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Autodock Tutorial

The document discusses the process of preparing files for autodock molecular docking simulations. It requires 4 input files - a PDBQT file for the ligand with a torsion tree, a PDBQT file for the receptor, a grid parameter file (GPF) for autogrid calculations, and a docking parameter file (DPF) for autodock calculations. It describes how to prepare these files, including editing PDB files to PDBQT format, adding charges and torsions to the ligand file, setting up the grid box and map types in the GPF, and configuring docking parameters like flexible residues and search algorithms in the DPF. It also provides commands to run autogrid and autodock simulations.

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799 views

Autodock Tutorial

The document discusses the process of preparing files for autodock molecular docking simulations. It requires 4 input files - a PDBQT file for the ligand with a torsion tree, a PDBQT file for the receptor, a grid parameter file (GPF) for autogrid calculations, and a docking parameter file (DPF) for autodock calculations. It describes how to prepare these files, including editing PDB files to PDBQT format, adding charges and torsions to the ligand file, setting up the grid box and map types in the GPF, and configuring docking parameters like flexible residues and search algorithms in the DPF. It also provides commands to run autogrid and autodock simulations.

Uploaded by

selnikraj
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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com

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 &)

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