AutoGrid requires an input grid parameter file, which usually has the extension ".gpf". The command is issued as follows:
% autogrid3 -p macro.gpf -l macro.glg &
where `-p macro.gpf' specifies the grid parameter file, and
`
-l macro.glg' the log file output during the grid calculation. The `
&
' ensures that the this job will be run in the background. This whole line can be prefixed with the `nice' command to ensure other processes are not unduly affected. The log file will inform the user of the maximum and minimum energies found during the grid calculations.
AutoGrid writes out the grid maps in ASCII form, for readability and portability; AutoDock expects ASCII format grid maps. For a description of the format of the grid map files, see the appendices.
Check the minimum and maximum energies in each grid map: these are reported at the end of the AutoGrid log file (here, it is "
macro.glg
"). Minimum van der Waals' energies and hydrogen bonding energies are typically -10 to -1 kcal/mol, while maximum van der Waals' energies are around +10
5
kcal/mol. Electrostatic potentials tend to range from around -10
3
to +10
3
kcal/mol: if these are both 0, this is a fairly clear indication that there are no partial charges on the macromolecule.
As well as the grid maps, AutoGrid creates two AVS-readable files, with the extensions `.fld', and `.xyz'. The former is a field file summarizing the grid maps, and the latter describes the spatial extent of the grids in Cartesian space. (To read the grid maps into AVS, use a "read field" module.)
The `-o' flag can be used on the AutoGrid command line to signify that the `.pdbq' file specified in the grid parameter file is in `old' PDBQ format (charges are stored in columns 55-61).