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

From: Suchetana Gupta via AMBER <>
Date: Fri, 6 Jan 2023 19:01:38 -0800

Thanks a lot David for the insightful points.
I will check these through. I have used a PDB structure that we have
obtained using Rosetta. Although it did have hydrogen in it, I had removed
them and just used the backbone to run LEaP since the presence of hydrogen
was throwing errors. I might try solving that problem first.
Thanks again

On Fri, Jan 6, 2023 at 6:40 PM David A Case <> wrote:

> On Fri, Jan 06, 2023, Suchetana Gupta via AMBER wrote:
> >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?
> Some extra comments, since I've just been doing some mixed D/L simulations:
> You don't say how you got your starting structure, but please check the
> starting coordinates carefully. Use ambpdb to get a PDB file, and a
> visualization program like VMD or Chimerax (etc.) Also, use the
> checkstructure option in cpptraj, which will flag the most common
> structural
> problems.
> One particular problem that can arise: if you don't have hydrogen positions
> in the original model, they may get added incorrectly if you "lie" and
> represent a D-amino acid as the L-version.
> >
> >The flip occurs right after LEaP.
> I'm not sure what "right after LEaP" means here, but it's certainly worth a
> double-check of what happens right at step 1. If you have bad forces to
> start with, a (non-physical) chirality flip might certainly occur.
> It's also possible for chirality flips to occur during an otherwise "good"
> simulation, but the barriers are quite high, so this is rare. You can use
> makeCHIR_RST to create artificial constraints to prevent chirality
> flips, but make sure you've eliminated other potential problems first.
> ....dac
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Received on Fri Jan 06 2023 - 19:30:03 PST
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