ff94 force field can be applied to D-amino acids in the same way as any other Amberforce field such as ff14/19SB, etc.
P.
On Tuesday, February 8, 2022, 09:58:31 AM PST, Nathan Guerin <nguerin.cs.duke.edu> wrote:
Thank you so much!
I know that ff94 is obsolete and has been so for some while, but to try
to reproduce prior results I'm interested in trying out ff94. There's no
chance that ff94 is compatible with D-amino acids, is there?
Thank you,
Nate Guerin
Duke University
On Mon Feb 7, 2022 at 9:04 PM EST, Carlos Simmerling wrote:
> 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 Thu Feb 10 2022 - 23:00:02 PST
