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?
There isn’t an off-the shelf method. You could potentially put something together using the core::scoring::rms_at_corresponding_atoms_no_super() function, but that’d be a little involved. You could also attempt to do something like create a params file for just the core atoms, and then have Rosetta use that instead of the normal ligand params file. Rosetta would discard the extra atoms and if you did your rmsd comparision would only be over the atoms in your reduced params file. This is a little kludgy, though.
It would probably be easier to use pymol to do it. Pymol is scriptable, so even if you have a large number of structures it shouldn’t be too painful.