HowTo:autodock

AutoDock

This is a short help file on the AutoDock suite of automated docking tools. This software allows the prediction of how small molecules bind to a receptor site of known structure. Since AutoDock is a rather sophisticated set of tools, this FAQ cannot replace the manual. It is rather meant as a starting point for using AutoDock, and to answer questions that are specific to our installation of the software.

Features AutoDock actually consists of three separate programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein AutoGrid pre-calculates these grids AutoTors sets up which bonds will be treated as rotatable in the ligand. AutoDock has been widely used and there are many examples of its successful application in the literature (see References). It is very fast, provides high quality predictions of ligand conformations, and good correlations between predicted inhibition constants and experimental ones. For a more complete list, see the official AutoDock homepage and click on "capabilities". Location of the program and setup The present version of AutoDock is 4.2.5, which is the latest as of early 2014. Before you can access AutoDock, you need to read our license agreement and sign a statement that you have done so and will abide by it. See the last section for details. The AutoDock program is located in the directory /opt/autodock. To access it, you have to do a setup using the usepackage facility: use autodock305 Of course, this may be included in your setup files (probably .bash_profile), so you don't have to type them each time you run AutoDock.

Running NWChem from a command line NAMD requires a number of input files to run. These include: A so-called "configuration file" that declares the initial configuration for a molecular dynamics run, the force field files, number of steps in the simulation, etc. A coordinate file that gives the coordinates of the participating atoms or molecules. A parameter file declaring bond-lengths, angles, dihedrals, non-bonded parameters etc. A force-field file declaring parameters associated with atomic and molecular interactions. Details about the supported format of these input files can be found in the NAMD User's Guide. NAMD supports several running modes. In the simplest case, it can be run in serial mode by typing: namd2 config_file where config_file is the configuration input file mentioned above. It is recommended to give the configuration file the file extension .namd to enable consistent naming of the output files. These will be generated automatically, and the progress of the program run will be tracked on the screen. NAMD is also able to run in parallel mode. For our shared-memory systems, it is easiest to run it by specifying the number of threads through the +p option: namd2 +pN config_file if N threads are requested. Submitting (parallel) NAMD jobs Only short test jobs of application software can be run interactively on HPCVL machines. Production jobs must be submitted via the scheduling software Grid Engine. For usage of this software, please consult our Grid Engine FAQ. In most cases, you will be running NAMD production jobs in parallel mode. This means that you need to specify a number of CPUs that should be reserved to run each independent NAMD thread. This is done in a Grid Engine submission script: #!/bin/bash #$ -S /bin/bash #$ -q abaqus.q #$ -l qname=abaqus.q #$ -V #$ -cwd #$ -M {email address} #$ -m be #$ -o {screen output file} #$ -e {screen error file} #$ -pe shm.pe {number of threads} namd2 +p$NSLOTS {namd configuration (input) file} The items in the template that are enclosed in {} be replaced by the appropriate values. Lines that start with "#$" contain information for Grid Engine. The "#$ -V" line tells GE to inherit the shell setup from the calling shell, for instance the $PATH variable. It is important to remember that you need to set up NAMD by issuing the "use namd" command before submitting the above script. "#$ -cwd" tells the system to start from the current working directory. "#$ -M" lets the system know you email address, so it can notify you when the job starts and ends. The "#$ -o" and "#$ -e" lines are there to define files that capture output that would go to the screen in an interactive run, coming from the program and the system, repsectively. Finally, the "#$ -pe" line serves to define the number of CPUs to be reserved. The number you insert here will be reused through the environment variable $NSLOTS, so that you do not have to type it again in the namd2 command line. Note that the name of the configuration file that replaces "configuration file" in the script template, should have file extension .namd, just as in the interactive run. Once you have a proper script file (let's call it namd.sh) you can submit your production job by typing qsub namd.sh The Grid Engine will take care of the rest.

Licensing NAMD is free for non-commercial use, but it is licensed. As with other licensed software, we ask our users to read through the license agreement that exists between the University of Illinois and HPCVL, and to sign a statement that they agree to abide by the terms of the license. The main issue in the NAMD case is that usage has to non-commercial. Once we have received the signed statement (FAX to (613) 533-2015 or scan/email to admin@hpcvl.org), we will enter the user to a Unix group namd which enables access to the software. More Information NAMD requires practice to be used efficiently. We cannot explain it use in any detail here, but Complete documentation for the program is available in the form of the User's Guide, which is an absolute must-have if you want to use this program. Check out the NAMD website. They feature a very useful FAQ and even a tutorial. There is an active NAMD Mailing List. Send to cac.help@queensu.ca. We're happy to help.