I know that AutoDock needs hydrogen atoms on the macromolecule and the ligand, but should I use polar hydrogens?

Yes, for both the macromolecule and the ligand, if you want to use the AutoDock 4 force field properly, you should always add all hydrogens, compute Gasteiger charges and then merge the non-polar hydrogens. This is because AutoDock 4 uses the united atom model to represent molecules, and the AD4 scoring function was calibrated using Gasteiger partial charges on both the ligand and the macromolecule. Polar hydrogens are hydrogen atoms that are bonded to electronegative atoms like oxygen and nitrogen.

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