ROCS

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

http://www.eyesopen.com/docs/rocs/3.0.0/html/usage.html

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

http://www.eyesopen.com/docs/rocs/3.0.0/html/tutorial.html#perform-a-rocs-run-from-the-command-line

 % rocs -query $PATH/query.oeb.gz -dbase $PATH/db_name.oeb.gz