Tehreem Tahir, I would like to compare the results of docking in Vina and AutoDock 4.2.6 and in some another free software. The problem is Vina gives negative binding energy as I expect while AutoDock gives positive binding energy for the same ligands. I can't understand what goes wrong with AutoDock.
I understand, as I have also used autodock once but every time I repeat the experiment, it gives far different values. So, I used free trial of schrodinger for reliable results