FAQ2019-08-01T14:40:38+00:00

Frequently-Asked Questions about the AutoDock Suite

FAQ

Where do I set the AutoDock 4 force field parameters?2019-03-18T21:11:48+00:00

The “parameter_file” command allows you to specify a new parameter library file that contains the various force field parameters.  In most cases, you will not need to modify these values, but you can make changes if you have special needs for your application.

The standard AutoDock 4 parameters are in the file “AD4_parameters.dat” which can be found in the “autodocksuite-4.n.m/src/autodock-4.x.y” directory of the AutoDock 4 distribution, where n and m are the major and minor version numbers of the AutoDock Suite, and x and y are the major and minor version numbers of AutoDock. These are the default values that are “baked in” to AutoGrid 4 and AutoDock 4, and are the values that will be used if you do not specify your own parameter file explicitly in your GPF or DPF with the “parameter_file” command.

You can add new atom types and parameters to this file, or modify the existing ones.  Please refer to the AutoDock4.2.6_UserGuide for information on the parameters and format of the file. If you come up with new or modified parameters, we would like to know about them, so we can incorporate them in future releases.  Thanks!

Can AutoDock be used for “Blind Docking”?2019-03-18T21:15:21+00:00

AutoDock can be used when the structure of the ligand and the protein are both known, but the location of the binding site is unknown.  This is often referred to as “blind docking.” This is a challenge because you need to set up the dockings to search the entire surface of the protein (or other macromolecule) of interest. This can be achieved using AutoGrid to create very large grid maps, with the maximum number of points in each dimension, and if necessary, creating sets of adjacent grid map volumes that cover the macromolecule. The third-party tool BDT can be used to set up such sets of grid maps.

You can also use AutoLigand to predict the probable binding sites on a protein surface, and limit docking simulations to those locations.

Several laboratories have used AutoDock to perform blind docking, for example:

  1. Hetenyi, C. and van der Spoel, D. (2002) Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Science, 11(7): 1729-1737.
  2. Kovacs, M., Toth, J., Hetenyi, C., Malnasi-Csizmadia, A., and Sellers, J.R. (2004) Mechanism of blebbistatin inhibition of myosin II. Journal of Biological Chemistry, 279(34): 35557-35563.
  3. Bikadi, Z., Hazai, E., Zsila, F., and Lockwood, S.F. (2006) