NAME
autogrid - preparing protein and ligand for AutoDock analysis
SYNOPSIS
autogrid4 [options] -p gridparameterfile
DESCRIPTION
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.
OPTIONS
-o Use old PDBq format (q in columns 55-61)
-u Usage information, also -h on Debian.
-d Increased verbosity of messages to help debugging.
-l logfile
-p filename Specifies Grid Parameter File
EXAMPLE
A range of tests is made available with the AutoGrid sources that can
be used as follows:
$ D=/usr/share/doc/autogrid/Tests
$ 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.
SEE ALSO
autodock(1), runAdt(1).
http://autodock.scripps.edu
LICENSE
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.
AUTHOR
The most prominent author of the version 4 of AutoDock is G. Morris
<garrett@scripps.edu>. See the AUTHORS file in /usr/share/doc/autogrid
for details.
This manual page was written by Steffen Moeller <moeller@debian.org>
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.
Juli 23, 2007 AUTOGRID(1)