AutoDock Examples and Test Systems

In order to use this test system, you will need to have obtained AutoDock and installed it - see How To Obtain AutoDock for more details.

3PTB: Benzamidine docking to beta-Trypsin

3PTB.tar.gz (4.3 MB)
This Gnu-zipped tar file contains all the files necessary to reproduce the benzamidine/beta-trypsin docking results reported in the JCAMD paper on AutoDock 2.4. It includes the grid parameter file (GPF), the macromolecule PDBQ file, the field and grid maps, the docking parameter file (DPF) set up for Simulated Annealing, and two docking log files (DLG), one which contains the lowest energy docking reported in the paper, and the second is a recent test run to ensure that all the necessary files were present. You can use these files to test that your installation of AutoDock is correct, and also to check against your own efforts in generating the same files. Click on the above link to download the compressed tar file, then type gunzip 3PTB.tar.gz, followed by tar xvf 3PTB.tar: this will create a directory called 3PTB and extract each of the files into here.

Note you will need gunzip, available from the GNU Project in the gzip-1.2.4.tar package.

Note also that earlier versions of the 3PTB.tar.gz examples were used with AutoDock version 2.4, and the DPF supplied was set up for Simulated Annealing (SA). SInce this was the only search method, when we introduced new search methods in AutoDock 3.0, we introduced two new commands, "simanneal" and "analysis", which must now be included in SA-based DPFs. The former command tells AutoDock to run the simulated annealing dockings (as many as the "runs" command specifies), and the latter tells AutoDock to run the conformational clustering after the dockings have completed.

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