Installed Versions
Installed version: 4.0.1
Latest version: 4.0.1
Description
This desciption of Autdock comes from the Autdock web site.
" AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock actually consists of two main programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid pre-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders. "
License
The following license conditions are taken from the Autodock web site. Please check that site for up to date license conditions.
"AutoDock 4 and AutoGrid 4 are free software, distributed under the GNU General Public License. The C and C++ source code of all the programs is provided, along with ready-to-run executables for several popular computers. If you plan to use AutoDock 4 for commercial purposes we encourage donations to the Olson laboratory to help support further development of the AutoDock 4 suite of programs. Donation information provided on the download page."
You can register to your usage of Autodock and donate here: http://autodock.scripps.edu/downloads/autodock-registration
Running Autodock on the NGS
Autodock may be run from the globus command line, as documented below, or from the GEMLCA P-GRADE portal.
On the web portal there is an example template for running a test run of Autodock, under the "Chemistry" applications category in the portal. This test can also be run on the command line as shown below.
Autodock consists of two executables, autodock and autogrid. These can be accessd via the /usr/ngs/AUTODOCK and /usr/ngs/AUTOGRID scripts passing the same arguments you would normally. For example: "/usr/ngs/AUTODOCK -p 1pgp.dpf -l 1pgp.dlg"
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 autodock in the following example) which will be the working directory.
Any input files required should be copied into the working directory (using gsiscp or gridftp or cp if local to the cluster) into the appropriate directory (/home/xxx/autodock in our example). The test files used in the example below can be found in the /usr/local/NGS/documentation/uee/autodock directory on ngs.wmin.ac.uk.
Example run of the AUTODOCK test on ngs.wmin.ac.uk at Westminster:
To submit the test job on ngs.wmin.ac.uk use the following command (one line ignoring the '\').
globus-job-submit ngs.wmin.ac.uk/jobmanager-pbs \
-x '& (jobType=single)(arguments=-p 1pgp.dpf -l 1pgp.dlg) \
(directory=/home/xxx/autodock) \
(stderr=/home/xxx/autodock/autodockErr.e) \
(stdout=/home/xxx/autodock/autodockErr.o)' \
/usr/ngs/AUTODOCK
Documentation
The online Autodock manuals and FAQs can be found on the Autdock web site here :
Getting help
The NGS cannot offer any scientific support for this package. However, if you believe there is a problem with the installation please contact the NGS helpdesk.
