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UMBC High Performance Computing Facility
Please note that this page is under construction. We are documenting the 240-node cluster maya that will be available after Summer 2014. Currently, the 84-node cluster tara still operates independently, until it becomes part of maya at the end of Summer 2014. Please see the 2013 Resources Pages under the Resources tab for tara information.
How to run DOCK on tara

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 tara, relevant executables are in the directory
[araim1@tara-fe1 ~]$ ls /usr/cluster/dock/6.3/bin/
For example
[araim1@tara-fe1 ~]$ /usr/cluster/dock/6.3/bin/sphgen
[araim1@tara-fe1 ~]$ /usr/cluster/dock/6.3/bin/grid
[araim1@tara-fe1 ~]$ /usr/cluster/dock/6.3/bin/dock6
Detailed information about running DOCK can be found in the user's manual