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

AUTODOCK MANUAL FOR WINDOWS

                                           (autodock –1.4 v, MGL Tool)

Protein: (Remove all hydrogen atoms manually before running)

File----- Read molecule----open “Protein.pdb”

Edit-----Hydrogen---Add---Polar only

Charges---add Kollman charges (e.g. -8.574)

File----save---write “protein.PDBQ”—click o.k

Ligand

Input----open “ligand.pdb”

Torsion tree---detect root

Output----save it a “ligand.PDBQT”

Grid

Macromolecule (protein)----Choose protein ---o.k---save it as “protein.PDBQT”

Set Map------directly---Accept

Grid box-----give X, Y, Z co-ordinates value (of active site from q-site finder server or from literature)

Grid Box

File----close saving current

Grid----output----save “protein.GPF”

Docking

Macromolecule----set rigid File name----open “protein.PDBQT”

Ligand------Choose----select a ligand----Accept

Docking-----search parameters----Genetic algorithm(GA)—Accept

Docking----other options---- choose AUTODOCK 4  parameter- Accept

Docking-----output(o/p)-----Lamarkian GA---save as protein.DPF

Run

Go to Run option

Run autogrid and then autodock (here change autogrid3 as autogrid4 and autodock3 as audodock4 while running autogrid and autodock.)
autogrid4 -p protein.gpf -l protein.glg
autodock4 -p protein.dpf -l protein.dlg

If you have problem during autogrid (Eg. Error such as “Cl.map file missing, then go to Grid option->edit GPF->rename C.map as Cl.map-Write it-Save and again run Autogrid.

Finally open DLG file through conformation option.

ANALYZING AUTODOCK RESULTS

STEP1. Load the docking solutions. Analyze --->Docking Logs --->Read Docking Log. (See page 27 of tutorial). 

STEP 2. View the individual docking solutions. Analyze-->Conformations-->Show Conformations. You'll get a window, you can slide the slider through the 10 different solutions. You'll see each docking site separately. (see page 29 of tutorial). 

STEP 3. View all the docked ligands at once to see how clustered the solutions are on the surface of the macromolecule. Analyze-->Molecules-->Visualize Dockings as Spheres. (see page 36 of tutorial). 

STEP 4. To get the coordinates of docked ligand in PDB format, type get-docked macro_ligand.dlg. You'll get a pdb file with 10 docked ligands. You'll have to split the file into individual molecules yourself, if you want.