AMBER: Preparing peptides with D-amino acids

From: David Watson <dewatson.olemiss.edu>
Date: Tue, 9 Sep 2008 19:06:58 -0500

Is it safe to generate sequences in xleap (say with ff03
parameterization) and "flip chirality" on the alpha-carbon to generate
the D-amino acid?
When I "desc myunit" I see that the residue name is unchanged.
I suppose what I am getting at is whether or not the dihedral force
constants are defined in a way so that chirality inversion is
penalized instead of promoted with such non-standard "standard" amino-
acid residues.

Thanks 


----
David Watson • Graduate Student • Medicinal Chemistry • 425 Faser Hall  
• University MS  38677 • 1.662.915.1663
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Received on Wed Sep 10 2008 - 06:07:52 PDT
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