I can't offer suggestions about force fields for the alternate backbone (I
don't know of any that have been developed, but maybe others here do). But
leap doesn't choose L or D by default if you are loading coordinates.
Indeed it will use these if you tell it to build from sequence, but that's
a challenge for a cyclic peptide anyway since leap won't ensure closure, so
I doubt that's what you're doing).
On Sun, Aug 25, 2024 at 11:02 AM Baker, Joseph via AMBER <amber.ambermd.org>
wrote:
> Dear all,
>
> My group is interested in a small cyclic peptide containing both D and L
> amino acids as well as a mix of peptide and ester links along the backbone.
> We have a structure, so the D and L amino bit is no problem (as I
> understand that tLeap only chooses L by default). But I'm wondering if
> there is some advice about how to handle the different ester backbone links
> between some of the aminos in a sensible way. Thanks for any thoughts!
>
> Kind regards,
> Joe
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Received on Sun Aug 25 2024 - 11:30:01 PDT
