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Frequently Asked Questions (& Answers!)

General Questions

How can I learn more about how to use Cygwin/Linux/Mac OS X?

AutoDock and AutoGrid run on UNIX systems like Cygwin, Darwin, Linux, and Mac OS X. I'm unfamiliar with using the command line in these operating systems. How can I learn more?

All Platforms

Use the man command to look up commands in the manual. From a Terminal or shell, type:

      man man

Remember to press the < Enter > or < Return > key at the end of every command: otherwise the computer will not do anything. For example, the command ls is short for "list" and lists all the files and directories in the current directory, so typing:

      man ls

and pressing < Enter > or < Return > would give you the manual page for the list command, ls. The behaviour of commands can be changed by typing a so-called flag after the name of the command, for example to get a simple listing of files, you would type ls, but to get a long listing, use the -l flag like this:

      ls -l

If you don't know the name of the command, you can use the apropos command (or type man -k, where k is short for "keyword") to get a list of all the commands that match, e.g. apropos python would list all the commands that refer to the word "python".

Cygwin

Linux

  • There is a nice series of interactive tutorials on using Linux, called Linux Survival.

Mac OS X

  • A gentle introduction to Mac OS X is available from Learning Mac OS X but this does not cover using the Terminal.
  • O'Reilly is a very well-respected publisher of books about UNIX and open source technologies; their "MacDevCenter" has a great series of hands-on tutorials about Learning the Mac OS X Terminal

How do I join the ADL (AutoDock mailing list)?

I've heard there is a mailing list for AutoDock, called "ADL". How do I join?

You can subscribe to the ADL by going to the ADL Info Page; you will need to give a valid email address, create a password, and decide if you want your messages to be sent as a daily digest or not.

About the AutoDock mailing list

This list is intended for novice and expert users of the ligand-protein and protein-protein docking software AutoDock, AutoGrid and ADT (AutoDockTools). This list will provide a forum for users to share experience, to ask questions about things not covered in the documentation, and hopefully, to get answers to these questions. Questions may range from technical to scientific, but should be about docking molecules using AutoDock and its associated programs and utilities. Suggestions for new features are also welcome. Announcements of new software versions and functionalities will be made on this list. In general, bugs should not be reported here but entered into our Bugzilla database. Just go to http://mgldev.scripps.edu/bugs/ and click on the "Open a new Bugzilla account" link.

This FAQ applies to: AutoDock 3, AutoDock 4

How do I search the ADL (AutoDock mailing list) archives?

I want to search the ADL (AutoDock mailing list) archives. How do I do it?

Go to the AutoDock List archives, and type in your query. If your query has more than one word, choose either "Match ALL words" or "Match ANY word".


This FAQ applies to: AutoDock 3, AutoDock 4

How do I report a bug?

Something didn't work as I expected, when using AutoGrid, AutoDock or ADT. How should I report a bug?

The MGL (Molecular Graphics Laboratory) has a special database called "Bugzilla" that we use to collect and track bug reports.

  • Click "Search existing bug reports" to see if your bug has been reported by someone else. If it has, then you don't need to file a new bug report.
  • If you have found a new bug, click on "Enter a new bug report" and select the appropriate "product", i.e. AutoGrid, AutoDock or "MGL Applications" for ADT (the AutoDockTools graphical user interface).
  • If you don't have a Bugzilla account, you will need to create one. Click on "Open a new Bugzilla account" to make one; you will need a valid email address, and this will also be your login name. The account will be created, and its password will be mailed to you. You will not be able to log in until you receive the password.

This FAQ applies to: AutoDock 3, AutoDock 4

Is there a graphical user interface to AutoGrid and AutoDock?

Is there a tool to help me set up my AutoGrid grid map calculations, and my AutoDock dockings? One that can help me analyse my docking results?

Yes, it is called ADT (also known as AutoDockTools), and is produced by the Olson Laboratory, here at The Scripps Research Institute.  ADT builds on Michel Sanner's PMV (Python Molecule Viewer) and MGLTools.

There is also BDT (Blind Docking Tool) which is produced by Facultat de Química de Tarragona, Universitat Rovira i Virgili, in Spain.

See the Resources section for more information.

This FAQ applies to: AutoDock 3, AutoDock 4

Can't find or open a file?

How do I tell AutoGrid/AutoDock where input files are?

Since AutoGrid/AutoDock look for input files in current working directory (cwd), you need to make sure that your cwd includes all input files necessary. Start your command line shell and run ls (POSIX) or dir (Windows). If the input file mentioned in error message is not listed, you need to change directory (cd) or move required input file to cwd. Please note that AutoDock is a command line application and you need to be able to navigate your file system in order to troubleshoot potential problems. See, for instance, File Systems - Unix and Dos.

The above is also true if you launch AutoDock using AutoDockTools (ADT). If you changed your directory while saving or opening an input file then chances are that you need to change current working directory in ADT.

Where can I find the Python scripts for preparing and analysing AutoDock dockings?

I've read about the Python prepare scripts like "prepare_dpf4.py" in places like the virtual screening tutorial. This FAQ answers the questions, "Which Python scripts are available?", "Where do I download the Python scripts from?" and "Where are these Python scripts installed?".


