", line
1684, in <module>
lig_prm, ligstart, INPUT['surften'], '', '_MMPBSA_')
File
"/home/bioinfp/jang/apps/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py",
line 124, in PrintDecompResults
return
_decoutput12(outfile,debug,verbose,frames,comres,recres,ligres,ligstart,type,idecomp,surften,stability,prefix)
File
"/home/bioinfp/jang/apps/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py",
line 263, in _decoutput12
eint = float(line[11:20])
ValueError: invalid literal for float(): *********
Looks like an issue during parsing of _MMPBSA_complex_gb.mdout. For
diagnosis, I've uploaded a gzipped version of this file here (25 MB):
http://vs241092.vserver.de/_MMPBSA_complex_gb.mdout.gz
Do you need more information?
Thanks,
Jan-Philip
--
Jan-Philip Gehrcke
PhD student
Structural Bioinformatics Group
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
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Received on Tue Oct 11 2011 - 06:30:04 PDT
