Re: [AMBER] L and D peptides

From: Jason Swails <>
Date: Wed, 21 Jul 2010 10:51:15 -0400


Here's a suggestion, though some others may have reasons that it is not very good... You can make a copy of the amino acid library templates (all_amino94.lib), and go through each atom and take Dr. Case's advice and invert each x-coordinate. This will give you templates for all of the D-amino acids. You'll have to rename the D-residues though, so leap doesn't confuse them with the regular amino acids. Then, if you're using a pdb, delete all of the side chains for the amino acids that you want to change to the D-form and change their name to whatever you called it in the library file. Alternatively, you can just use the sequence command as you normally would using the D-names where you want them instead of the normal names.

Hope this helps,

Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
On Jul 21, 2010, at 3:39 AM, FyD <> wrote:
> Jorgen,
>> 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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Received on Wed Jul 21 2010 - 08:00:03 PDT
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