It depends on the specific force field, but the ff14SB and ff19SB are
applicable to D amino acids as well. The standard name can be used, as long
as the D conformation is present in the input coordinates.
On Mon, Feb 7, 2022, 8:17 PM nguerin <nguerin.cs.duke.edu> wrote:
> Dear Amber Community,
>
> I've looked through the archives and I've seen some notes about some of
> the protein forcefields are compatible with D-amino acids, but I didn't
> find anything specific about whether there were special steps one has to
> take to simulate protein systems with mixed D and L amino acid
> chiralities. Are there?
>
> One thing I've noticed is that programs like pdb4amber doesn't recognize
> amino acid names like 'DLY' for D-lysine, so I've been changing the
> names back to their L- versions.
>
> Thank you for your help,
>
> Nate Guerin
> Duke University
>
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Received on Mon Feb 07 2022 - 18:30:02 PST
