Tools for AutoDock

Contents:

AutoDockTools, ADT - Tools to Set Up, Run and Analyze AutoDock Dockings
Format-Conversion Tools
Graphical Tools
Superimposing Molecules
Structural Data
Lists of Software and Sites
Extra AutoDock UNIX Shell Scripts, Python & Awk Programs
General

AutoDockTools, ADT - Tools to Set Up, Run and Analyze AutoDock Dockings

AutoDockTools, or ADT,is the ultimate GUI to set up, launch and analyze AutoDock runs. With ADT, you can:

View molecules in 3D, rotate & scale in real time.

Add all hydrogens or just non-polar hydrogens.

Assign partial atomic charges to the ligand and the macromolecule (Gasteiger or Kollman United Atom charges).

Merge non-polar hydrogens and their charges with their parent carbon atom.

Set up rotatable bonds in the ligand using a graphical version of AutoTors.

Set up the AutoGrid Parameter File (GPF) using a visual representation of the grid box, and slider-based widgets.

Set up the AutoDock Parameter File (DPF) using forms.

Launch AutoGrid and AutoDock.

Read in the results of an AutoDock job and graphically display them.

View isocontoured AutoGrid affinity maps.

And much, much more...

Downloading AutoDockTools:

After you have clicked on this AutoDockTools link, you will be taken to our lab's Python Home Page.

Click on the "DOWNLOADS" link at the top;

Register to create a login in and then you can use the Packager. This clever piece of code takes care of all the dependencies for the different downloading options.

When you are given the option to Either:

( ) Download a pre-compiled Python Interpreter for Unix,
( * ) Download Python Packages, or
( ) Download MSMS binaries,
you should click on the "Download Python packages" radio button.
Then click "Start".

Select your platform (SGI, Linux, Sun, Win) and the version of Python (1.5 or 2.0).

Now you can select the "AutoDockTools" package: click on the check box next to this, then click the "Select dependent packages" button. The Packager will figure out which of the other packages you will need.

On the next page you can click on the "OK" button to proceed to the download.

If you choose to download Michel Sanner's Molecular Surface Library MSLIB, the Fast Isocontour Library, or the Stride Secondary Structure Assignment Library, you will be presented with additional licenses that you must accept before you can download these packages.

Finally, you will be sent email, within about 30 minutes, containing instructions on how to download the tar file containing the packages you selected.

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Format-Conversion Tools

Babel

Converts between many different kinds of molecular formats, including SYBYL mol2, PDB, InsightII car, and MDL SD formats. Available for UNIX, DOS and Mac OS.
hin2pdbq.py

Converts a HyperChem .hin-file to an AutoDock PDBQ-file. [Python script; needs "python", free from http://www.python.org/.]
AutoDock Utilities Documentation

These utilities are available with the AutoDock distribution.
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Graphical Tools

gOpenMol

has, amongst other things, various AutoDock tools, including the ability to read and view trajectories from simulated annealing dockings. Written by Leif Laaksonen. Free.
RasMol

can be used to view PDB files. Free. RasMol Manual and Quick Reference Card
Chemscape Chime^TM

From MDL Information Systems. Allows visualisation of structures within WWW browser pages. Download from USA or UK
Swiss-PDB Viewer

can read in electron density maps, show sequence alignments, superimpose molecules, and easily create files for POV-Ray, a free ray tracer. Runs on Apple Macintosh, iMacs and Power Macintoshes; & IBM PC clones.
XtalView

for fitting electron density maps in x-ray crystallography. Has support for Raster 3D.
MacMolecule 2 and PCMolecule 2

From Molecular Ventures Inc.
MolView and MolView Lite

Free software for Macintosh
WebLab ViewerLite and ViewerPro

From Molecular Simulations Inc. For Macintosh and PC.
MolScript

Display structures as images in various formats, or VRML
Ribbons

General molecular illustration and error analysis in protein crystallography
MolMol

For displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. Imports: Residue Library, PDB, DIANA, DG, SYBYL(Mol2), XYZ. Exports: same as Imports, and... PostScript, MIF, EMF, TIFF, JPEG, PNG, BMP, POV-Ray, VRML.
MolPOV

David E. Richardson's Win95/3.1 freeware program to convert PDB files into POV-Ray input files.
PovChem

Non-graphical utility to convert PDB files into CPK, Ball and Stick, etc. POV-Ray input files. Runs under MSDOS, Irix(5.x), Mac (68k/PPC).
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Superimposing Molecules

ProFit

Protein least squares fitting.
Swiss-PDB Viewer

free, for Mac, PC and SGI; can be used to superimpose proteins (use "Iterative Magic Fit").
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Structural Data

PDB

the Protein Data Bank from the Research Collaboratory for Structural Bioinformatics.
SearchLite

for simpler searches of the PDB.
SearchFields

a customizable form for more advanced searches of the PDB.
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Lists of Software and Sites

Software for structure determination and analysis from the PDB.

Crystallography

NMR

Structure analysis and verification

Modeling and simulation

Molecular Graphics

Education

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Extra AutoDock UNIX Shell Scripts, Python and Awk Programs

rem-lp

usage: rem-lp file.pdbq
needs: file.pdbq or file.mol2
creates: file.pdbq-lp or file.mol2-lp

Merges charges of lone pairs with their sulfur atoms; assumes lone pairs are called ''LP'', and occur with SG or SD atoms only. Appends "-lp" to original file name; NOTE: doesn't work if x,y or z coord is the same as the charge.

lj4.py

usage: python lj4.py > new_parameters.txt
needs: lj4.py
creates: new_parameters.txt
This is a python program to calculate new Lennard-Jones parameters for new atom types you decide you need to add to AutoDock. You need to understand python and be able to edit the "lj4.py" file in order to add new atom types. The output of "lj4.py" is in various formats, including "awk" and AutoDock GPF and DPF formats. You can then cut-and-paste the relevant sections into your own GPF or DPF files, or into your copies of "gpf3gen.awk" and "dpf3gen.awk" program files. Then the next time you use "mkgpf3" or "mkdpf3", the new parameters will always be available.
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General

Gzip

File compression utility
Python

All purpose, object-oriented, interpreted programming language. Powerful Numeric extensions - check out the Scientific Computing page at the Python web site. Much easier to learn and more powerful than Perl.
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AutoDock

Useful Tools