> I am having issues generating an amber force field for a protein
> containing my non-standard amino acid. I generated the helix itself
> in Macromodel and then modified the amino acid to my side chain
> (Cysteine -> Cys + side-chain, labeled DMV in this model).
When you want to develop a force field library for a new amino-acid,
you first need to decide which type of FF library you wish to build:
N-terminal, C-terminal or a central fragment.
(Usually, you only need the central fragment).
