Yes, you can use the script, rmsd.py, which is available in your software installation. This script computes the RMSD after automatically renumbering the atoms. It is a command-line script, which you can run as follows:

$SCHRODINGER/run rmsd.py file1file2

where file1 and file2 are the Maestro files that contain the co-crystallized ligand and the pose file. If you have generated ionization or tautomeric states of your ligand, you should use the -use_neutral_scaffold option to ensure that the multiple bonds patterns and ionization states are ignored when calculating the RMSD.