AMBER Archive (2005)

Subject: Re: AMBER: D-enantiomers

From: David A. Case (case_at_scripps.edu)
Date: Tue Sep 20 2005 - 18:07:53 CDT


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
leap.

...good luck....dac

-- 

================================================================== David A. Case | e-mail: case_at_scripps.edu 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 | http://www.scripps.edu/case ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu