AUTODOCK TOOLS:

1. File-> read molecule-> select ur protein in pdb format

2. Edit-> hydrogen-> add (polar only):OK
3. Edit-> charges-> add kollman charges
4. Edit-> atoms -> assign AD4 type
5. File-> save-> write PDBQT->(a box will open) browse-> go to the same folder from which
protein.pdb is taken nd save this file as protein.pdbqt ->> ATOM to END-> add -> check SORT
NODES AND SAVE TRANSFORMED-> then click OK
6. Ligand-> input->open->ligand.pdb
7. Ligand->torsion tree->choose root torsion tree(again)->detect root
8. Ligand->output->save as .pdbqt
9. Grid->macromolecule->choose-> select protein warning vl come…..click OK
Save protein.pdbqt again-> replace existing
10. Grid-> set map types-> choose ligand-> select ligand.pdb
11. Main menu-> select from string (active site residue number) in input-> add
12. Grid->grid box-> grid options-> center-> pik an atom( click on any + sign)->no. of points in X,Y
and Z= 60,60,60-> file->close saving current
13. Grid-> output->save gpf-> protein.gpf( save in the same folder
14. Docking ->macromolecule->set rigid filename->goto your folder->select protein.pdbqt
15. Docking-> ligand ->choose-> select ligand……….default parameter-r window opens…..accept it
16. Docking -> search parameter-> genetic algorithm-> default para-> accept
17. Docking-> output-> Lamarckian GA-> got our folder……….protein.dpf saved

After .gpf and .dpf files are made I used two commands in cygwin and there were .exe files in my folder
that were autodock4.exe and autogrid4.exe……………

Commands in cygwin :-

./autogrid4.exe –p protein.gpf –l protein.glg &

./autodock4.exe –p protein.dpf –l protein.dlg &

Now .dlg files will be prepared.