The Prime MM-GBSA panel is bellow.
As you can see, the first section is about choosing the structures to calculate the MM-GBSA energy.
The marked option works only for pose viewer files. IFD don't create this kind of file. If you want to use it, you need to work with some scripts/export in order to convert a mae (or maegz) file into a .pv.mae (or .pv....
Based on what you have said, a phonon calculation is likely what you want. You should see imaginary frequencies in the output if you do infact have a transition state. You may need stricter convergence for the phonon calculation than the geometry relaxation.
From the MAESTRO help system we got that the calculation is run using the driver periodic_dft_driver.py:
usage: $SCHRODINGER/run periodic_dft_gui_dir/periodic_dft_driver.py
[-h] -cfg_file CFG_FILE [-TPP THREADS] [-nimage NIMAGE]
[-npools NPOOLS] [-ntg NTG | -nband NBAND] [-qargs QARGS]
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).