The parallel version of MMPBSA.py is installed in AmberTools, not Amber
anymore. Thus, you have to run "make parallel" in the
$AMBERHOME/AmberTools/src directory to install parallel MMPBSA.
If you want to, you can just go to the directory
$AMBERHOME/AmberTools/src/mmpbsa_py and run the command "make parallel" and
that should do it.
HTH,
Jason
On Thu, Sep 29, 2011 at 10:07 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Thank you Bill.
>
> My bin directory has MMPBSA but not MMPBSA.MPI. sander.MPI and pmemd.MPI
> are there. I did run pmemd.MPI successfully.
>
> Any ideas why so?
>
>
> On Sep 29, 2011, at 3:59 PM, Bill Miller III wrote:
>
> > In AmberTools 1.5 the executables have changed to MMPBSA and MMPBSA.MPI
> > instead of MMPBSA.py and MMPBSA.py.MPI, respectively. The original
> scripts
> > are still present they are just in the src directory, though. The new
> > executable files call those python scripts when executed.
> >
> > -Bill
> >
> > On Thu, Sep 29, 2011 at 9:54 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> Hi everybody,
> >>
> >> Having installed AmberTools1.5 and Amber11 in parallel, I tried to run
> >> mmpbsa.py. I don't see in the bin directory a MMPBSA.py.MPI as in
> >> AmberTools1.4v.
> >>
> >> I run the tests of both serial and parallel installations (see below).
> So
> >> where's MMPBSA.py.MPI????
> >>
> >> Thanks in advance
> >>
> >> George
> >>
> >>
> >> Finished serial test suite for Amber 11 at Wed Sep 28 20:46:28 CEST
> 2011.
> >>
> >> 363 file comparisons passed
> >> 15 file comparisons failed
> >> 4 tests experienced errors
> >> Test log file saved as logs/test_amber_serial/2011-09-28_20-19-31.log
> >> Test diffs file saved as logs/test_amber_serial/2011-09-28_20-19-31.diff
> >>
> >> Finished parallel test suite for Amber 11 at Wed Sep 28 23:30:44 CEST
> 2011.
> >> Some tests require 4 threads to run, while some will not
> >> run with more than 2. Please run further parallel tests with the
> >> appropriate number of processors. See README for details.
> >>
> >> 296 file comparisons passed
> >> 0 file comparisons failed
> >> 4 tests experienced errors
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> 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
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Received on Thu Sep 29 2011 - 07:30:03 PDT
