I tried to dock protein and ligand in discovery studio after applying Charmm force field and minimization for both ligand and protein. defined binding sites from receptor cavities (here my ligand is not is not getting fit in the cavity instead it gets fits some part of protein or even outside/away from protein)
how to correct it?
Used CDOCKER for docking. but got failed results " failed ligands" stating "No refined poses found for ligand deoxy".
How to sort out the errors in both the above mentioned cases?