DOCK

The DOCK suite of programs is designed to find favorable orientations of a ligand in a "receptor." It can be subdivided into (i) those programs related directly to docking of ligands and (ii) accessory programs.

Before using DOCK you should read the extensive documentation, either the hard copy in the CSB core user area or the on-line documentation at UCSF, or the local PDF version.

Worked examples are in /srv/local/dock/examples/ and subdirectories therein. These are well documented.

To put the executables for DOCK in your path, type the following:

setup dock (or source /srv/local/setup/dock.set)

Note: You must create a dot surface of your "receptor" molecule to use DOCK. We have both MS and DMS here in the CSB core in /srvlocal/bin/. These are discussed in the documentation for DOCK but they are separate programs. The prefered program however, is qcpe_ms which is in /srv/local/dock/bin/ and is called by autoMS by default.