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dock3.5

version 1.0,1.1
Robert Sheridan, Renee DesJarlais, Irwin Kuntz

version 2.0
Brian Shoichet, Dale Bodian, Irwin Kuntz

version 3.0
Elaine Meng, Brian Shoichet, Irwin Kuntz

version 3.5
Mike Connolly, Daniel Gschwend, Andrew Good, Connie Oshiro, Irwin Kuntz

Overview / Input / Output / Sample INDOCKs / DOCKOPT

Input

The input file names and parameters are read from a file called INDOCK. The INDOCK file has undergone extensive changes in version 3.5. It is now based upon keywords. Although the old (3.0) format INDOCK and DOCKOPT files can be read by DOCK 3.5, it is strongly recommended that these files be updated to the new keyword format with the tonew utility. The following guidelines apply to the 3.5 keyword format input files:

the first line must be

           DOCK 3.5 parameter      for an INDOCK file
   or,     DOCK 3.5 option         for a DOCKOPT file

otherwise the old 3.0 format is assumed and read accordingly.

all lines except the header line are free format
the order of parameters is irrelevant
blank lines are allowed
anything following a # is treated as a comment
tab characters are not permitted
keywords which have defaults (see below) may be omitted entirely
logical keywords (yes/no choices) assume the affirmative when the keyword is specified in the input file but no value is provided
extraneous parameters, i.e. those that do not apply for the particular DOCK run, are disregarded (e.g. specifying force-field scoring related keywords when using the "contact scoring only" option)

The following tables present all keywords available for interacting with DOCK. The allowed values that may accompany a given keyword is given, along with a default should the keyword be omitted.

Note that the scoring option can be either a number or a word. That is, you can have scoring_option 3 or scoring_option contact+forcefield. For logical parameters, specify yes or no, which may be abbreviated y or n, and which may be in upper or lower case. For the sake of backward compatibility, if 1 and 0 were used for a logical parameter previously, then they are still acceptable. The match keyword is peculiar, because it may be repeated (up to 60 times).

Click to see a particular set of input parameters:

Curator: Daniel Gschwend, gschwend@cgl.ucsf.edu (rev. 1 September 1995)