dock
| Description | ||
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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. |
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| Site | Version (Latest: v6.1) | Notes |
| ngs.rl.ac.uk | v6.1 | 64 bit |
License
The following license conditions are taken from the Dock web site. Please check that site for up to date license conditions.
"Dock is available free of charge for academic institutions, but there is a licensing fee for industrial organizations."
The NGS requests that you register online so that there is a record of your use with the developers.
You can register to use Dock here http://dock.compbio.ucsf.edu/Online_Licensing/index.htm then contact the NGS helpdesk to access the software on the NGS.
Running the Dock on the NGS (General)
There a multiple ways in which jobs can be launched on the NGS
- Submission Using UI/WMS
- NGS Web Portal Submission
Submission Using Globus
On the web portal there are three example templates for running each of the three parts/executables of the MPI-demo Dock tutorial (showbox, gird, dock6.mpi executables), under the "RAL Chemistry" applications category in the portal. These three parts can be run on the command line as below.
There are many programs that come with the Dock package, all (including the mpi versions of the codes) are accessed by using the /usr/ngs/DOCK script with the first argument being the executable name. For example
"/usr/ngs/DOCK dock6.mpi -i mpi.in -o mpi.out"
The list of available executables that can be specified is below:
The string 'xxx' in the subsequent commands is to be replaced with your id on NGS.
You can also create a directory within your home directory (named mpi_demo in the following examples) which will be the working directory.
Any input files required should be copied onto ngs.rl.ac.uk (using gsiscp or gridftp or cp if local to the cluster) into the appropriate directory (/home/xxx/mpi_demo in our example).
Compilation Information for ngs.rl.ac.uk
If you need information on how this application was compiled please contact the NGS support centre.
Further Information
The online dock manuals can be found on the Dock web site here : http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm
There are example test input files available (eg the mpi_demo subdirectory) above, and others at ngs.rl.ac.uk:/apps/dock/examples
Applications Support
The NGS cannot offer scientific support for applications. However if you require further information or believe there is something wrong with the installation, please contact the NGS support centre.
Acknowledgements
Please note: When publishing work based on use of the NGS, users should acknowledge both the authors of any programs used (see the individual program web sites, or contact the authors directly) and the NGS directly using the following line:
"The authors would like to acknowledge the use of the UK National Grid Service in carrying out this work"
This line must also accompany any use of the NGS logos.
