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.

DOCK Home Page

Version

6.5

Authorized Users

CIRCE account holders

Platforms

CIRCE cluster

Running DOCK jobs on CIRCE

Modules

Dock6 requires the following module file and some prerequisites to run:

apps/dock/6.5

To run Dock6 on the cluster, ensure that you use module add apps/dock/6.5 in your submit script. See Modules for more information.

Running dock6

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

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 ./abinit-test.sh

You can view the status of your job with the “squeue -u <username>” command

Additional Documentation

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

DOCK

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