On Fri, 12 Sep 2014 11:16:55 -0400
David A Case <case.biomaps.rutgers.edu> wrote:
> On Fri, Sep 12, 2014, sunita.tifrh.res.in wrote:
> >
> > After going through the literature I find ff99SB*-ILDN is the one
> > which gives comparable result to the experimental observations.
>
> Just to add a small note to Jason's excellent reply:
>
> The types of side-chain torsional modifications that were made in the
> "ILDN" modifications to ff99SB are also present in ff14SB. That is to
> say, the same problems with side-chain behavior (plus some additional
> difficulties with other side chains) have been addressed; the specific
> changes from ff99SB are different. We expect that (like ff99SBildn)
> ff14SB will generally show improved physical fidelity, compared to
> ff99SB.
>
> For more details, please see the paragraph on "side chain dihedral
> parameters" on p. 31 of the Amber14 Reference Manual.
>
> Like Jason, I don't know what the "*" means in ff99SB*ildn.
According to this paper
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032131
it is a combination of the ff99SB* modifications plus ILDN. The ff99SB*
(and ff03*) parameters are apparently from
http://pubs.acs.org/doi/abs/10.1021/jp901540t
Cheers,
Hannes.
--
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Received on Fri Sep 12 2014 - 09:00:02 PDT
