I need to calculate the RMSD between a co-crystallized ligand and my ligands and a non-co-crystallized ligand with GLIDE but I don't know how. Could someone explain to me how to do it? Many thanks in advance.
The software GLIDE is not used for RMSD calculation. GLIDE is dedicated to do small ligand/protein docking (rigid/rigid and flexible/rigid).
You can calculate the RMSD by hand, using MAESTRO, CHIMERA and VMD interfaces (all free for academics) among many other software (also free).