Currently i am doing a fragment based drug design for an antibacterial drug target. I am totally new in this area and would like to ask for advice in using this software. I have prepared my protein and the only problem i experience now is that I don't know which protocol should i use to screen the library. What is the different between de novo fragment based drug design and pharmacophore drug design?  My tutor has prepared three different libraries for me and asking me to screen and link one of each from each libraries based on the distance of the fragments to become a lead. Is that possible if i screen three libraries at the same time so that i can visualize the binding mode for three  fragments in the same pocket?