AUTODOCK -protein ligand docking (Easy Steps) Running in WINDOWS

AUTODOCK MANUAL FOR WINDOWS

(Autodock version -1.4 v, using MGL Tool)

Preparing Protein File

Go to File -> Read molecule -> open pdb file

Go to Edit -> Hydrogen -> Add -> choose polar only

Edit -> Charges -> Add -> Kollman Charges (Eg.-8.91)

Go to File -> Save -> Save as protein.pdbq

Preparing Ligand File

Go to ligand -> Input -> open ligand or drug file in pdb format (do not open mol file or any other format - For molecular file conversion use DUNDEE PRODRG Server)

Go to ligand -> Torsion Tree -> Detect Root

Go to ligand -> Output -> Save as ligand.pdbqt

Preparing Grid Parameter File

Go to Grid -> Macromolecule -> select molecule -> choose protein file -> click O.K-> save as protein.pdbqt

Go to Grid -> Set Map type -> Click Directly - Click Accept

Go to Grid -> Grid Box -> Enter X,Z,Y value of your preferred active sites (For predicting active sites, use Q-Site Finder server and submit your protein, there choose minimum x,z,y coordinate values of active sites as a Grid Box value)

Go to File -> Click Saving Current

Go to Grid -> output -> save as protein.gpf

Preparing Docking Parameter Files

Go to Docking -> Macromolecule -> Set Rigid File Name -> open protein.pdbqt

Go to Docking -> Ligand -> Choose -> select a ligand file -> Accept

Go to Docking -> Search Parameters -> Genetic Algorithm (GA)--> Accept

Go to Docking -> other options -> choose -> Autodock4 parameters

Go to Docking -> output -> Lamarkian GA -> save as protein.dpf

Running AutoGrid

Click - Run Autogrid

Change autogrid3 to autogrid4

Running AutoDock

Click - Run Autodock

Change autodock3 to autodock4

ANALYZING AUTODOCK RESULTS

Open dlg file in notepad and check the rank (Control+F three times), and find the RUN of rank 1. choose the pdb coordinates of rank 1. copy and paste the coordinates and paste it in protein pdb file. Open the saved pdb file in Pymol or any visualization software.