Hi Rosetta team,
I am trying to learn ligand docking using Rosetta. In my ligand docking trials, I have docked a different ligand in to a protein in which the original ligand was replaced. In this case both (original and new) ligands have similar core structure but they are different in substitution groups. Since core atoms and core structure of both ligands are similar, is there a way to calculate RMSD for ligand core atoms?
Thanks in advance.