Dock 6.2
Last Modified: 07/31 9:44
Description
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. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.
From: http://dock.compbio.ucsf.edu/Overview_of_DOCK/index.htm
Version
- 6.2
Authorized Users
- circe account holders
Platforms
- circe cluster
Local Documentation
Modules
Dock6 requires the following module file and some prerequisites to run:
- apps/dock/6.2
- Prerequisites: compilers/gcc/4.1.2 openmpi/1.2.6-x86_64-gcc-4.1.2
To run Dock6 on the cluster, ensure that you use module initadd to make the changes persistent. See Modules for more information.
Running dock6.mpi on the Grid
The following script will execute the parallel version of dock6, dock6.mpi. You'll need to set the number of processors to the number you wish to use as well as modify the input and output file parameters to suit your environment:
#!/bin/bash #$ -N job_name #$ -cwd #$ -j y #$ -o output.$JOB_ID #$ -l h_rt=04:00:00 #$ -pe ompi* 4 sge_mpirun /opt/apps/dock-6.2/bin/dock6.mpi -i job.in -o job.out
Local Documentation
Parameter files, the tutorials, and the source code are located in /opt/apps/dock-6.1 under the respective directories
- parameters/
- tutorials/
- src/
More Job Information
See the following for more detailed job submission information:
Reporting Bugs
Report bugs directly to Research Computing: mailto:support@rc.usf.edu
