I agree with Hannes, ff99SB* is different from ff99SB. Overall, though, I
still recommend ff14SB as being better, but we have not made a systematic
comparison.
On Fri, Sep 12, 2014 at 11:35 AM, Hannes Loeffler <
Hannes.Loeffler.stfc.ac.uk> wrote:
> 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.
> --
> Scanned by iCritical.
>
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Received on Fri Sep 12 2014 - 14:00:02 PDT
