Hi all,
We're trying to do some tests to compare mm-pbsa and mm-gbsa calculations
for a protein/DNA complex. We've now got our mm-pbsa calculations mostly
working. For the mm-gbsa calculation, in our &gb section of the mmgbsa.in
script to MMPBSA.py we are trying igb=5 and igb=8 (both with mbondi2 for
the radius set, though we've also tried mbondi3 for the igb=8 case). In the
igb=5 case we are getting a negative dG, while using igb=8 with either
mbondi2 or mbondi3 we are getting very positive dG values. I've seen some
previous discussions here about folks having some difficulty with mm-gbsa
for protein/nucleic complexes, but it seemed that those were prior to the
optimized nucleic gb parameters of igb=8. Can anyone provide any input on
whether mm-gbsa is a reasonable approach for relative dG's with either of
these GB models? Thanks for your input.
Kind regards,
Joe
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Received on Tue Jun 27 2017 - 20:30:03 PDT
