Command line arguments in DOCK6

Command-line Arguments

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

 dock6 -i dock.in [-o dock.out] [-v]

DOCK may be executed in either interactive or batch mode, depending on whether the 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.

Command line Arguments

-i dock.in =#input file containing user-defined parameters

-help= #emit the usage statement.

-v #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

 dock6 -i dock.in

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 the dock.in file using a text editor.

Batch mode

  dock6 -i dock.in -o dock.out

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

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

If DOCK has been built for parallel processing (see Installation) then DOCK can be run in parallel. Parallelization employs a single master processor with the remaining processors acting as slaves. If np = 1, the code defaults to non-MPI behavior. There is a minimal difference in performance between 1 and 2 processors. Improved performance is only evident with more than 2 processors.

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

MPICH2 QUICK START: MPICH2, unlike MPICH, requires command line initialization. If your system administrators have not initialized MPICH2 then follow these steps: Create a .mpd.conf file in your home directory containing secretword=mysecretword. Create a .mpd.hosts file in your home directory containing a list of machine names, one per line. Start the MPICH2 daemons by executing mpdboot. Verify the start up of the MPICH2 daemons by executing mpdtrace -l. Finally execute DOCK using mpiexec or mpirun. For further information see the MPICH2 README.

PB/SA DOCK

 dock6.pbsa -i dock.in [-o dock.out] [-v]

If you have compiled DOCK for use with the ZAP library (see Installation), DOCK can be run using the ZAP PB/SA scoring function. The environment variable OE_LICENSE must be defined to the full path of the license file.

DOCK 6 Parameter Parser

In Interactive Mode, dock will dynamically ask the user to enter the appropriate user parameters. The generic format for the questions is:

parameter_name [default value] (legal values):

The parameter parser requires that the values entered for a parameter exactly match one of the legal values. For example:

 Example A: program_location [Hello_World!] ():
 Example B: #_red_balloons [99] ():
 Example C: glass_status [half_full] (half_full half_empty):

In Example A, the parameter "program_location" can be assigned any string value, and in Example B, the parameter "#_red_balloons" can be assigned any integer value. However, in Example C, the parameter value "glass_status" can only be assigned the strings "half_full" or "half_empty". If no parameter are assigned by the user, the default value--in brackets--will be used.

In Batch Mode, all parameters in the dock.in file, must be:

 parameter_name value 

Note that the parameter_name and corresponding value must be separated by white space, namely, blanks or tabs.