Which Python scripts are available?

In version 1.5.0 of MGLTools, these scripts include:
compute_AutoDock41_score.py
compute_consensus_maps_from_dlgs.py
compute_rms_between_methods.py
dpf3_to_dpf4.py
energy_average_maps.py
gpf3_to_gpf4.py
gpf4_to_gpf3.py
pdbq_to_pdbqt.py
pdbqs_to_pdbqt.py
pdbqt_to_pdb.py
pdbqt_to_pdbq.py
pdbqt_to_pdbqs.py
prepare_dpf.py
prepare_dpf4.py
prepare_flexreceptor4.py
prepare_gpf.py
prepare_gpf4.py
prepare_ligand.py
prepare_ligand4.py
prepare_ligand_dict.py
prepare_receptor.py
prepare_receptor4.py
repair_ligand4.py
rotate_molecule.py
summarize_docking_directory.py
summarize_results.py
summarize_results4.py
summarize_time.py
summarize_wcg_docking.py
superimpose_based_on_subset.py
write_all_complexes.py
write_clustering_histogram_postscript.py
write_component_energies.py
write_largest_cluster_ligand.py
write_lowest_energy_ligand.py
write_random_state_ligand.py
Note that the scripts that end in "4.py" are for AutoDock 4.  See the "How to" section to learn more about these scripts.



Where do I download the Python scripts from?

All the AutoDock Python scripts are distributed as part of AutoDockTools, which is distributed as part of the MGLTools bundle.



Where are these Python scripts installed?

They can be found at the following locations, depending on your platform (Linux, Mac OS X or Windows) and on the version of MGLTools you installed (1.5.0):
 

Linux

    <InstallationDirectory>/MGLToolsPckgs/AutoDockTools/Utilities24

    If you install as root, <InstallationDirectory> is:

    /usr/local/MGLTools-1.5.0

    If you install as a regular user, <InstallationDirectory> is:

    $HOME/MGLTools-1.5.0

Mac OS X

    /Library/MGLTools/1.5.0/MGLToolsPckgs/AutoDockTools/Utilities24

Windows

    <InstallationDirectory>\MGLToolsPckgs\AutoDockTools\Utilities24

    Note that by default,  <InstallationDirectory> is:

    C:\Program Files\MGLTools 1.5.0

This FAQ applies to: AutoDock 3, AutoDock 4

How should I prepare a ligand for docking with AutoDock?

Where can I obtain 3D coordinates for my ligand? What do I have to do before I can use AutoDock?

Steps to Generate a Ligand Input File for AutoDock

  1. Convert a 1D description (SMILES string, e.g.) or 2D description (from a molecule sketching program such as ChemDraw, Ghemical or PRODRG) of the ligand into 3D coordinates.  Pay attention to the stereoisomeric form, especially chirality.
  2. Alternatively, obtain the structure of the ligand from a database.
  3. Generate the correct tautomeric form.  If this is not known, all tautomers should be generated and docked independently.
  4. Add all the hydrogen atoms, to make sure all the valencies of the heavy atoms are satisfied.
  5. Compute partial charges for the ligand using your preferred method and level of theory.
  6. AutoDock 3 and AutoDock 4 use the United Atom model.  This means only polar hydrogens are included in the coordinates file. A molecule with all hydrogens can be converted into a United Atom model using AutoDockTools (ADT)'s "Edit > Hydrogens > Merge Non-Polar" menu option.
  7. The ligand needs torsion information to be added depending on which torsions are to be treated as rotatable during the docking.  Then it needs to be saved in PDBQ format for AutoDock 3, and PDBQT format for AutoDock 4. There are more details on how to do this using ADT in the tutorials, "Using AutoDock 3.0.5 with AutoDockTools", "Using AutoDock 4 with AutoDockTools" and  "Using AutoDock for Virtual Screening".

Obtaining 3D Coordinates for a Ligand

There are a variety of ways of obtaining coordinates for a small organic molecule ('ligand')—this list is by no means exhaustive:
  • Databases
    • CSD (Commercial, Cambridge Structural Database) — this is the "world repository of small molecule crystal structures".
    • PDB — (Free) — RCSB Protein Data Bank — great if you are looking for a structure of a small molecule in complex with a protein or other macromolecule.
    • ZINC (Free) — ZINC Is Not Commercial! — "a free database of commercially-available compounds for virtual screening. ZINC contains over 4.6 million compounds in ready-to-dock, 3D formats".
  • Chemical Drawing Software

Requirements for AutoDock


  • AutoDock 3 requires 3D coordinates and partial charges for all the heavy atoms and polar hydrogens in the ligand; these must be given in PDBQ format.
  • AutoDock 4 requires 3D coordinates, partial charges and AutoDock 4 atom types for all the heavy atoms and polar hydrogens in the ligand; these must be given in PDBQT format.

This FAQ applies to: AutoDock 3, AutoDock 4

How to cite AutoDock?

Link to AutoDock references.

by morris last modified 2007-07-19 17:31
Contributors: Ruth Huey, Garrett M. Morris, Sargid Dallakyan, Stefano Forli

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