Just brief addition.
chi correction (OL) should be used only for RNA,
as it was not possible to simultaneously refine
ff for DNA and RNA via 1D reparametrization
of the chi dihedral of the force field.
Real RNA and DNA have different chi preferences,
RNA for chi anti, DNA for chi high-anti.
Without chi correction RNA would sooner or later degrade
to ladder-like structure, so it is quite essential in longer
sims and also improves syn region.
The entirely independent alpha/gamma correction (bsc0) works very well with
OL and improves RNA sims. There appears to be a synergy between
the chi and alpha/gamma corrections for RNA. So while bsc0 is
may be dispensable for RNA, it is definitely recommended,
based on existing experience.
For DNA bsc0 is critically important as without bsc0
DNA would degrade, and does it actually very swiftly.
Description of reasons (ladders etc), consequences and limits are in:
Zgarbova et al Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
J. Chem. Theor. Comput. 2011, 7, 2886
Sklenovsky et al Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs
J. Chem. Theor. Comput. 2011, 7, 2963
Banas et al Performance of molecular mechanics force fields for RNA simulations. Stability of UUCG and GNRA hairpins. Journal of Chemical Theory and Computation J. Chem. Theor. Comput. 6, 2010, 3836
Perez et al. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of alpha/gamma Conformers. Biophysical Journal 92, 2007, 3817-3829.
best wishes, Jiri
> OK, you mean probably that differences between RNA and DNA in
> "reparameterized glycosidic torsions".
>
> If I understood well for both (RNA,DNA) is possible to use ff10 but only
> in case
> of RNA, "reparameterized glycosidic torsions" are used.
>
> My previous question was more "user based" taking care here just
> what is the best option to load in tleap when creating systems a), b), c).
>
> Best wishes,
>
> Marek
>
>
>
> Dne Thu, 22 Sep 2011 18:15:28 +0200 Jason Swails <jason.swails.gmail.com>
> napsal/-a:
>
> > 2011/9/22 Marek Maly <marek.maly.ujep.cz>
> >
> >> OK,
> >>
> >> perfect that.s what I wanted to know.
> >>
> >> So just to be really sure:
> >>
> >> In case of simulation:
> >>
> >> a)
> >> Nucleic acids systems: BEFORE bsc0 NOW equivalent with using ff10
> >>
> >
> > Not quite. This is what Tom said:
> >
> >>> > For nucleic acids:
> >>>
> >>> ...to clarify: for RNA:
> >>>
> >>> > ff10 = ff99 + bsc0 + reparameterized glycosidic torsions
> >>>
> >>> ...for DNA,
> >>>
> >>> ff10 = ff99 + bsc0
> >>>
> >>> (since the reparameterized glycosidic torsions do not work particularly
> >>> well for DNA).
> >
> >
> >>
> >> b)
> >> Proteins systems: BEFORE ff99SB NOW equivalent with using ff10
> >>
> >> c)
> >> Proteins + nucleid acids systems: BEFORE (ff99SB + bsc0) now equivalent
> >> with using just ff10
> >>
> >>
> >> Am I right ?
> >>
> >> Best wishes,
> >>
> >> Marek
> >>
> >>
> >>
> >> Dne Thu, 22 Sep 2011 17:24:56 +0200 Brian Radak <radak004.umn.edu>
> >> napsal/-a:
> >>
> >> > I believe ff99SB is only for amino acids (improves helicity or
> >> > something).
> >> > It is almost certainly included in ff10 by default.
> >> >
> >> > On Thu, Sep 22, 2011 at 11:15 AM, Thomas Cheatham <tec3.utah.edu>
> >> wrote:
> >> >
> >> >>
> >> >> > For nucleic acids:
> >> >>
> >> >> ...to clarify: for RNA:
> >> >>
> >> >> > ff10 = ff99 + bsc0 + reparameterized glycosidic torsions
> >> >>
> >> >> ...for DNA,
> >> >>
> >> >> ff10 = ff99 + bsc0
> >> >>
> >> >> (since the reparameterized glycosidic torsions do not work
> >> particularly
> >> >> well for DNA).
> >> >>
> >> >> --tec3
> >> >>
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> >> >
> >> >
> >>
> >>
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> >
>
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Received on Thu Sep 22 2011 - 12:00:03 PDT
