I am working on Rosetta Enzyme Design Application trying to design a protein with a particular ligand in desired geometry. I wanted to define a bridged hydrogen bond interaction between the carboxylate group on the ligand and the arginine residue in protein via water molecule.
I thought of adding two separate constraint blocks in the constraint file: one representing interaction of ligand with water and the other representing interaction of water with arginine. I am using two ligands in my design (ligand and water). I tried to do something similar to the way metal ion interactions are defined but I cannot find the residue name or code or abbreviation to use in the constraint block ATOM_MAP row. (TEMPLATE:: ATOM_MAP: 2 residue1: ??????? )
Also, if there is another way to approach the problem, any suggestions would be appreciated.
Thank you in advance !