Command Line Arguments

DOCK must be run command line from a standard unix shell. It reads a parameter file containing field/value pairs using the following command:

USAGE: dock6 -i dock.in [-v2] [-help] [-o dock.out]

DESCRIPTION:

DOCK may be executed in either interactive or batch mode, depending on whether output is written to a file. In interactive mode, the user is requested only for parameters relevant to the particular run and default values are provided. This mode is recommended for the initial construction of the input file and for short calculations. In batch mode, input parameters are read in from the input file and all output is written to the output file. This mode is recommended for long calculations once an input file has been generated interactively.

OPTIONS -i dock.in #input file containing user-defined parameters -help #emit the usage statement. -v2 #verbosity flag that prints additional information and warnings for scoring functions -o dock.out #output file containing the parameters used in the calculation, summary information for each molecule docked, and all warning messages

Interactive mode

USAGE: dock6 -i dock.in

DESCRIPTION:

When launched this way, DOCK will extract all relevant parameters from dock.in (or any file supplied by the user). If additional parameters are needed (or if the dock.infile is non-existent or empty), DOCK will request them one at a time from the user. Reasonable default values are presented. Any parameters supplied by the user will be automatically appended to the dock.in file. If the user would like to change any previously entered values, the user can edit in the dock.in file using a text editor.

Batch mode

USAGE: dock6 -i dock.in -o dock.out

DESCRIPTION:

When launched in this way, DOCK will run in batch mode, extracting all relevant parameters from dock.in (or any file supplied by the user) and will write out all output to dock.out(or any file supplied by the user). If any parameters are missing or incorrect, then execution will halt and an appropriate error message will be reported in dock.out.

Parallel DOCK

USAGE: mpirun [-machinefile machfile] [-np #_of_proc] dock6.mpi -i dock.in -o dock.out [-v2]

DESCRIPTION:

If you have compiled DOCK for parallel processing (see Installation), DOCK can be run in parallel. Parallelzation is set up to have a single Master node with the remaining nodes act as slaves. The Master node performs file processing and input/output, whereas the slaves perform the actual calculations. If np = 1, the code defaults to non-MPI behavior. As a result, there will be minimal difference in performance between 1 and 2 processors. Improved performance will only become evident with more than 2 nodes.

ADDITIONAL OPTIONS

-machinefile #simple text file containing the names of the computers (nodes) to be used -np # specifies the number of processors which typically is the same as the number of lines in the machinefile

PB/SA DOCK

USAGE: dock6.pbsa -i dock.in [-o dock.out][-v2]

DESCRIPTION:

If you have compiled DOCK for use with the ZAP library (see Installation), DOCK can be run using the ZAP PB/SA scoring function.