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

From: Suchetana Gupta via AMBER <amber.ambermd.org>
Date: Fri, 6 Jan 2023 09:22:22 -0800

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.

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Received on Fri Jan 06 2023 - 09:30:02 PST
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