Running DOCK 3.7

Jump to navigation Jump to search

Setting up an alias for the dock37tools directory in $DOCK_BASE/src/dock37tools/ is highly recommended, though you don't need it if you don't want it. Assume you have it set as $d37 from here on out with a command line this

setenv d37 $DOCK_BASE/src/dock37tools/

In that directory, there are 3 scripts for setting up a dock run. The first script will send setup a docking run where each file will be relegated to a separate node, fine for quick jobs.

$d37/setup_db2.csh /full/path/to/db2/files/

Another script, useful for testing on DUD-E targets, is:

$d37/setup_db2_own.csh /full/path/to/db2/files/

A file script, useful for running many db2.gz files, sometimes with a few files grouped together, like for prospective screening against lead-like is:

$d37/ desiredDirectoryCount prefixName  /full/path/to/db2/files/

After setting up any of these runs, you can run them with the following:


or $d37/subdock.csh /path/to/dock.csh if you have compiled your own version of DOCK3.7.

Runs should proceed on the cluster. Problems will show up in the stderr files, further diagnosis can be attempted by looking at the various OUTDOCK files produced. If you've used lots of sampling, expect slower results. If you've asked for hundreds of poses, expect large files. You should not combine prospective screening, hundreds of poses and high sampling.

If a few jobs crash (shouldn't happen but anything is possible) and you need to complete them, run

$d37/ -f

This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License. To view a copy of this license, visit This page is adapted from "DOCK3.7 Documentation" by Ryan G. Coleman. Based on a work at