autogrid4 - Online in the Cloud

PROGRAM:

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.

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