AMBER Archive (2009)

Subject: Re: [AMBER] parameter files for D-amino acid

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Feb 05 2009 - 09:00:55 CST

Quoting vijayaraj_at_clri.res.in:

> There are some discussions in this forum regarding the D amino acid
> incorporation into the protein. But there is no clear definition for
> setting up parameters in ff99sb. Can someone give suggestion on this
> regard?

I think you just use a D-amino acid as you would use a L-amino acid.
LEaP does not differentiate enantiomers or even diastereoisomers...
Recognition is only based on the atom names and residue name available
in the force field library. That's it.

regards, Francois

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber