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

From: Thomas Fox <thomas_fox.gmx.net>
Date: Tue, 23 Oct 2018 23:24:20 +0200

   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 - 14:30:02 PDT
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