DOCK

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.

Version

  • 6.5

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

DOCK requires the following module file to run:

  • apps/dock/6.5

Running DOCK on CIRCE/SC

The DOCK user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting a Job

In order to use DOCK, you must agree to the following: “I agree that any public reports or publication of results obtained using DOCK will acknowledge its use by an appropriate citation.” 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/sh
#
#SBATCH --job-name=dock-test
#SBATCH --ntasks=4
#SBATCH --time=01:00:00

#### SLURM 4 processor DOCK test to run for 1 hour.

module purge
module load apps/dock/6.5

mpirun /opt/apps/dock/6.5/bin/dock6.mpi -i dock.in -o dock.out

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./dock-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

  • Parameter files
    • /opt/apps/dock/6.5/parameters
  • Tutorials
    • /opt/apps/dock/6.5/tutorials
  • Source Code
    • /opt/apps/dock/6.5/src

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with DOCK to the IT Help Desk: rc-help@usf.edu