Command line arguments in DOCK6 - Revision history

Khtang at 22:49, 10 January 2019

2019-01-10T22:49:05Z

← Older revision		Revision as of 22:49, 10 January 2019
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	Note that the parameter_name and corresponding		Note that the parameter_name and corresponding
	value must be separated by white space, namely, blanks or tabs.		value must be separated by white space, namely, blanks or tabs.

			[[Category:NEED ATTENTION]]

Sudipto at 23:23, 23 March 2016

2016-03-23T23:23:30Z

← Older revision		Revision as of 23:23, 23 March 2016
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	shell. It reads an input parameter file containing field/value pairs:		shell. It reads an input parameter file containing field/value pairs:

	~~USAGE:~~ dock6 -i dock.in [-o dock.out] [-v]		dock6 -i dock.in [-o dock.out] [-v]

	~~DESCRIPTION:~~

	DOCK may be executed in either interactive or batch mode, depending on		DOCK may be executed in either interactive or batch mode, depending on
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	calculations once an input file has been generated interactively.		calculations once an input file has been generated interactively.

	= ~~OPTIONS~~ =		= Command line Arguments =

	-i dock.in =#input file containing user-defined parameters		-i dock.in =#input file containing user-defined parameters
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	and all warning messages		and all warning messages

	=Interactive mode=		= Interactive mode =

	dock6 -i dock.in		dock6 -i dock.in

	~~DESCRIPTION:~~

	When launched this way, DOCK will extract all		When launched this way, DOCK will extract all
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	mpirun [-machinefile machfile] [-np #_of_proc] dock6.mpi -i dock.in -o dock.out [-v]		mpirun [-machinefile machfile] [-np #_of_proc] dock6.mpi -i dock.in -o dock.out [-v]


	If DOCK has been built for parallel processing		If DOCK has been built for parallel processing
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	dock6.pbsa -i dock.in [-o dock.out] [-v]		dock6.pbsa -i dock.in [-o dock.out] [-v]


	If you have compiled DOCK for use		If you have compiled DOCK for use
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	The environment variable		The environment variable
	OE_LICENSE must be defined to the full path of the license file.		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.

Sudipto: Created page with "=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: USAGE: dock6 -i do..."

2016-03-23T23:18:54Z

Created page with "=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: USAGE: dock6 -i do..."

New page

=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:

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

DESCRIPTION:

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.

= OPTIONS =

-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

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
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.