You are now ready to run DOCK . Since dock can use a substantial amount of CPU time, it is a good idea to check whether there are other jobs running on the same machine. Consider any other users sharing your computers when deciding whether to start more than one run at a time. Be aware of any policies your site has regarding submitting background jobs.
The easiest way to select dock parameters is to run dock interactively. Do this by typing dock -i dock.in. You will be prompted for a value for each parameter. Any value you enter will be stored in the file dock.in. This file does not need to exist beforehand. If it does exist, then dock will extract all the relevant parameters it can find from the file. For each parameter, dock will supply a default value. If you want to use the default value, just hit return. The following tables list recommended values for running dock in two different ways: first to dock a single ligand, and second to dock a database of ligands. If you are viewing this manual on-line, then click on any of the keywords to view the reference entry for it.
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Enter the ligand MOL2 file name here (including the directory path if this file is not in the current directory). |
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first try 10 to make sure everything is working, then set it to a number larger than the number of molecules in input file |
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If you happen to enter the wrong value for any parameter and wish to change it, then you may edit the dock.in file directly and modify the parameter value. Once all parameters have been entered, dock should begin the calculation and the dock.in file is complete. You may kill the process with a CTRL-C and relaunch the process in background by typing "dock -i dock.in -o dock.out&". If you would like to run dock multiple times from the same directory, then you may use a different name for dock.in and dock.out. Just be sure to change the names of the output files inside the new dock.in file so that two processes don't end up overwriting each other's output files.
Check a few minutes after you start the run to be sure that it is still going; if it has stopped, look for mistakes in the input. Beginners should check disk usage occasionally while the job is running, just in case the program is creating incredibly large files which might overflow the available space.
During a database search run (which can take anywhere from hours to days to weeks to finish), you can follow dock's progress through the database by inspecting the *.info file.
In database search mode of dock (when multiple_ligands, orient_ligand, and rank_ligands are selected), dock periodically saves information necessary to restart the search from its current location in the database in a *.rst file. If there is a power failure or the system crashes, you can set up a new run to start where the last one was stopped. First, make a copy of dock.out so that status of the previous run are saved. Then relaunch the job using the -r flag at the command line. (Do not change the remaining files, since dock needs them to restart successfully.) When the restarted run finishes, the sorted list of ligands in the output file will include the top scorers from the entire database.
Dock puts the resulting molecule orientations in a file for each type of scoring function used. The scores are given in the comment records at the beginning of each molecule record. If you have selected MOL2 format for your output files and your graphical viewer does not read this format, then convert the file to PDB by typing dock -i dock_nrg.mol2 -o dock_nrg.pdb.
Depending on your particular project, you might be interesting in any one or several of the following post-docking techniques: