On Tue, Oct 11, 2011 at 9:20 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> 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(): *********
>
Try looking at the energies. It appears that some of the energies are
overflowing the fixed format. Are the energies for the same frames
identical for both simulations? Try visualizing the created trajectories
with VMD or something to make sure that they look OK.
HTH,
Jason
> 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
>
>
>
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 11 2011 - 07:00:03 PDT
