You can use either substructure or Atomic Property Field Templates for docking.

• Setup the ligand and receptor.
• File/Open a 3D template structure and place in the pocket.
• Click on the Edit Tools panel button.
• Click on the Impose Template Restraint button.
• Select the template object from the drop down menu and choose whether you wish to impose substructure or 3D pharmacophore APF template.
• A table will be displayed called DOCK_RESTRAINTS where you can turn the template on or off.