I try both vinblastin and taxol using 1z2b and 1jff without ab-initio. I am using all interacting residue (hydrogen bond and non-hydrogen bond stated in PDBsum) as active residue, passive resiude define automatically. However, both docked result seem close but not expectantly same with reference ligand crystal using ligplot. Some of the interaction is not the same with PDBSUM.
ligand taxol not bind into binding site
original taxol bind directly into binding site
Would appreciate if anyone can explain how to improve the docking ?