Re: AMBER: D-enantiomers

From: David A. Case <>
Date: Tue, 20 Sep 2005 16:07:53 -0700

On Tue, Sep 20, 2005, M. Scott Shell wrote:
> I am relatively new to Amber, but have not found any information on the
> following topic. Is there an easy way to implement the D amino acids in
> Amber? I am looking to simulate a short peptide which contains one or more
> D-enantiomers along the backbone.

The force field for D-amino acids is the same as for L. You just need to make
sure that your starting geometries have the right chirality; after that, they
should remain with the correct chirality. (Of course, you should check that
this is true.)

That said, Amber doesn't provide any simple way to create starting geometries
for D-amino acids. In many cases, you can get something useful by using xleap
to graphically swap the HA and CB...(Sidechain) positions. Or, use other
tools to build the initial structure, save it in pdb format, and read it into

....good luck....dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Sep 21 2005 - 00:53:00 PDT
Custom Search