The files distributed in the toppar directory in the original format do contain D amino acids--

Code:
% ls stream/prot
toppar_all36_prot_aldehydes.str          
toppar_all36_prot_arg0.str
toppar_all36_prot_c36_d_aminoacids.str   
toppar_all36_prot_c36m_d_aminoacids.str
toppar_all36_prot_fluoro_alkanes.str     
toppar_all36_prot_heme.str
toppar_all36_prot_model.str              
toppar_all36_prot_modify_res.str
toppar_all36_prot_na_combined.str        
toppar_all36_prot_pyridines.str
toppar_all36_prot_retinol.str


A stream file for the recent c36m protein FF is available, as well as one for the older c36 FF. The residue names all have the letter D added, the chiral Calpha configuration is inverted, and the CMAP correction is modified accordingly.

I do not know if they are included in the GROMACS conversion, however.


Rick Venable
computational chemist