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
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Mar 20 2011 - 08:00:02 PDT
