How to run DOCK on taki

Note: This page has not been updated to reflect the move to taki from maya.

Introduction

DOCK addresses the problem of “docking” molecules to each other. In general, “docking” is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. To run the DOCK software on maya, relevant executables are in the directory

[araim1@maya-usr1 ~]$ ls /usr/cluster/dock/6.3/bin/

For example

[araim1@maya-usr1 ~]$ /usr/cluster/dock/6.3/bin/sphgen
[araim1@maya-usr1 ~]$ /usr/cluster/dock/6.3/bin/grid
[araim1@maya-usr1 ~]$ /usr/cluster/dock/6.3/bin/dock6

Detailed information about running DOCK can be found in the user’s manual