Preparing protein and ligand for autodock analysis
autogrid4 [options] -p gridparameterfile
AutoGrid prepares a 3D grid representation of the non-covalent interaction energies that various user-specified ligand atom types will experience around a user-specified target macromolecule. In addition, the electrostatic potential and desolvation free energy grid maps may also be calculated. The grid maps are stored in plain text files with the extension '.map' and are required by AutoDock 4 to perform dockings. AutoGrid also outputs a '.xyz' file which describes the spatial extents of the grid box, and an AVS field '.fld' file which describes the consistent set of atomic affinity grid maps that were calculated together for a given target macromolecule. Note: it is necessary to compute grid maps for all the atom types in the ligand or set of ligands that will be docked, as well as an electrostatic potential grid map and a desolvation free energy map. For example, if a ligand has an aliphatic carbon and a hydrogen-bond-accepting oxygen atom, it would be necessary to compute both a 'C' map and an 'OA' map. See http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters for more information about AutoDock 4 atom types.
The input to AutoGrid is best prepared with the program suite AutoDockTools. There is no way to run autodock4 without a grid.
-o Use old PDBq format (q in columns 55-61)
Usage information, also -h on Debian.
Increased verbosity of messages to help debugging.
filename Specifies Grid Parameter File
A range of tests is made available with the AutoGrid sources that can be used as follows:
$ cd /tmp
$ ln -s $D/AD4_parameters.dat .
$ gunzip -c $D/hsg1_sm.pdbqt.gz > hsg1_sm.pdbqt
$ autogrid4 -p $D/hsg1_no_receptor_types.gpf -l hsg1_no_receptor_types.glg
This command prepares grid map files for each of the AutoDock atom types specified in the grid parameter file (in this case: hsg1_sm.A.map, hsg1_sm.C.map, hsg1_sm.d.map, hsg1_sm.e.map, hsg1_sm.HD.map, hsg1_sm.NA.map, hsg1_sm.N.map, hsg1_sm.OA.map), the AVS field file (hsg1_sm.maps.fld) and hsg1_sm.maps.xyz. To perform the cocking calculation, AutoDock should be executed, though it demands a separate docking parameter file (with extension .dpf). The 'DPF' refers to the grid map files that are necessary to the docking and allows the setting of other important parameters, such as the search method and how many dockings to perform.
This software is made available under the terms of the GNU Public License version 2 or later. This implies that this software may be redistributed if the source is made available. It would however help the future development of the AutoDockSuite if you register yourself at http://autodock.scripps.edu/downloads.
The most prominent author of the version 4 of AutoDock is G. Morris <[email protected]>. See the AUTHORS file in /usr/share/doc/autogrid for details.
This manual page was written by Steffen Moeller <[email protected]> and much revised by upstream author Garrett Morris. It was prepared for the Debian project but may be used by others and is hopefully adopted by the upstream developers.