for linking seeds into ligands is the 'Top Percent' parameter which is crucial to selecting the number of seeds used to generate potential conformations via the maximum clique algorithm. If this number is too small, then there will not be enough potential conformations generated to sample the conformational space of the ligand properly. In fact, there is a possibility that no conformations are generated during the linking step, causing CANDOCK to fail to produce any conformations. If the 'Top Percent' is too large, then the conformational search space is too large, and CANDOCK will become computationally inefficient (especially in the case of fully-flexible protein docking).