Re: [AMBER-Developers] mmpbsa tests (perl and python)

From: Jason Swails <>
Date: Mon, 29 Mar 2010 12:12:24 -0400

On Mon, Mar 29, 2010 at 11:56 AM, case <> wrote:
> Hi everyone:
> It seems that neither the perl nor the python version of mmpbsa are being
> tested in the current release candidate(!?!).  And, neither seem to pass
> the tests ("make test.mm_pbsa" and "make test.mmmpbsa_py")

I don't know if they should necessarily be tested by default... The
mmpbsa_py test takes a couple minutes (I could probably change the
test so as not to take as long). It's easy enough to add both test
rules to the master rule and have them tested alongside everything
else by the scripts.

Also, what part of the test fails? In my experience, it has been the
fact that the PBSA has been changing a lot recently and giving
slightly different numerical results and at some point I had stopped
updating the test files with the new results. If you would like, I
can have new test files with a new test that won't take nearly as long
(and another test for sander.APBS if it exists, since that
functionality is built into

> Can people associated with these figure out what is going on?  These should
> be a part of the master test file.  Is "test.mmmpbsa_py" just a typo?

It used to be test.mmpbsa in the Makefile_at. I don't remember if I
moved it to the Makefile or not, but test.mmpbsa_py would probably be
less confusing.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Mon Mar 29 2010 - 09:30:03 PDT
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