Hello,
I've come to realize that, in GAFF, Junmei is playing a very sophisticated
game. The parameters listed in gaff.dat aren't precisely what appears in
the resulting prmtops. There are, instead, a rich set of rules listed
elsewhere on our website by which those parameter prototypes get
post-translational modifications to make a functioning system. In light of
this, I'm trying to figure out how one can go about parameterizing a ligand
with mostly GAFF yet introduce some specific modifications of his own (the
new modifications would not be meant to go through the mixing and
modification that other GAFF parameters do).
Looking at the sustiva ligand parameterization tutorial and the general
strategy with paramfit, it seems the things to do is write a frcmod file
that then gets read in to supplement or overwrite the original parameters.
So... is the answer that GAFF can be modified with a frcmod file, and tleap
knows to apply various mixing rules and contexts to modify GAFF's prototype
parameters, but if it then sees a frcmod file with relevant parameters it
will apply those at face value, overwriting the GAFF-generated numbers?
Cheers,
Dave
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Received on Mon Mar 28 2016 - 15:00:05 PDT
