Small-molecule (ligand) conformer generation is usually performed prior to protein-ligand docking.
RDKit uses the ETKDG method to generate a collection of diverse low-energy conformers.
Generation may take a while depending on how many conformers are being generated. Specifically intended for small-molecules, not proteins (look into molecular dynamics).
Note: Avoid ambiguities in PDB files. Caution is warranted when providing ligands in PDB format, as conversion is prone to errors. It is advised to use SDF/Mol or preferably SMILES representation for larger molecules.
Reference: https://pubs.acs.org/doi/10.1021/acs.jcim.5b00654