>If I were to do a protein-RNA simulation with what is generally available
>today, I would likely use one of the modified phi/psi protein parameter
>sets by the Simmerling group (see the JACS 2002 article on TrpCage
>folding); if you have amber9 (or are getting AMBER9), this is the
>frcmod.ff99SB.
>
ff99SB is a newer update than the JACS 2002 parameters, in that paper we
had not
yet refit the glycine backbone. we think that ff99SB is much better and
a manuscript
is under review.
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Received on Sun Apr 16 2006 - 06:07:06 PDT
