AutoDock Vina protocol: For Molecular Docking

There are many softwares available for carrying out molecular docking calculations. Many of these softwares are paid, while some of them are free. AutoDock is one such freely available software. Earlier, there was AutoDock 4.0 version available. One of the problem with the software was the space it would occupy, if you attempt to do multi docking.
Recently, there is another algorithm made available under autodock. It is called AutoDock Vina.
This is more efficient, robust and fast algorithm.
There are many tutorials available to learn AutoDock Vina including:
http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf

and also a video tutorial
http://vina.scripps.edu/tutorial.html 

 But for some reason, few changes or explanation in little detail is always required to make it understandable for a beginner to follow. 
Here is a protocol designed in our group, which our Master's student follow to get acquainted to Molecular Docking studies.
This protocol can be pretty much followed for any molecular docking study:
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*You need to download files for ligand and target form the link as suggested in the tutorial

Or else you may directly attempt to work with your set of ligands and targets. 

Step I: Preparation of Ligand PDBQT files:

1)       Open AutoDockTools.

2)      On the Menu bar Click on File --- Read Molecule --- Desktop---Docking_Files---ind.pdb.

3)      Press Open

Below Menu bar you will find an option named Ligand.

4)      Click on Ligand --- Input --- Choose --- ind

5)      Press  Select Molecule for AutoDock 4.

A widget appears on the screen describing the chemical nature of the Drug Molecule. Press OK

6)      Click on Ligand --- Output --- Save as PDBQT.

7)      Save the PDBQT file on Desktop in Docking_Files folder.

In the Dashboard Click on the red circle (fig.1) beside the name of the drug molecule ind.

Drug molecule will disappear from the screen.

 

Step II: Preparation of  Protein PDBQT files.

1)      On the Menu bar Click on File --- Read Molecule --- Desktop---Docking_Files---1hsg.pdb.

2)      Press Open

3)      On the Menu Bar, click on Select --- Select From String.

     A Dialogue Box appears on the screen  with the name Select From String

4)      Type HOH* within the Residue Box.

5)      Type * within the Atom Box (fig.2).

1)       Click Add and then Press Dismiss.

2)       On the Menu Bar click on Edit --- Delete Water

This step deletes all water molecules from the PDB files.

Below the Menu bar you will find an Option named Grid.

3)      Click on Grid --- Macromolecule --- Choose ---- hsg1.

4)       Press Select Molecule.

A WARNING widget appears on the screen.

5)       Click on OK.

6)      A Dialogue Box appears on screen for saving the PDBQT.

7)      Save this file within the folder named Docking_File on Desktop as hsg1.pdbqt.

8)      Click on Grid --- Grid Box

Change the X,Y and Z dimension to 26.

Enter the values 3.18, -0.294 and -3.784 in x, y and z center respectively.

9)      Increase Spacing from 0.375 to 1 (fig.3).

Before Closing this widget, open notepad and enter the following.

receptor = hsg1.pdbqt

ligand = ind.pdbqt

center_x = 3.18

center_y = -0.294

center_z = -3.784

size_x = 26

size_y = 26

size_z = 26

1)      Save this file as conf.txt (fig.4).

 

1)       In Grid Option widget, Click on File--- Close Saving Current

Close AutodockTools.

Before starting with Docking check whether  hsg1.pdbqt, ind.pdbqt and conf.txt files are all saved in the Docking_Files folder.

Step III: Running Autodock Vina.

1)      Press start button and click on Command Prompt

2)      In the command prompt type cd, press space and drag the folder Docking_Files over the command prompt, Press enter .

3)      Open Docking_Files folder drag the file named Vina over the command prompt, press space and type --config, again press space then drag the conf.txt file over the command prompt.

4)      Press Space and type --log log.txt. Press enter.

Command Prompt should be similar to fig.5

 

Wait for the Docking Process to complete. A file with the name ind_out.pdbqt will be generated in the folder Docking_Files folder

Step IV: Analysing Vina Result.

1)      Open AutodockTools.

2)      Click on Analyze --- Docking --- Open AutodockVina Result --- Desktop --- Docking_Files --- ind_out.pdbqt.

Click on the option Single molecule with muliple conformations and press OK.

3)      Click on Analyze --- Macromolecule --- Open --- Desktop --- Docking_Files --- hsg1.pdbqt.

4)      Click in Analyze --- Docking --- Show Interaction.

Study the interactions between the protein and ligand. Check for hydrogen bond interactions in different ligand conformers. Use left and right arrow keys on the Keyboard to change conformations.

Close AutodockTools.

5)      Open DiscoveryStudio from Desktop Icon.

6)       Drag hsg1.pdbqt , then drag ind_out.pdbqt.

7)      Click on Scripts --- Ligand Interactions --- Show ligand binding site atoms.

8)      Below the Menu Bar Click on Receptor-Ligand Interactions.

9)      In the Tools explorer widget click on Hydrophobic.

10)  Right click on Black window Labels--- Object --- from the Drop Down Menu select Amino Acids and press OK.

Repeat the Steps I, III and IV for other ligand file. Remember to  change the ligand name in the conf file accordingly.