Optional Parameters

Execute Options

-param

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.

File Options

-log

The argument for this flag specifies the name of the log file. The level of detail for logfile information can be altered using the -verbose flag. Generation of an output log may be disabled by providing nul as a argument in Windows and /dev/null as an argument on Linux and macOS. [default = prefix _log.txt]

-prefix

The argument for this flag defines the prefix to be used for various information and data files generated. Most important among these is the ‘prefix_parm.txt’ file which includes a copy of all the parameters used in the run. The prefix is also used to generate a default log file name if not explicitly specified with the -log flag. [default = <app_name>].

-verbose

This is a boolean flag that controls the level of detail written to the log file. By default only minimal information is written to the log file. Verbose logging will cause more information to be written to the log file in order to follow behavior during program execution. [default = false]

-molNames

This parameter takes 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 input file(s) (see parameter -in) 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 file, without having to extract those molecules by hand from the input molecules file. [default = NONE].

-progress

Show progress on screen. Options are ‘none’, ‘dots’, ‘log’ and ‘percent’. The ‘dots’ options will displays dots on screen to show molecules completed. The ‘log’ option will duplicate the log file on screen. The ‘percent’ option will track progress through the input file. [default = none]

EON App Options

-scdbase

Treat the database file as a single-conformer input (when the format is not OEB). [Default=true]

-fixpka_query

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]

-fixpka_dbase

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]

-writegrid

Whether or not to output electrostatic grid when writing to .oeb file. [Default=false]

-charges

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]

-num_top_scores

When potential mode is engaged, the shape and charge overlay will keep this many best hits, and score them all with potential to choose best combo hit. [Default=5]

-potential

Scoring done with shape and potential similarity combo. [Default=false]

-scoreonly

Whether or not to score only or do full overlay. [Default=false]

EON Hitlist Options

-besthits <N>

Keep a hitlist and find best N hits. Zero implies no hitlist, and streaming all scored input in the order of appearance. [Default=500]

-maxhits <N>

When this parameter is greater than zero, stop after N hits, otherwise find all hits. [Default=0]

-rankby

Score to use when ranking the hitlist.

Value	Meaning
ET_pb	Poisson-Boltzmann ET score
ET_coul	Coulomb ET score
ET_combo	Combined ET score (default)

[Default=ET_combo]

-cutoff <N>

Minimum score to keep. [Default=-1.0]

-outputquery

Output query molecule at the beginning of the hits file. [Default=true]

-sdTags

Attach score information to output molecules as SD data. [Default=true]

[Aliases=**-sdtags**]

-nostructs

Do not output any structures to the hits file. [Default=false]

-hitsfile <filename>

Absolute filename for the output hits file. Must be a valid molecule file. Use none for no hit file output. Overrides the name generated from -prefix.

-reportfile <filename>

Absolute filename for the report file. Use none for no report file output. Overrides the name generated from -prefix.

-oformat <extension>

Format for the output structure file. Legal values: sdf, mol, mol2, pdb, ent, mmod, oeb, sdf.gz, mol.gz, mol2.gz, pdb.gz, ent.gz, mmod.gz, oeb.gz. [Default=oeb]

-logfile <filename>

Absolute filename for the log file. Use - for stdout, none for no log output. Overrides the name generated from -prefix.

-statusfile <filename>

Write status information to this file. Use none for no status file.

ZAP/PB Options

-salt

Salt concentration (in mol/L) to use in the PB calculation. [Default=0.04]

-spacing

Grid spacing for internal ZAP grid. [Default=0.75]

Omega Conformer Options

-ewindow

Energy window (kcal/mol) used for conformer selection. [Default=10.0]

-rms

RMS threshold used to identify and remove duplicate conformations. [Default=0.3]

-sampleHydrogens

Sample hydrogen positions for hydroxyl (OH), thiol (SH), and amine groups during conformer generation. [Default=false]

[Aliases=**-sampleH**,**-samplehydrogens**]