On Thu, Sep 22, 2011 at 10:54 AM, Marek Maly <marek.maly.ujep.cz> wrote:
> Hello Hugh,
>
> just to be sure:
>
>
> ff10 = ff99 + bsc0 + reparameterized glycosidic torsions ?
>
> or
>
> ff10 = ff99SB + bsc0 + reparameterized glycosidic torsions ?
>
Yes. ff99 = ff99SB for nucleic acids (only protein backbone torsions were
reparametrized in going from ff99 to ff99SB). For any useful advice/info
see Tom's response :).
All the best,
Jason
>
> Thanks in advance !
>
> Best wishes,
>
> Marek
>
>
>
>
>
> Dne Thu, 22 Sep 2011 17:02:40 +0200 Hugh Heldenbrand <helde010.umn.edu>
> napsal/-a:
>
> > For nucleic acids:
> >
> > ff10 = ff99 + bsc0 + reparameterized glycosidic torsions
> >
> > The paper describing the glycosidic torsion reparametrization is here:
> >
> > Performance of Molecular Mechanics Force Fields for RNA Simulations:
> > Stability of UUCG and GNRA Hairpins
> > Banas et al. J. Am. Chem. Soc. 2010 v6 pp 3836-3849
> >
> > http://pubs.acs.org/doi/abs/10.1021/ct100481h
> >
> > Unless you have a specific reason not to, you would want to use ff10
> > rather than ff99bsc0 to simulate a nucleic acid.
> >
> > To answer the OP's other question, ff10 and ff99bsc0 are compatible with
> > AMBER9, no need to upgrade.
> >
> > -Hugh Heldenbrand
> > Graduate Student, University of Minnesota
> >
> > On 09/22/2011 08:50 AM, Brian Radak wrote:
> >> If I'm not mistaken (and someone please correct me if I am wrong), for
> >> nucleic acids ff10 is exactly equivalent to ff99 + the bsc0
> >> parameters. Of
> >> course, ff10 also includes the non-trivial shift to new solvent models
> >> (TIP4P-Ew and the Joung/Cheatham alkali and halide ions).
> >>
> >> In short, I believe the conventional wisdom now is to always use ff10
> >> whenever possible. I don't know of any reasons why you wouldn't be
> >> able to
> >> do this with any recent release of AMBER (9, 10, 11, etc)
> >>
> >> Brian
> >>
> >> On Thu, Sep 22, 2011 at 9:41 AM, souvik sur<souviksur.hotmail.com>
> >> wrote:
> >>
> >>>
> >>> Hello,
> >>>
> >>>
> >>> Can the ff99 force field is comparable with parm bsc0 ?
> >>>
> >>> Is it possible to run
> >>> parm bsc0 in amber9 ? or higher version of amber is required for that?
> >>>
> >>>
> >>>
> >>> regards,
> >>> Souvik Sur
> >>> Ph. D. Student
> >>> Department Of Chemistry
> >>> University Of Delhi
> >>> India
> >>>
> >>> _______________________________________________
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> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >
> >
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> >
> >
>
>
> --
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 22 2011 - 08:30:07 PDT
