Hi Ilyas,
The extent of my knowledge on these parameters are what I read in the
manual. The paragraph on "chi.OL3" corrections are:
3. ff99bsc0 and chi.OL3 for nucleic acids. The nucleic acid force fields
have recently been updated from those in ff99, in order to address a
tendency of DNA double helices to convert (after fairly long simulations) to
extended forms in the \alpha and \gamma backbone torsion angles.(Perez07)
Another change updates the glyocosidic torsional parameters for RNA.
(Banas10)
The citations listed there are
.Article{Perez07,
author = {Perez, A. and Marchan, I. and Svozil, D. and Sponer, J. and
Cheatham, T.E. and Laughton, C.A. and Orozco, M.},
title = {{Refinement of the AMBER Force Field for Nucleic Acids: Improving
the Description of alpha/gamma Conformers}},
journal = {Biophys. J.},
volume = {92},
pages = {3817-3829},
year = {2007}
}
and
.Article{Banas10,
author = {Ban\'{a}\v{s}, P. and Hollas, D. and Zgarbov\'{a}, M. and
Jurecka,
P. and Orozco, M. and Cheatham, III, T.E. and \v{S}poner, J. and Otyepka,
M.},
title = {{Performance of molecular mechanics force fields for RNA
simulations: Stability of UUCG and GNRA hairpins}},
journal = {J. Chem. Theory. Comput.},
volume = {6},
pages = {3836-3849},
year = {2010}
}
Outside of this, I don't know exactly what parameters were put into ff10.
Hopefully some of the designers of that force field can chime in here and
see if we've forgotten to add a reference or something.
All the best,
Jason
On Sun, Mar 27, 2011 at 11:49 AM, <yildirim.pas.rochester.edu> wrote:
> I've published a paper regarding revision of chi torsion for RNA last
> year, which I think most of you are aware of. We tested it on the smallest
> structures; mononucleosides of A,G,C,U. It was even tested on hairpin
> structures in Banas et al. 2010 paper. I have spent almost my whole phd
> year to figure out why RNA single strands were not behaving right. At the
> end I revised the chi torsions, and tested on (both computationally and
> experimentally) on mononucleosides. We did a similar analysis on single
> strand GACC tetramer RNA and submitted to JPC B to show that chi revision
> is important. There is another paper in line to be submitted that shows
> its importance on free energy predictions.
>
> I would like to know if my work has been ignored and chi1.OL3 (which I am
> not sure if it is even published or published before my work) is included
> in ff10.
>
> Sincerely,
>
> Ilyas Yildirim, Ph.D.
> -----------------------------------------------------------
> = Department of Chemistry - 2145 Sheridan Road =
> = Northwestern University - Evanston, IL 60208 =
> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> = http://www.pas.rochester.edu/~yildirim/ =
> -----------------------------------------------------------
>
>
> On Sun, 27 Mar 2011, Jason Swails wrote:
>
> > According to the manual, ff10 has the chi1.OL3 modifications. It should
> be
> > part of parm10.dat.
> >
> > I'm in the process of checking this out now ;).
> >
> > All the best,
> > Jason
> >
> > On Sun, Mar 27, 2011 at 11:23 AM, <yildirim.pas.rochester.edu> wrote:
> >
> >> I have a question regarding the amber ff10 force field. Is there any
> >> revision for chi torsions? If yes, which parameter set is used?
> >>
> >> Ilyas Yildirim, Ph.D.
> >> -----------------------------------------------------------
> >> = Department of Chemistry - 2145 Sheridan Road =
> >> = Northwestern University - Evanston, IL 60208 =
> >> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> >> = http://www.pas.rochester.edu/~yildirim/ =
> >> -----------------------------------------------------------
> >>
> >>
> >> On Sun, 27 Mar 2011, Jason Swails wrote:
> >>
> >>> On Sun, Mar 27, 2011 at 4:39 AM, case <case.biomaps.rutgers.edu>
> wrote:
> >>>
> >>>> Hi everyone:
> >>>>
> >>>> I have posted a new release candidate here:
> >>>>
> >>>> http://ambermd.org/downloads/AmberTools.26mar11.tar.bz2
> >>>>
> >>>> Still needed:
> >>>>
> >>>> 1. Proofreading of Users' Manual.
> >>>> 2. Testing of the ff10 force field files
> >>>>
> >>>
> >>> How would we check that the RNA/DNA force fields act as advertised?
> Are
> >> the
> >>> chi.OL3 parameters found in a separate frcmod file somewhere that we
> >> could
> >>> add onto ff99bsc0?
> >>>
> >>> 3. Minor tweaks to the tests, esp. MMPBSA.py
> >>>>
> >>>
> >>> What tweaks are needed here?
> >>>
> >>>
> >>>>
> >>>> I know lots of people are at ACS, but any help you can give
> (especially
> >> for
> >>>> item 2) would help us get this baby out the door.
> >>>>
> >>>> ...thanks...dac
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER-Developers mailing list
> >>>> AMBER-Developers.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Jason M. Swails
> >>> Quantum Theory Project,
> >>> University of Florida
> >>> Ph.D. Candidate
> >>> 352-392-4032
> >>> _______________________________________________
> >>> AMBER-Developers mailing list
> >>> AMBER-Developers.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>
> >>
> >> _______________________________________________
> >> AMBER-Developers mailing list
> >> AMBER-Developers.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Mar 27 2011 - 13:00:03 PDT
