To calculate the RMS difference between two geometries, use the GEO_REF keyword and 0SCF. This calculation is very fast, it typically only takes a few seconds of CPU time. For this type of calculation, a convenient option is to also use GEO_DAT, so the data-set could be as short as one line(although three lines would allow the job to have a title and comment).
Caveats:
Both systems must have the same number of atoms and the same empirical formula.
If PDB information is present, this will be used, in which case every atom must have a unique PDB label. Atom numbers in labels do not count in determining the PDB label.
If the RMS can be reduced by swapping pairs of atoms, this will be done. To prevent swapping, add NOSWAP.