AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Feb 05 2009 - 09:06:09 CST

correct- building an initial model if you do not have one can be
challenging, but otherwise nothing specific needs to be done for the
parameters, they have the correct symmetry.

On Thu, Feb 5, 2009 at 10:00 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
> 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
>
>
>
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