Optional Parameters

Input Options

-param <parameter filename>    [No Default]

A parameter file is a text file that lists parameter settings to be used during a run. If a parameter is specified both on the command line and in the parameter file, the value specified on the command line is used.

The format of the parameter file is as follows:

• One parameter per line

• For non-list parameters one key-value pair per line. (e.g., -receptor rec.oedu).

• For list parameters a key followed by all the values (e.g., -dbase lig1.oeb.gz ligs2.oeb.gz)

• Boolean parameters must be listed as a key followed by true or false (e.g. -annotate_poses true).

• The parameter file may not contain the -param parameter.

• Lines beginning with # are considered comments

-molnames <input filename>    [No Default]

This parameter specifies a text file containing a list of molecule names (one name per line in the file). If this parameter is set then only molecules in the database file(s) (see parameter -dbase) with names that match those in the text files will be read in.

The general purpose of this flag is to provide an easy mechanism for reading a few specific molecule(s) that are contained in a large database, without having to extract those molecules by hand from the database.

Dock Options

-dock_resolution <setting> [Default: Standard]

The parameter controls the resolution of the docking both during the exhaustive search and the optimization. The resolution of the exhaustive search at each setting is as follows.

Setting	Translational Stepsize	Rotational Stepsize
High	1.0 Ångström	1.0 Ångström
Standard	1.0 Ångström	1.5 Ångströms
Low	1.5 Ångströms	2.0 Ångströms

During the optimization step the resolution is half that of the exhaustive search.

Output File

-docked_molecule_file <filename> [Default: docked.oeb.gz]

File docked molecules will be written to. The file format is controlled by the extension of the filename. The following output formats are supported.

Format	Extension
OEBinary	.oeb
SDF	.sdf
Gzipped OEBinary	.oeb.gz
Gzipped SDF	.sdf.gz

Scores will be attached as SD data to each pose with the tag FRED Chemgauss4 Score, unless the -score_tag option is used to specify another tag.

The number of top scoring molecules outputted is controlled by the -hitlist_size option (which has a default value of 500).

Note

If this flag is not set by the user the default filename (i.e., docked.oeb.gz) will be automatically prefixed with the setting of the -prefix flag.

[ Aliases = -docked_mol_file, -docked_file, -docked, -out ]

-undocked_molecule_file <filename> [Default: undocked.oeb.gz]

Specifies an output file in which to place molecules that could not be docked into the active site (this generally occurs when a molecule is too large to fit in the site, or unable to match user specified docking constraints). The format of this file is determined by the filename extension. The following output formats are supported.

Format	Extension
OEBinary	.oeb
SDF	.sdf
Isomeric SMILES	.ism
Gzipped OEBinary	.oeb.gz
Gzipped SDF	.sdf.gz
Gzipped Isomeric Smiles	.ism.gz

Note

If this flag is not set by the user the default filename (i.e., undocked.oeb.gz) will be automatically prefixed with the setting of the -prefix flag.

[ Aliases = -undocked_mol_file, -undocked_file, -undocked ]

-score_file <filename>   [Default: score.txt]

Specifies a tab separated text file with the name and scores of the molecules.

Note

If this flag is not set by the user the default filename (i.e., score.txt) will be automatically prefixed with the setting of the -prefix flag.

[ Aliases : -score ]

-report_file <filename> [Default: report.txt]

Specifies a file that a text report of the run will be written to.

Note

If this flag is not set by the user the default filename (i.e., report.txt) will be automatically prefixed with the setting of the -prefix flag.

[ Aliases : -report ]

-settings_file <filename> [Default: settings.param]

Writes the settings of all parameters of the run to the specified output file. The settings will be listed in plain text with one parameter name follow by its value(s). This format is compatible with the format of parameter files, and therefore a settings file from a previous run can be passed to the -param flag to re-run the program with the same settings.

Note

If this flag is not set by the user the default filename (i.e., settings.param) will be automatically prefixed with the setting of the -prefix flag.

[ Aliases : -settings ]

-status_file <filename> [Default: status.txt]

If this parameter is set then the status of the run will be written to the given output file every few seconds (the previous contents of the file will be overwritten) during the run.

Note

If this flag is not set by the user the default filename (i.e., status.txt) will be automatically prefixed with the setting of the -prefix flag.

[ Aliases : -status ]

Output Options

-hitlist_size <num>  [Default: 500]

This parameter controls the number of top scoring molecules that will be outputted at the end of the run (sorted by score), or can be used to specify that all molecules should be outputted as they are processed (unsorted).

If -hitlist_size is non-zero a sorted hitlist of the best scoring molecules is produced that will be maintained and output at the end of the run. The maximum size of the hitlist is -hitlist_size. If more than this number of molecules are in the input database only the top scoring molecules will be outputted and the rest will be discarded.

If -hitlist_size is zero the run will be in serial mode, i.e. each molecule will be outputted as it is processed (unsorted). For single processor runs this will be the order the molecules appear in the database file(s). For MPI runs the order will not be strictly the order the molecules appear in the database file(s).

There is no formal limit on the number of molecules that can be sorted and outputted at the end of the run. However, retaining a large number of molecules significantly increases the memory requirements. A good rule of thumb is that the setting -hitlist_size times the setting of -num_poses should not be larger than 10,000.

[ Aliases = -hitlist_size, -hitlist ]

-num_poses <num> [Default: 1]

Specifies the maximum number of docked poses to output for each docked molecule.

There is no formal limit on the number of poses per molecule that can be outputted, however, retaining a large number of alternate poses significantly increases the size of the molecules in memory and when outputted to disk. A good rule of thumb is that the setting -hitlist_size times the setting of -num_poses should not be larger than 10,000.

[ Aliases = -numposes ]

-score_tag <score tag> [No Default]

This parameter overrides the default SD data tag used to store molecule scores.

[ Aliases = -scoretag ]

-annotate_scores [Default: false]

If the value of this flag is set to true VIDA score annotations will be added to the processed molecules. These annotations are visible in VIDA (OpenEye’s molecular visualization program) and show a per atom breakdown of the score.

Note

The docked molecule output file format (see fred -docked_molecule_file) must be OEBinary when using score annotations.

[ Aliases = -annotate ]

-save_component_scores    [Default: false]

If the value of this flag is set to true individual components of the total score will be saved to SD data on each pose and appear in the score file (see -score_file).

[ Aliases = -component_scores, -component ]

-no_extra_output_files [Default: false]

When this flag is set to true the only default output to the program will be the docked structure file (see -docked_molecule_file).

Using this flag suppresses the default output of the following

Output	Default	Parameter
filename
Undocked molecule file	undocked.oeb.gz	-undocked_molecule_file
Text score file	score.txt	-score_file
Report file	report.txt	-report_file
Settings file	fred.param	-settings_file
Status file	status.txt	-status_file

Only default output is suppressed. If any of these output parameters are explicitly set by the users the relevant output file will still be written even if this switch is turned on.

[ Aliases = -no_extra, -noextra, -noextraoutputfiles, -no_extra_output, -noextraoutput ]

-no_dots [Default: false]

When this flag is set to true, a dot is being written to standard error for each docking molecule (or x in the case of a failure). Setting this flag to false to suppress dot/x writing.

[ Aliases = -nodots ]

-prefix <value> [Default: fred]

This flag prefixes all default output filenames with the specified value.

Note

This flag does not affect output filenames explicitly set by the user.

-nostructs [Default: false]

When this flag is set to true, both the docked and undocked structure files will be suppressed. The flag overrides -docked_molecule_file and -undocked_molecule_file.