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? *
p.s. The results of mmGBSA (igb = 1, 2, 5, 7, 8) from AmberTools 12 & 13
are similar.
Please forgive the ignorance, if any.
Cheers,
Henry
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Received on Thu Jun 27 2013 - 09:30:02 PDT
