Using AutoDockTools to run Autodock
You can download the files for this tutorial here
1. Create PDBQ for the ligand
File -> Read Molecule -> ap.pdb
Ligand -> Input Molecule -> Choose Moleclue -> ap
Ligand -> Define Rigid Root -> Automatically
Ligand -> Rotatable Bonds -> Define Rotatable Bonds
Double-click 'Make all active bonds rotatable'
Ligand -> Write PDBQ ... -> ap.pdbq
2. Create PDBQS for the macromolecule
Often it is a good idea to use PDB2PQR to fix the surface side-chain rotamers
pdb2pqr.py --ff=amber acp.pdb acp.pqr
File -> Read Molecule -> acp.pqr
Edit -> Hydrogens -> Add -> Polar only -> OK
Grid -> Macromolecule -> Choose Macromolecule -> acp -> Select Molecule
Save the file as acp.pdbqs
3. Set up the GPF file for autogrid
Grid -> Set Map Types -> By Choosing Ligand -> ap
Grid -> Set Grid
This
will open up a menu-interface. You will need to set the center fo the
grid as well as the x,y,z dimensions of the grid. The grid box set the
boundary of the docking. If you do not know the active site of the
protein, and would like to search all available surfaces, the grid box
should cover the whole macromolecules:
- Set the number of points in x, y, z dimension to 80.
- Center -> Center on macromolecules
- View -> Show box as lines
- File -> Close saving current
Write GPF -> out.gpf
4. Set up the DPF file for autodock
Docking -> Set Macromolecule -> Choose Macromolecule -> acp
Docking -> Set Ligand Parameters -> Choose Ligand -> ap
Write DPF -> GALS.dpf -> out.dpf
5. Run autogrid and then autodock
autogrid3 -p out.gpf -l out.glg
autodock3 -p out.dpf -l out.dlg
6. Output docked conformations
To extract the PDB files for the docked conformations:
get-docked out.dlg
This will output the coordinates to the out.dlg.pdb
I have written a perl script to rank the energies of the docked conformation
rank_ene.pl out.dlg.pdb
7. Visualize the docked conformation using ADT
You can view the docked conformations by:
Analyze -> Conformations -> Show Conformations
You can use this command to select the cluster with the lowest docked energy.
Analyze -> Clusterings -> Show Clustering
Double-click the bar to select the cluster of docked conformations with the lowest docked energies