You can allow certain defined residues in the receptor to be flexible during docking. To do this:

• Setup the ligand and receptor.
• Select the residues you wish to be flexible using the residue selection button.
• Select Advanced/Defined Flexible Receptor Groups
• Choose full side-chains or hydroxy and water.
• The side chains you have selected will then be displayed in thicker stick and will be flexible when you dock or edit a ligand.