ROCS: Difference between revisions
Jump to navigation
Jump to search
(adding useful links) |
m (5 revisions) |
||
(3 intermediate revisions by one other user not shown) | |||
Line 1: | Line 1: | ||
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 | 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 | ||
Preparing a database | |||
== '''1. Preparing a database''' == | |||
http://www.eyesopen.com/docs/rocs/3.0.0/html/usage.html | http://www.eyesopen.com/docs/rocs/3.0.0/html/usage.html | ||
Running ROCS | The database file must be a multi-conformer OEBinary file created by OMEGA | ||
http://www.eyesopen.com/docs/rocs/3.0.0/html/tutorial.html# | % 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 | |||
[[Category:Tutorials]] |
Latest revision as of 20:32, 8 October 2012
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