AUTOGRID(1)						      General Commands Manual						       AUTOGRID(1)

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 nec-
       essary 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  poten-
       tial  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)