Optional Parameters

Execute Options


The argument for this flag is the name of a file containing control parameters. The control parameter file acts to either replace or augment the command line interface. All parameters necessary for program execution may be provided in the control parameter file, although any command given explicitly on the command line will supersede options found in the parameter file. The application generates a new parameter file containing the full set of execution parameters upon every execution. The name of the parameter file is created by combining the prefix base name with the ‘.param’ extension.

-mpi_np <n>

Specifies the number of processors n when the application is run in MPI mode.

-mpi_hostfile <filename>

Specifies the name of the file containing processors configuration. For every host this file should contain a line host_name slots=n where n is the number of processors on the host.

Input Options

-query <filename>

File containing one 3D molecule to use as a query. File format can be any of the formats given in the table for -dbase above.


Specifies charges to be used on the query and the database. Default is to calculate them internally with mmff. The option -charges existing will use precalculated charges that must be set in the input files. If existing is selected and any molecule doesn’t have charges then EON will default to mmff for those molecules. Both -fixpka_query and -fixpka_dbase should be set to false if -charges is set to existing; otherwise EON will fail.

[default = mmff]


Since EON reads multi-conformer input molecules, when reading from non-binary files, EON will compare consecutive molecules and if they are determined to be the same structure, they will be concatenated into a single, multi-conformer molecule. If the user desires to score each input conformation independently, then using this flag will turn off the conformer comparison step.

[default = false]

Output Options

-oformat <extension>

Format of output structure file(s). The default is oeb so that ET score can be included as tag data. The format for the file is determined by giving the extension. Valid values include all formats listed above for -query

[default = oeb]

-prefix <prefix>

Defines a prefix used to name output files. Using -prefix FOO will create a hits structure file named like FOO_hits.oeb and a report file, FOO.rpt

[default = EON]

-besthits <N>

Process entire dbase file but only keep N best scores sorted by property specified by -rankby. Using a value of 0 implies no hitlist will be maintained and structures will all be scored and output in input order.

[default = 500]

-maxhits <N>

Stop after finding first N hits. This option overrides any setting for -besthits


-rankby <score>

Property to use to sort hitlist. Values include ET_combo, ET_pb and ET_coul.

[default = ET_combo]

-cutoff <score>

Minimum score to keep as a hit.

[default = -1.0]


Write the query to the top of the hits file. This make visualization of results much easier inside VIDA.


Turn off the terminal torsion conformer search and just score each input conformation as-is.

-hitsfile <filename>

Explicit filename for writing hits. Overrides the default filename created from -prefix.

-reportfile <filename>

Explicit filename for writing hits. Overrides the default filename created from -prefix.


This parameter controls whether to attach score information to output molecules as SD data.

Log Output Options

-logfile <filename>

Filename for log file. Overrides log filename created from -prefix.


Method for showing job progress on the command line. Choices include:

  • percent - show a percent complete progress bar (DEFAULT)

  • log - echo the log message for each molecule

  • dots - show dots as in EON 1.1

  • none - print nothing to console

[default = percent]


Write status info to this file. Use “none” for no status file.


Give verbose output to console instead of simple progress.

[default = false]

ZAP/PB Options


Apply a neutral pH model to the query molecule. It should be set to false if -charges is set to existing; otherwise EON will fail.

[default = true]


Apply a neutral pH model to the database molecules. It should be set to false if -charges is set to existing; otherwise EON will fail.

[default = true]


Add salt to the Zap calculation. To aid in moderating large, local charges, salt is added into the calculation. Legal values are between 0.0 and 0.1 (mM).

[default = 0.04]


Sets the grid spacing for the internal Zap calculations.

[default 0.5]


Write ET grid to output attached to each molecule. Useful for visualization in VIDA but this only works when writing hits to an OEB (.oeb or .oeb.gz) file. Note that while this feature is quite useful, grids do take a large amount of memory so care should be taken when using this feature for hit lists of more than 500 molecules.

[default = false]

Omega Options


Omega energy window used for conformer selection.

[default = 10.0]


Omega RMS threshold used to determine duplicate conformations

[default = 0.3]


Sets whether hydrogens will be sampled. This option enables sampling of hydrogen locations for -OH, -SH, and amines.

[default = false]