> You are making exactly the confusion I was referring to .... "ff99SB" is
> yet another protein-only force field .... I was not referring in any
> line of my comment to this force field. Again, everything denoted with
> "SB" are protein-only force fields ....
While this may be true (the nomenclature ff14SB refers to the protein
part), the "leaprc" file named leaprc.ff14SB contains both protein and
nucleic acid parameters, as noted. Perhaps we should have named the
default and recommended leaprc as of 2014:
leaprc.ff14.recommended
As noted, to understand what parameters are in a particular leaprc file,
you have to read the manual and/or understand what is in the leaprc file
(and also study the output from LEaP when building topologies).
We have discussed separating out leaprc's for proteins vs. nucleic vs.
lipid, etc and we admit that it can be very confusing with the current
force field alphabet soup and many options available. However, the
updated manuals in the current AmberTools do attempt to describe the force
fields more clearly; if you have ideas how to improve further, we are
happy to consider...
--tec3
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Received on Thu Aug 06 2015 - 19:00:02 PDT
