My problem is with LigandFit docking. I am using this module for docking of multiple ligands into target protein. I have a .SDF file containing 17932 ligands. When I tried to dock these ligands then it shows 0 poses. So I concluded that none of the ligands can be docked into the protein. But this is not the case. Because when I am using another .SDF file containing 17933 ligands (previous 17932 ligands + another ligand which can be docked into the target protein if used separately) it also shows 0 poses, though it definitely contain one known ligand which can be docked into the protein. It shows no error. So I am totally clueless in this matter. PLease help me.