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

From: Thomas Fox <thomas_fox.gmx.net>
Date: Tue, 23 Oct 2018 23:53:01 +0200

   And what about electrostatics? It feels wrong, but my intuition may fail
   me...
   Th.
   --
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   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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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
   4. http://lists.ambermd.org/mailman/listinfo/amber
   5. http://lists.ambermd.org/mailman/listinfo/amber
   6. http://lists.ambermd.org/mailman/listinfo/amber
   7. http://lists.ambermd.org/mailman/listinfo/amber
   8. http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Oct 23 2018 - 15:00:03 PDT
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