On Wed, Aug 11, 2010, Jason Swails wrote:
>
> ff99SB is the ff99 force field that fixes a couple torsion parameters (4 of
> them total). All other parameters are those of ff99. If you want to
> simulate Nucleic acids, you should probably load leaprc.ff99bsc0 instead of
> leaprc.ff99SB. This will load ff99SB parameters to be used for proteins
> along with parmbsc0 for nucleic acids (which is updated from ff99).
Just an update/clarification: for historical reasons, ff99bsc0 only
applies the "Barcelona modifications" to DNA, not to RNA. If you want
RNA to have those modifications (and you will have to read the literature
carefully to decide this), use leaprc.ff10 (which is not well documented,
but with uses ff99SB for proteins, and ff99bsc0 for both DNA and RNA.)
....dac
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Received on Wed Aug 11 2010 - 09:30:08 PDT
