Personal tools
You are here: Home FAQs & Help How-tos
Document Actions

How-tos

Audiences
User
Developer
This section provides step-by-step instructions for how to accomplish common tasks with AutoDock. There are two intended audiences, named "User" and "Developer", each with their own sections of How-tos. Let us know your suggestions for new How-tos.

User

General

How to use this resource
A brief description of how you use and contribute to the Help Center.
Positioning ligands with ADT
This explains how to move a ligand independently of the macromolecule using our GUI.
Setting up AutoDockTools utility scripts
Describes how to configure Python interpreter so that it can find packages from MGLTools. This How-to is intended for users who use pre-compiled Python interpreter that comes with MGLTools.
Fixing "All energies are equal in population; re-initializing" Message
The dlg file continues to fill with this line.
Force a non-rotatable bond to be considered rotatable in ADT
ADT discriminates between rotatable bonds and non-rotatable bonds during ligand preparation. If bonds are classified as rotatable when they should be non-rotatable, they can be made non-rotatable using the GUI. However, if a bond is classified as non-rotatable when it should be rotatable, making the change is more complicated. This how-to explains the necessary steps to be taken in ADT.
How to compile autodock as native 64 bit windows application
This Guide explains the compilation of the autodock software, resulting in the executable that will be executed faster than the standard 32 bit application. To use the resulting faster application you will need 64 bit Windows installed such as Windows 7 X64, Windows Vista X64, Windows XP X64 or Windows Server X64.

How To Get Help

How to Subscribe to ADL
How to Subscribe to ADL, the AutoDock Mailing List.
How to Unsubscribe from ADL
How to Unsubscribe from ADL, the AutoDock Mailing List

How To Get Started

How to prepare a ligand file for AutoDock 4
This How-to explains how to use the Python script 'prepare_ligand4.py' to format a ligand file for AutoDock 4. Input files for this script can be in PDB, PDBQ, PDBQT, SYBYL mol2 or PQR format. Output files from the script are in PDBQT format and include special keywords establishing the torsional flexibility. Optional arguments invoke adding hydrogens, preserving input charges, merging non-polar hydrogens, etc. (NOTE: You must have installed MGLTools).
How to prepare a receptor file for AutoDock4
This How-to addresses using the python script 'prepare_receptor4.py' to format a receptor file for AutoDock4. Input files for this script can be in pdb, pdbq, pdbqt, mol2 or pqr format. Output files from the script are in pdbqt format. Optional arguments invoke adding hydrogens, preserving input charges, merging non-polar hydrogens et al. (NOTE: You must have installed MGLTools).
How to prepare a grid parameter file for AutoGrid 4
This How-to addresses using the python script 'prepare_gpf4.py' to create a grid parameter file for AutoGrid4. This grid parameter file specifies the 3D search space by setting the number of points in each dimension, the center of the grids and the spacing between points. It also specifies the types of probe atoms to use, the filename of the receptor and the names of each the output gridmaps. (NOTE: You must have installed MGLTools).
How to prepare a docking parameter file for AutoDock4
This How-to addresses using the python script 'prepare_dpf4.py' to create a docking parameter file for AutoDock4. This docking parameter file specifies the ligand to move during the search, the gridmap files to use for the energy evaluations, which search algorithm to use and parameters for it as well as how many separate docking runs to perform and how many energy evaluations to use in each run. (NOTE: You must have installed MGLTools).
How to prepare a flexible residue file for AutoDock4
This How-to explains how to use the python script "prepare_flexreceptor4.py" to create two input receptor files for AutoDock4, one containing the rigid residues and one containing flexible residues. The input file for this script should be in PDBQT format. Output files from the script are in PDBQT format. The flexible file includes special keywords establishing the torsional flexibility. Optional arguments can be used to disallow rotation around specified types of bonds or between specified atoms. (NOTE: You must have installed MGLTools).

How To Run AutoDock

How do I run AutoDock at Scripps?
instructions to run AutoDock at The Scripps Research Institute.
How to Launch AutoDock Using AutoDockTools
A troubleshooting guide on how to launch AutoGrid/AutoDock using AutoDockTools' GUI.

How To Analyse AutoDock Results

How to prepare a text summary of a directory of AutoDock4 docking results
This How-to explains how to use the python script "summarize_results4.py" to create a text file which summarizes the results of all the AutoDock4 log files in a single directory. The output from this script is in CSV (comma separated value) format. Optional arguments can be used to set the rmsd tolerance used for clustering and to specify which results to report. The clustering is based on the input ligand coordinates unless a reference file is specified. (NOTE: You must have installed MGLTools).

Developer

General

How to compile autodock as native 64 bit windows application
This Guide explains the compilation of the autodock software, resulting in the executable that will be executed faster than the standard 32 bit application. To use the resulting faster application you will need 64 bit Windows installed such as Windows 7 X64, Windows Vista X64, Windows XP X64 or Windows Server X64.

Powered by Plone CMS, the Open Source Content Management System

This site conforms to the following standards: