Re: [AMBER] Amber force field for non-natural amino acids

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Tue, 23 Oct 2018 18:06:35 -0400

The charge distributions of D and L are the same during fitting (since they
are just mirror images) so the partial charges are the same. They would
interact with other chiral molecules differently, but so would the same
ligand docked in 2 poses. So it's the same as the rest of our
electrostatics model. The only real concern is making sure the dihedral
parameters have the right phases to be invariant to the D/L change,and
that's been tested.

On Tue, Oct 23, 2018, 5:53 PM Thomas Fox <thomas_fox.gmx.net> wrote:

>
> And what about electrostatics? It feels wrong, but my intuition may fail
> me...
> Th.
> --
> Diese Nachricht wurde von meinem Android Mobiltelefon mit GMX Mail
> gesendet.
>
> Am 23.10.18, 23:44, Carlos Simmerling <carlos.simmerling.gmail.com>
> schrieb:
>
> 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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Received on Tue Oct 23 2018 - 15:30:02 PDT
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