Once the grid maps have been prepared by AutoGrid and the docking parameter file, or DPF, is ready, the user is ready to run an AutoDock job. A docking is started from the command line using the following command:
% autodock3 [-o][-k][-i][-u][-t] -p lig.macro.dpf [-l lig.macro.dlg] &
Input parameters are specified by "
-p lig.macro.dpf
", and the log file containing the output and results from the docking is defined by "
-l lig.macro.dlg
". This is the normal usage of AutoDock, and performs a standard docking calculation.
-o
This can be added to the command line, to signify that the input file specified in the docking parameter file is in old PDBQ format, with charges in columns 55-61.
-k
keep the original residue number of the input ligand PDBQ file. Normally AutoDock re-numbers the starting position to residue-number 0, and any cluster-representatives are numbered incrementally from 1, according to their rank (rank 1 is the lowest energy cluster).
-i
This is used to ignore any grid map header errors that may arise due to conflicting filenames. This overrides the header checking that is normally performed to ensure compatible grid maps are being used.
-u
This returns a message describing the command line usage of AutoDock .
-t
This instructs AutoDock to parse the PDBQ file to check the torsion definitions, and then stop.
The Unix script "
job
" can be used to submit an
AutoDock
job, and then perform additional post-processing, such as profiling, extracting job-information and creating a field file for AVS display of the docked results. See the Appendix for more details.