Thanks! That is very clear-cut.
Krisztina
--- On Tue, 6/18/13, David A Case wrote:
> From: David A Case
> Subject: Re: [AMBER] D amino acids
> To: "AMBER Mailing List"
> Date: Tuesday, June 18, 2013, 5:19 PM
> On Tue, Jun 18, 2013, FyD wrote:
> > > Charges and atom types I imagine would be same.
> >
> > Yes, although putting a D-amino-acid in the middle of
> L-amino-acids
> > leads to diastereoisomers, which would have different
> charge values
> > and identical atom types.
>
> No existing Amber protein model has charges that depend on
> the nature of
> adjoining amino acids. So, results for mixed L- and D-
> amino acids should be
> as accurate (or as inaccurate) as "standard" calculations
> with just L-amino
> acids.
>
> > > It is not clear to me if there is an
> improper term that is applied
> > > to the inverted chirality.
>
> There are not. Bottom line is that you should be able
> to handle D-amino
> acids with no change in libraries or force fields.
>
> ...dac
>
>
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Received on Tue Jun 18 2013 - 09:00:03 PDT
