I have a macrocycle peptide obtained with simple_cycpep_predict, cycled between a Lys (Dap, Dab, and Orn too) side chain and the C-terminal carboxyl. I want to dock this peptide in a binding site with FlexPepDock. During the prepacking step, the bond between the Lys_NZ and the C atom that make the cyclization is lost and a carboxyl is restituted in the C-terminal.
What patch or similar can I use to preserve the cyclization during the prepacking for docking purposes?
I checked in database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation and there are some params files (e.g LYX.param) that seems to be useful for this.