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.
>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?
Best regards,
Jesper
On Sep 15, 2011 04:15 "Jason Swails" <jason.swails.gmail.com>
<jason.swails.gmail.com> wrote:
> Oh, one thing I forgot to mention, because this edits MMPBSA.pypp,
> you'll
> have to re-install MMPBSA.pypp. You can do this by going to
> $AMBERHOME/AmberTools/src/mmpbsa_py and running the commands
>
> make serial
>
> and
>
> make parallel
>
> in succession. No need to reconfigure (it doesn't make use of any
> compilers, just the Python interpreter). You just need to have *some*
> config.h file available.
>
> HTH,
> Jason
>
> On Wed, Sep 14, 2011 at 10:09 PM, Jason Swails
> <jason.swails.gmail.com>wrote:
>
> >
> >
> > On Wed, Sep 14, 2011 at 9:52 PM, Jesper Soerensen <lists.jsx.dk>
> > <lists.jsx.dk> wrote:
> >
> > > Hey all,
> > >
> > > I am running an alanine scanning calculations with the new 3DRISM
> > > solvent model. I have used default settings.
> > >
> > > The error I get is this:
> > >
> > > getpdb: can't open file _MMPBSA_mutant_complex.pdb
> > >
> > > close failed in file object destructor:
> > >
> > > IOError: [Errno 9] Bad file descriptor
> > >
> > >
> > This is a bug. Please see the attached bugfix. You could either
> > apply it
> > by hand if you know how to read patch files (and even if you don't,
> > it's not
> > a very difficult format to learn) or apply it with the command:
> >
> > patch -p0 -N < bugfix.17
> >
> > while you are in AMBERHOME. The fix is, I would say, less than a
> > 1-liner.
> >
> > Let me know if this fixes things.
> >
> > Thanks for the report!
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> >
>
>
>
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Received on Fri Sep 23 2011 - 10:00:02 PDT
