On Wed, May 23, 2012 at 11:24 AM, marawan hussain
<marawanhussain.yahoo.com>wrote:
> Dear AMBER developers,
> I feel like there are some issues with the MMPBSA.py in this version of
> AMBER (12)..From the bunch of posts i have seen i'm a bit afraid to use the
> results i got form the script..Some errors even may be silent and can't be
> easily figured out..I appreciate if you can release a new version of the
> script that we can safely use...
>
The test cases for MMPBSA.py changed slightly due to variations in the
coordinate files (slightly different RMSD behavior, which causes small
numerical differences since MDCRD files has such limited precision for the
coordinates). This affects results by well less than 1%.
Outside of this, and some slightly modified PBSA defaults (these change
slightly from version to version as further work suggests a better set of
defaults), the test results are unchanged since the last version.
There have been a number of issues that have cropped up, but these have all
been either poor error handling or attempts to get AmberTools12 working
with Amber11 for decomposition (there was a recent thread talking about
this). To clarify, the errors reported here have been instances in which
MMPBSA.py was not used correctly, but the error message was not helpful.
Anything tested for in the test suite (AmberTools/test/mmpbsa_py/) should
be as reliable as the previous version was. As deficiencies in the error
messages are reported, we will fix them.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 23 2012 - 03:30:02 PDT
