Re: [AMBER] How do I simulate D-amino acids?

From: Suchetana Gupta via AMBER <>
Date: Fri, 6 Jan 2023 10:18:11 -0800

I was using ff12SB

Somehow, trying to use Amber20 and ff14sb or ff19sb was giving me issues to

On Fri, Jan 6, 2023 at 9:22 AM Suchetana Gupta <>

> Hi Amber Community
> I have been trying to simulate a cyclic peptide containing L and D amino
> acids. I am noting a flip in stereochemistry. The method that I am using is
> simply renaming the D-amino acids to their regular L-counterparts and then
> running LEaP as usual. I was thinking that Amber does not affect the
> stereochemistry and would just make sure that the coordinates are taken
> care of, as they were from the beginning.
> My question is, how can I make sure that this flip does not happen?
> The flip occurs right after LEaP.
> Thanks
> Suchetana
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Received on Fri Jan 06 2023 - 10:30:03 PST
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