Same protein and ligand but different active residues


Im performing a docking analysis with a protein and a small ligand and doing two different runnings with the same files and parameters, but Im selecting differents active residues.

Can I compare these two results? Is it correct to assume if the smallest score may indicate the better binding site for the ligand?


Best would be to compare the score of the two runs after removing the restraint energy from the score (subtract 10% of the restraint energy from the HADDOCK score).