As far as I have learned, after the necessary pre-processing, I prepare my protein and ligand for molecular docking with AutoDockTools with the following workflow.

For protein preparation, respectively: Edit→Misc→Check for Missing Atoms→Select All Residues→Dismiss; Edit→Misc→Repair Missing Atoms→Save as 2 sets→Dismiss; Edit→Hydrogens→Add→Polar Only; Edit→Charges→Add Kollman charges; Edit→Charges→Check totals on residues→Spread charge deficit over all atoms in residue.

For ligand preparation, respectively: Ligand→Torsion tree→Choose root; Ligand→Torsion tree→Choose Torsions.

However, I usually get an error after the "Spread charge deficit over all atoms in residue" command when applying these steps to the A chain of the protein with PDB ID: 4m0e. On the other hand, after giving the Dismiss command and adding Kollman charges again, all charges are distributed without errors with the Spread charge deficit over all atoms in residue command.

Are all these steps I applied correct? If they are incorrect, what is the correct workflow?

Also, after the Dock Prep process with chimeraX, will our protein be ready for docking or do we have to do other processes?