AMBER Archive (2008)

Subject: Re: AMBER: Preparing peptides with D-amino acids

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Sep 09 2008 - 19:26:20 CDT

we carefully checked ff99SB to make sure that D amino acids had the
right behavior.
all you have to do is read a pdb with D coords, or if you don't have
one then we often swap the HA and CB, heavily restrain all but the
side chain and minimize. for chiral side chains (Thr, Ile, etc) check
them carefully when you're done.
carlos

On Tue, Sep 9, 2008 at 8:06 PM, David Watson <dewatson_at_olemiss.edu> wrote:
> 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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-- 
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Carlos L. Simmerling, Ph.D.
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