I'm trying to design a peptide that binds to an enzyme. The tricky bit is that the peptide needs to be "grown" off of one end of a small molecule ligand that should dock into the active site. The ligand in question has an amide group at one of the ends, and we want to add amino acids to it. It also has a chlorine atom (pdb file attached).
What would be the best way to proceed with this problem? I'm unsure of how to let Rosetta's pepspec application know that it can add amino acids at the amide group.
Any help would be appreciated!