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 - 08:30:13 PDT
