Protein and Ligand docking with AutoDock4.2

·         Ligand & receptor both should be in Pdb format

·         Inside a folder keep the receptor & ligand

Prepare the RECEPTOR

1.       Read MOLECULE >> receptor.pdb

2.       Edit >>Hydrogen >> add-all hydrogens

3.       Edit >> Charge >> Compute Gasteiger – ok

4.       Edit >> Atoms >> assign AD4 type

5.       Edit >> Bond

6.       Save >> write PDBQT >> click on short notes- ok

7.       Edit >> Delete >> Delete all molecule

 Prepare the LIGAND

1.       Ligand >> input >> open ligand.pdb file

2.       Ligand >> Torsion tree >>. Choose root

3.       Ligand >> Torsion tree >>. Detect root

4.       Ligand >> Choose torsion >> Done

5.       Ligand >> Output >> Save as PDBQT

6.       Edit >> Delete >> Delete all molecule

RIGID DOCKING

Grid >> Macromolecule >> Open >> receptor.pdbqt >>  preserve good change >> No >> Ok >> Ok

SETTING GRID

1.       Grid >> Set map types >> Open ligand

*If you know about the active site residues then go to select option and then select the residues one-by-one and if don’t have any information about the active site residues, then directly create the box covering the whole or particular active site of the protein.

Select >> Select from string >> residue >> put active site residue one by one >> add

2.       Grid >> Grid box >> X- Dimension = XX

                                    Y- Dimension = XX

                                    Z- Dimension = XX

          Grid Center* >> X center = XX

                                     Y center = XX

                                        Z center = XX

3.       Grid >> Center >> Go to center >> pick an atom

Click one atom of the all residues; after setting the proper grid save the grid file

4.       Grid box >> file >> Close saving file

AUTOGRID RUN

1.       Grid >> Output >> Save gpf >> give one file name

2.       Run >> Run autogrid >> Launch

After autogrid run delete macromolecule along with ligand

DOCKING

1.       Docking >> Macromolecule >> Set rigid filename >> receptor.pdbqt

2.       Docking >> ligand >> open >> ligand.pdbqt >> Accept

3.       Docking >> Search parameter >> GA ( set the parameter ) >> accept

4.       Docking >> Docking parameter >> Set docking run option >> accept

5.       Docking >> Output >> Lamarckian GA

6.       Run >> Run Autodock >> Launch

.dlg file will be generated automatically

ANALYSE

1.       Analyse >> docking >> open.dlg file

2.       Analyse >> macromolecule >> open >> receptor.pdb

3.       Analyse >> Confirmation >> Play 

4. Can write out the conformations from the Analyse Window