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

From: Jason Swails <>
Date: Mon, 29 Mar 2010 15:07:54 -0400

On Mon, Mar 29, 2010 at 2:17 PM, case <> wrote:
> On Mon, Mar 29, 2010, Jason Swails wrote:
>> I don't know if they should necessarily be tested by default..
> I think it should.  Otherwise, we don't find problems, such as the one being
> dicsused here.
>> 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
> can't find ptraj:
> cat mmbpsa.out:
> Error: ptraj is needed for MMPBSA
> NOTE: All files have been retained for debugging purposes. Type
> --clean to erase these files.
> Note: the first thing the "Run" script does is to check for ptraj, but that
> test passes (because ptraj is indeed in $AMBERHOME/bin.)  But 'utils.which'
> is failing to find ptraj.  I would really appreciate it if someone who knows
> something about mmpbsa_py could look at this; I'm really not familiar at all
> with this part of the code, or with python.  Is 'utils.which' a standard
> module?  Is it somehow relying on the $PATH variable? I don't think the latter

utils.which does indeed search through PATH (not a standard python
function). Should it instead depend on AMBERHOME being present? I
just figured PATH was safer due to the confusion with where AMBERHOME
should point to (which is solved by the upcoming release, but not if
someone tries to use with anything earlier than Amber11 +
AmberTools1.3 and greater). The test could also be changed to look
for ptraj in the PATH rather than AMBERHOME/bin. I'll see what I can
do and get back to you with a fixed version of that searches
the PATH and AMBERHOME/bin if that's not already there.


> should be required for running the tests.
> ...thx...dac
> _______________________________________________
> AMBER-Developers mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Mon Mar 29 2010 - 12:30:02 PDT
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