> I am doing simulation on system that with various compounds bonded to the
> N-terminal of certain peptide, like shown in the following picture. Now I
> am facing the problems with creating unit for such N-Cap residue.
>
> ?
> 1. Should I treat R1 combined R' as a N-Cap residue or just the R' only?
> 2. In any case above, is there any method available to assign correct
> partial charge and atom type for such non-standard residue?
