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INPUT FILE -- Parameters are extracted from input_file, or dock.in if not specified. |
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OUTPUT FILE -- Results are written to output_file, or dock.out if not specified. If a -o flag is present then dock runs in batch mode, otherwise it runs interactively (see below). |
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STANDARD INPUT -- Parameters are entered interactively without the construction of an input file. This option is generally not recommended. |
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RESTART -- Run is initialized with information from a restart file. This option is used to restart a rank_ligands docking run that was terminated prematurely. |
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PROFILE -- Time spent in docking routines and minimizer statistics are profiled. This option helps the user to identify the bottleneck of a particular calculation and to choose optimal minimizer parameters. See Performance on page 73 . |
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TERSE -- Reduced output level. This option helps reduce the size of the output file when docking a large number of molecules. |
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VERBOSE -- Increased output level. This option allows additional data to be included in the output. Recommended for single molecule runs. |
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.
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.in file 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.
dock will behave as above, but will assume the input file to be dock.in.
dock will run interactively, but will not check any input file for parameters and will not append any entered parameters to a file.
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.
dock will behave as above, but will assume the i/o files to be dock.in and dock.out.
If a file called INDOCK is present in the current working directory, then dock will use it as an input file. Output will be written to a file called OUTDOCK. This mode is present for reverse compatibility with previous versions of dock.
If the input and output file have recognized coordinate file extensions (*.mol2, *.pdb, *.xpdb, *.sph, *.ptr), then dock will automatically construct its own parameter input file to perform a file conversion operation.