On Fri, Sep 23, 2011 at 12:58 PM, Jesper Soerensen <lists.jsx.dk> wrote:
> Hi Jason,
>
>
>
>
> Sorry it has taken me a while to get the bugfix patched and the
> calculation tested. So to follow up I was able to patch it and it moves
> past this "bugged" point now. However, a new error surfaced:
>
>
>
>
> >Error: Could not combine output files from different threads. Check
> >output files for errors.
>
Can you run in serial on a couple frames and see if it works? I'll try to
see why it's not working... Can you look at _MMPBSA_complex_rism.out.0 and
see if there are any errors in it?
>
> >NOTE: All files have been retained for debugging purposes. Type
> >MMPBSA.py --clean to erase these files.
>
>
>
>
> Now I checked the size of the combined output files:
>
> >184K_MMPBSA_complex_rism.out
>
> >184K_MMPBSA_ligand_rism.out
>
> >184K_MMPBSA_receptor_rism.out
>
> >4.0K_MMPBSA_mutant_complex_rism.out
>
> >0_MMPBSA_mutant_ligand_rism.out
>
> >0_MMPBSA_mutant_receptor_rism.out
>
>
>
>
> And as you can see there is a problem, with some of them not having the
> expected size. I have checked and all the output files per node are
> present and all have the same file size. Where should I look for the
> error would you think?
>
>
>
>
> Another thing that I wonder about is why it calculated the mutant_ligand
> "structure", when the mutation was performed on the enzyme, thus the
> "wild type" ligand should be the same as the ligand one. Is that a bug?
>
No. It copies over the normal ligand files (trajectories, topologies, etc.)
and re-runs the calculations. This wasn't considered a huge deal since the
mutation was almost always in the receptor and the ligand was so cheap to
calculate.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Sep 24 2011 - 07:30:04 PDT
