The simplest way to run EON is to use the -eon_input flag in ROCS to create a set of ROCS-aligned structures with the ROCS query at the top of the file. By default, if EON is only provided a dbase file, it will assume the first molecule is the query.
prompt> eon -dbase rocs_eon_input.oeb.gz
Or you can provide a single molecule in a query file and a set of molecules in a dbase file. A common example would be to use a ROCS query as the EON query and the ROCS hits file as the dbase file for EON.
So for example:
prompt> eon -dbase rocs_hits_1.oeb -query rocsquery.sdf
will score all the structures in rocs_hits_1.oeb against the molecule in rocsquery.sdf and place the structures in EON_hits.oeb (with ET scores in SD tag data) and a table of results in EON.rpt.
To keep only the best 100 hits, use:
prompt> eon -dbase rocs_hits_1.oeb -query rocsquery.sdf -besthits 100
Note that the use of an output structure file is mostly for generation of a single file containing structures and tag data such that loading this single file into VIDA provides easy analysis of the results. If however, the only real desire is for the numerical scores, use -nostructs to suppress the creation of an output structure file.
prompt> eon -dbase rocs_hits_1.oeb -query rocsquery.sdf -nostructs
By default, EON calculates partial charges using MMFF94. However, if you have structure files that already contain good partial charges in both your dbase file and query file, you can tell EON to use them instead:
prompt> eon -dbase rocs_hits_chgs.mol2 -query rocsquery_chg.mol2 -charges existing -fixpka_query false -fixpka_dbase false
To prevent continually over-writing output files, the -prefix flag allows you to give unique names to these files.
prompt> eon -dbase rocs_hits_1.oeb -query rocsquery.sdf -prefix FOO
will write the hit structures into a file named FOO_hits.oeb and the numerical values will be in FOO.rpt. The parameter file for this run will likewise be named FOO.parm.
To prevent EON for searching alternate terminal torsions, use the -scoreonly flag.
prompt> eon -dbase rocs_eon_input.oeb.gz -scoreonly
Finally, to create ET grids as used in the calculation and attach them to each output molecule. Note, this only works for OEB output and can be very memory intensive.
prompt> eon -dbase rocs_eon_input.oeb.gz -oformat oeb.gz -writegrid