Running AUTODOCK 4.0 (blind docking): Protocol Ligand and protein file is needed in .pdb or .mol2 or .

dbq or in pdbqt format A. Preparing Ligand: 1.Open Autodock tools click ligand click input choose open browse the ligand

2. Detecing root: Click ligand click torsion tree select detect root Save it in .pdbqt format

B. Preparing macromolecule(protein) Click grid choose macromolecule Click open load the macromolecule(Protein) Save it in .pdbqt format

C.Preparing GPF file for Autogrid :

click grid select set Map types choose open ligand load saved ligand in .pdbqt format

click grid

select grid box

click center select center on macromolecule choose your paramter

Click grid select output choose save GPF save the file

Click Docking choose macromolecule Click Set Rigid Filename load the macromolecule(Protein) saved in .pdbqt format

Click Docking choose Ligand Click open load the ligand saved in .pdbqt format

Click search parameters Click Genetic Algorithm

Click Docking choose Output Click lamarckian GA

Running Autogrid

Click Run choose Autogrid

Browse autogrid.exe C:\cygwin\usr\local\bin\ autogrid.exe Browse locate your gpf file location Click launch Running Autodock:

Click Run choose Autodock

Browse autodock.exe C:\cygwin\usr\local\bin\ autodock.exe Browse locate your dpf file location Click launch