Q:

How to handle D-amino acids in peptides or proteins in a DS CHARMm simulation?

A:

In Discovery Studio, the CHARMm forcefield parameters are able to handle both L- and D-form amino acids equally well.

If you select the C-alpha atom of an L-amino acid and use the command: Chemistry> Stereochemistry > Invert Center, it will be converted to the D-form amino acid. Forcefield typing with CHARMm will be completely successful with no warning of missing parameters, and you can run CHARMm energy minimization and dynamics simulation as usual.