Currently I am using ligandfit to dock multiple number of ligands into a particular cavity of a protein. I have several number of .SDF file containing round about 25000 ligand each of them. whenever I am docking the file into the protein, it is always giving 178 poses docked for each file regardless whichever file I am using. Is it due to any limitation. In fail ligand list, it is written filtered for which it is not docked, but why is it being filterd when I dont choose anything to be filtered. Please help me, I am clueless. Thanks in advance.