Thank you, I'll try to install the new version of MMPBSA.py script.
David
On Sun, Mar 20, 2011 at 9:33 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> The first error is a failure with mm_pbsa.pl. To find out why it really
> failed, you'd have to look at some of the temporary files created during
> that program's execution and look for error messages. Since mm_pbsa.pl is
> a
> self-contained program, as long as you don't plan on using it for stability
> calculations, you can safely ignore that error.
>
> As for the other error -- that relates to the other MM/PBSA script,
> MMPBSA.py. This can also be safely ignored since the version bundled with
> Amber11 should be discarded in favor of the version that is downloadable on
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/compile.html.
>
> Hope this helps,
> Jason
>
> On Sun, Mar 20, 2011 at 1:45 AM, David Cantu <cantudav.gmail.com> wrote:
>
> > Dear Amber Users/Developers:
> >
> > I installed the serial version of Amber 11 and during the tests one error
> > and one failure came up.
> >
> > Here is the error on the log file:
> > ==============================================================
> > CALCULATING TEST: 02_MMPBSA_Stability
> > ./Run.mmpbsa.test: Program error
> > make[1]: *** [test.mm_pbsa] Error 1
> > cd qmmm2/input_validation && ./Run.invalid_atom_ids
> > diffing invalid_atom_ids.out.save with invalid_atom_ids.out
> > PASSED
> > ==============================================================
> >
> > And one test experience failure. On the log file:
> > ==============================================================
> > diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
> > possible FAILURE: check FINAL_RESULTS_MMPBSA.dat.dif
> > ==============================================================
> >
> > and on the .dif file (last lines):
> >
> > < DELTA G binding = -38.7089 +/- 1.9350
> > 1.3683
> > <
> >
> >
> -------------------------------------------------------------------------------
> > <
> >
> >
> -------------------------------------------------------------------------------
> > < RESULT OF ALANINE SCANNING: (D231A MUTANT:) DELTA DELTA G binding =
> > 0.4443 +/- 2.6654
> > <
> >
> >
> -------------------------------------------------------------------------------
> > <
> >
> >
> -------------------------------------------------------------------------------
> > < WARNINGS:
> > < igb=5 should be used with either mbondi2 or bondi pbradii set. Yours
> are
> > modified Bondi radii (mbondi)
> > ---------------------------------------
> >
> >
> > Should I be concerned about this error and failure? Any ideas as to why
> > they
> > came up? How can I correct them?
> >
> > Thank you,
> >
> > David
> > _______________________________________________
> > 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
>
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Received on Mon Mar 21 2011 - 19:00:02 PDT
