On Fri, Jul 07, 2017, Elvis Martis wrote:
> inp=2 is default.
My personal advice, based mainly on looking at other people's results:
inp=1 is a more stable option, and "works" for a wider range of inputs (e.g.
nucleic acids, odd ligands, odd geometries). I would recommend using this
option first, especially when you are trying to see if things make sense.
inp=2 can work well in cases close to what it was designed for. But note
that the absolute energies for inp=2 may be quite different from those for
inp=1, even when trends in binding affinities are the same as (or better than)
those from inp=1.
Ray can weigh in here with more detailed advice. My conclusions should be
taken with caution, since I don't do very many of these calculations any more.
And I don't know what the defaults are--may depend on how you invoking the
pbsa codes.
....dac
[Shameless plug: MM/RISM avoids the issue of dividing the solvation free
energy into to polar and non-polar terms. But it hasn't been used nearly as
widely, and one has to be careful to use "corrected" estimates of the
solvation free energy.]
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Received on Fri Jul 07 2017 - 07:00:02 PDT
