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Autodock Vina

1. Download autodock in Windows

Vina1.1.2
How to install vina on ubuntu
MGLtools1.5.6

AutoDockTools (ADT)
AutoDockTools AutoDockTools is graphical front-end for setting up and running AutoDock - an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

Python Molecular Viewer (PMV)
PMV PMV is a powerful molecular viewer that has a number of customizable features and comes with many pluggable commands ranging from displaying molecular surfaces to advanced volume rendering.

Vision
PMV Vision is a visual-programming environment in which a user can interactively build networks describing novel combinations of computational methods, and yielding new visualizations of their data without actually writing code.

2.Official tutorial

http://vina.scripps.edu/tutorial.html
This tutorial demonstrates molecular docking of imatinib using Vina with AutoDock Tools and PyMOL
Imatinib is in a class of medications called kinase inhibitors. It works by blocking the action of the abnormal protein that signals cancer cells to multiply. This helps stop the spread of cancer cells.

Steps:

 1. Open ADT-file- read protein.pdb
 2. Add polar-only hydrogens
 3. Grid-macromolecule-choose-protein
 4. Save protein.pdbqt
 5. Gridbox
 6. Ligand choose ligand.pdb
 7. Ligan Torsion tree-choose torsion
 8. Ligand-output ligand.pdbqt
 9. exit ADT
 10.Go to Command Prompt
 C:\>"\Program Files (x86)\The Scripps Research Institute\Vina\vina.exe" --help

        Input:
              --receptor arg        rigid part of the receptor (PDBQT)
              --flex arg            flexible side chains, if any (PDBQT)
              --ligand arg          ligand (PDBQT)

            Search space (required):
              --center_x arg        X coordinate of the center
              --center_y arg        Y coordinate of the center
              --center_z arg        Z coordinate of the center
              --size_x arg          size in the X dimension (Angstroms)
              --size_y arg          size in the Y dimension (Angstroms)
              --size_z arg          size in the Z dimension (Angstroms)

            Output (optional):
              --out arg             output models (PDBQT), the default is chosen based on
                                    the ligand file name
              --log arg             optionally, write log file

            Misc (optional):
              --cpu arg                 the number of CPUs to use (the default is to try to
                                        detect the number of CPUs or, failing that, use 1)
              --seed arg                explicit random seed
              --exhaustiveness arg (=8) exhaustiveness of the global search (roughly
                                        proportional to time): 1+
              --num_modes arg (=9)      maximum number of binding modes to generate
              --energy_range arg (=3)   maximum energy difference between the best binding
                                        mode and the worst one displayed (kcal/mol)

            Configuration file (optional):
              --config arg          the above options can be put here

            Information (optional):
              --help                display usage summary
              --help_advanced       display usage summary with advanced options
              --version             display program version
  11. Create a conf.txt include options:
      receptor = protein.pdbqt
      ligand = ligand.pdbqt

      out = out.pdbqt
      center_x =11
      center_y = 90.5
      center_z = 57.5

      size_x =22
      size_y=24
      size_z=28

      exhaustiveness = 8
        D:\Docking-Practice\vina_tutorial>"C:\Program Files (x86)\The Scripps Research Institute\Vina\vina.exe" --config conf.txt  --log log.txt