On Thu, Jun 27, 2013 at 12:02 PM, <psu4.uic.edu> wrote:
> Dear Amber 12,
>
> We found that the mmPBSA calculation results are quite different from
> MMPBSA.py in AmberTools 12 & AmberTools 13. The MMPBSA.py AmberTools 12
> results (dG) seem to be very negative just like AmberTools 1.5 (dG= -30~-40
> kcal/mol) while MMPBSA.py AmberTools 13 results are less negative. (dG= -7
> ~ -9 kcal/mol).
>
> We find that the default setting of "radiopt" has been changed from 1
> (AmberTools 12) to 0 (AmberTools 13). However, even set radiop = 1 in
> AmberTools 13 and use the same other settings and parameter files (radi) to
> run mmPBSA, MMPBSA.py results in AmberTools 13 are still less negative than
> AmberTools12. *May we know if there is a major change of the MMPBSA.py
> algorithm in AmberTools 13? *
>
>
MMPBSA.py itself has not changed how it works. It continues to call
external programs to compute the energies of each snapshot. If the binding
free energy results change between two versions of MMPBSA.py, that's a
result of changes to whichever programs that it calls.
The PB code changes a lot more than the GB code (the latter should never
change), so differences in results between two versions are unfortunately
not unusual. In my experience the differences have never been that large,
though.
However, where is the bulk of the difference in the binding free energy
coming from? Is the electrostatic energy largely the same? Is most of the
difference coming from big changes to the non-polar solvation free energy?
Looking at the actual energy terms that change significantly will help
narrow down what might have changed from one version to the next. Not
being an active PBSA developer, though, I'm not sure what has changed
between AmberTools 13 and AmberTools 12.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 27 2013 - 10:00:03 PDT
