Re: [AMBER] L and D peptides

From: Karl N. Kirschner <>
Date: Wed, 21 Jul 2010 12:26:21 +0200 (CEST)

Hi Jorgen,

  A while back I was working with a polymer with enantiomeric centers. I created two different residues files to represent two enatiomeric configurations. However, I was having difficulty getting Leap to recognize the enantiomeric center, as there was a bug in Leap (tleap and sleap) at the time when trying to connect the residues together to form a chain. I am not sure if this is corrected yet, but I know the Amber development team was working on it. I suggest that you double check Leap's output to verify that your enantiomeric centers in your peptide are what you think they are before you run a production run simulation.


----- Original Message -----
From: "FyD" <>
To: "AMBER Mailing List" <>
Sent: Wednesday, July 21, 2010 9:39:32 AM
Subject: Re: [AMBER] L and D peptides


> I am simulating a L-Tyr-L-Tyr-L-Tyr-L-Tyr-LTyr ect peptide and want to
> observe if the same is true for the D-isomer.

Yes, replacing x by -x in the PDB file will allow to generate
enantiomers for PDB files.

Now mixing different enantiomer units (D & L) will be more tricky and
will lead to diastereoisomers which should present different
properties... I wonder if C. Simmerling did not work on
enantiomers/diastereoisomers. But I cannot find the reference here...

regards, Francois

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