Same protein and ligand but different active residues

HADDOCK
1

Hello

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?

Thanks!

2

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).