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Each docking requires at least four input files.

PDBQT file for the ligand that encodes a torsion tree.
PDBQT file for the receptor;
grid parameter file (GPF) for the AutoGrid calculation, and
docking parameter file (DPF) for the AutoDock calculation.
Editing PDB files to Autodock input files(PDBQT)
File ➞ Open ➞ Macromolecule.
Edit ➞ Hydrogens ➞ Add.
File ➞ Save ➞ Write PDB.

Preparing ligand for autodock

Ligand ➞ Input ➞ Open

(ADT detects whether the ligand already has charges or not.If not, ADT computes Gasteiger charges; remember that for the Gasteiger
calculation to work correctly, the ligand must have all hydrogen atoms added, including both polar and non-polar ones. If the charges are all

zero, ADT will try to add charges. It checks whether the total charge per residue is an integer)

Ligand ➞ Torsion Tree ➞ Detect Root

Ligand ➞ Torsion Tree ➞ Choose Torsions

Ligand ➞ Tor sion Tree ➞ Set Number of Tor sions

Ligand ➞ Output ➞ Save as PDBQT

Preparing a macromolecule file

Grid ➞ Macromolecule ➞ Open

Output ➞ save as pebqt file.

Preparing the grid parameter file

Grid ➞ Set Map Types

Grid ➞ Set Map Types ➞ Open Ligand

Close this widget with the Accept button

Grid ➞ Grid Box

File ➞ Close saving current

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Grid ➞ Output ➞ Save GPF

Grid ➞ Edit GPF

Starting Autogrid
Run ➞ Run AutoGrid

(autogrid4 –p protein.gpf –l protein.glg &)

Preparing the docking parameter file
Docking ➞ Macromolecule ➞ Set Rigid Filename…

Docking ➞ Ligand ➞ Choose

Docking ➞ Macromolecule ➞ Set Flexible Residues

Docking ➞ Search Parameters… ➞ Genetic Algorithm

Docking ➞ Docking Parameters

6. Docking ➞ Output ➞ Lamarckian GA…

Starting autodock
AutoDock 4 must be run in the directory where the macromolecule, ligand, GPF and DPF
files are to be found.
(% autodock4 –p ligand.dpf –l ligand.dlg &)