yes - the intrinsic bond/angle/dihedral parameters are indifferent to D or
L, and in the context of mixed D/L the energies differ but it would all be
in the nonbonded terms. So at least within the approximations of decoupled
force field terms it wouldn't matter if your bonded terms are fit to D or
L.
On Tue, Oct 23, 2018 at 5:24 PM Thomas Fox <thomas_fox.gmx.net> wrote:
>
> This is something I was always wondering... It is certainly true that
> the FF
> ist the same if you have an all-L or an all-R peptide/protein, but what
> when
> you combine R and L in one system? Probably the effects are small and
> also
> small compared to the general force field errors, but is it really
> rigorously true?
> Best,
> Th
> --
> Diese Nachricht wurde von meinem Android Mobiltelefon mit GMX Mail
> gesendet.
>
> Am 22.10.18, 15:46, Mijiddorj B <b.mijiddorj.gmail.com> schrieb:
>
> Dear Carlos,
> Thank you very much for the helpful reply.
> Best regards,
> Miji
> On Sat, Oct 20, 2018 at 7:11 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
> > You can use the same force field as for L-Phe. This is a
> conformational
> > difference, not a chemical one, and our parameters in ff14SB will
> work
> for
> > both. Other force fields may or may not.
> >
> > On Sat, Oct 20, 2018, 12:54 AM Mijiddorj B <b.mijiddorj.gmail.com>
> wrote:
> >
> > > Dear AMBER users,
> > >
> > > I would like to simulate a system that contains D-phenylalanine
> residue.
> > Is
> > > there any possible force field? Please advice me any possible
> chance.
> > >
> > > Best regards,
> > > Miji
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> References
>
> 1. http://lists.ambermd.org/mailman/listinfo/amber
> 2. http://lists.ambermd.org/mailman/listinfo/amber
> 3. http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Oct 23 2018 - 15:00:02 PDT
