Just to be sure, these references were given in the manual. Should we
include these as well?
Krepl, M.; Zgarbova, M.; Stadlbauer, P.; Otyepka, M.; Banas, P.; Koca, J.;
Cheatham, T.E. III; Sponer, J. Reference simulations of noncanonical
nucleic acids with different chi variants of the AMBER force field:
Quadruplex DNA, quadruplex RNA, and Z-DNA. J. Chem. Theory Comp.,2012, 8,
2506–2520
Zgarbová, Marie; Luque, F. Javier; Šponer, Jiˇri; III, Thomas E. Cheatham;
Otyepka, Michal; Jureˇcka, Petr. Toward improved description of dna
backbone: Revisiting epsilon and zeta torsion force field parameters. J.
Chem. Theory Comput.,2013, 9, 2339–2354.
Zgarbová, M.; Sponer, J.; Otyepka, M.; Cheatham, T.E. III;
Galindo-Murillo, R.; Jureˇcka, P. Refinement of the Sugar-Phosphate Backbone
Torsion Beta for AMBER Force Fields Improves the Description of Z- and
B-DNA. J. Chem. Theor. and Comp.,2015, 12, 5723–5736
On Thu, Mar 5, 2020 at 1:25 AM Christina Bergonzo <cbergonzo.gmail.com>
wrote:
> This info can be found at the top of the leaprc.DNA.OL15 file:
>
> # Uses ff99bsc0+OL15 for DNA
> # (ff99): Wang et al. J. Comp. Chem. 21: 1049, 2000
> # (bsc0): Perez et al. Biophys J. 92: 3817, 2007
> # (OL15): Zgarbova et al. JCTC 11: 5723, 2015
>
> On Wed, Mar 4, 2020 at 2:15 PM Sruthi Sudhakar <
> sruthisudhakarraji.gmail.com>
> wrote:
>
> > Respected group members,
> > Could anyone tell me how to cite the DNAOL15 forcefield in our papers? I
> > have read about how to cite the other force fields, except this one.
> > Thanking you in advance.
> >
> > Sruthi
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> -----------------------------------------------------------------
> Christina Bergonzo
> Research Chemist
> Biomolecular Measurement Division, MML, NIST
> -----------------------------------------------------------------
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 05 2020 - 01:30:02 PST
