AMBER Archive (2008)

Subject: AMBER: Preparing peptides with D-amino acids

From: David Watson (dewatson_at_olemiss.edu)
Date: Tue Sep 09 2008 - 19:06:58 CDT


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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