This is more of a guide to how to run ROCS on the Shoichet cluster than what ROCS is, for that, see the OpenEye webpage: http://www.eyesopen.com/products/applications/rocs.html
1. Preparing a database
The database file must be a multi-conformer OEBinary file created by OMEGA
% omega -in db_name.mol2 -out db_name.oeb.gz
ROCS also accepts list files as input (.list or .lst), with one molecule file per line. The entire set of molecules will be treated as a single db.
% cat db.list part1.oeb.gz part2.oeb.gz part3.oeb.gz
2. Running ROCS
% rocs -query $PATH/query.oeb.gz -dbase $PATH/db_name.oeb.gz