Peptide with a new crosslinker

[lelaihoangson]

I want to create a PDB structure of a peptide with a new crosslinker (the one in red) that does not have a params file in Rosetta. I used PyRosetta to create the structure of the peptide, and chemdraw to make the linker. Then I connected them in Avogadro. However, Rosetta could not read it, even when I generated the params file (mol_to_params). I want to know what protocol do we use to incorporate the new linker to a peptide structure so that Rosetta can understand. Also, for the linker, should I keep COOH group or just CO group and define the atom that forms the bond?

Thank you