AUTODOCK VINA TUTORIAL

SOFTWARES REQUIRED:
1. Autodock Tools
Link: http://mgltools.scripps.edu/downloads

2. Autodock Vina
Link: http://vina.scripps.edu/

PREPARING PROTEIN PDBQT FILE:

1. Download/obtain 3D protein structure / the pdb file from online data bank such as
http://www.rcsb.org/pdb/home/home.do .

2. In Autodock Tools, click on File Read Molecule Select .pdb file of protein.

3. Next, we remove the waters. On the main menu bar, choose Select, Select from String. In the
Residue entry box, type HOH*. The asterisk is a “wild card”, used in case the waters are
numbered. It means accept any character at all following the H. Then type * in the Atom entry
box; again the * is a wild card, this time meaning “any atom”. Click add and then ok. On the main
menu bar, choose Edit Delete Delete Selected Atoms. Click Continue. (The waters are
already removed in the PDB file we are going to use)

4. Now, we need to add hydrogen because X-ray crystallography usually does not locate
hydrogens; hence most PDB files do not include them. Choose Edit Hydrogens Add.
Usually, you will choose Polar Only in the widget that pops up, using Method noBondOrder, and
renumbering OK.

5. Adding Charges: We need to add charges to the charged residues

Edit-> Charges-> Add Kollman Charges

6. To add an autodock_element, which is the autodock4 atom type, to

each atom, you can use
Edit-> Atoms-> Assign AD4 type

7. For generating .pdbqt file of protein, click on Grid Macromolecule Choose Select
Protein Click on “Select Molecule” Save with .pdbqt extension. (make sure you write the
name: filename.pdbqt)

SETTING SEARCH BOX:

8. Open the Grid Options widget: Grid Grid Box Adjust the box and record the
coordinates to somewhere else in a file.

PREPARING LIGAND PDBQT FILE:

1. Download/obtain 3D ligand structure / the pdb file from online data bank such as
http://www.rcsb.org/pdb/home/home.do .
2. In Autodock Tools, click on Ligand Input Open Select .pdb file of ligand.

3. Now go to Ligand Torsion Tree Choose Torsions. Using this option, you can make
some bond rotatable or non-rotatable.

4. Choose Ligand Output Save as .pdbqt

GENERATING CONFIGURATION FILE:

11. An example configuration file is given below.

receptor = renin1.pdbqt
ligand = inhibitor1.pdbqt

center_x = 172.963
center_y = 202.419
center_z = 103.192

size_x = 34
size_y = 30
size_z = 36

Make a file named “conf.txt” and save it in same where .pdb and .pdbqt files of protein and ligand
are present. Copy above code in conf.txt file and replace center and size values with the one you
chose while setting Grid Box. Here out.pdbqt file is the output file which Vina will generate.

RUN VINA:
VINA can be run in command prompt.

1. Run cmd on windows. Check if Vina has been successfully installed by writing the command
given below:

“C:\Program Files (x86)\The Scripps Research Institute\Vina\vina.exe” --help

The path given in above command can change slightly in your computer. The output on
successful installation of vina is the list of arguments.

2. Now, using “cd” command go to the folder where pdb, pdbqt and configuration files are
located. Now run the command given below:

“C:\Program Files (x86)\The Scripps Research Institute\Vina\vina.exe” --config conf.txt

--log log.txt

Here, log.txt is another output file which will consist of all the text printed on cmd by Vina.

ANALYZING & VISUALIZATION OF RESULTS:

1. Delete both protein and ligand molecule in Autodock Tools.
2. Go to File Read Molecule Select protein.pdbqt
3. Select Analyze Docking Open Autodock Vina Results Select output.pdbqt
4. Go to Analyze Macromolecule Choose
5. Now, again go to Analyze Docking Show interactions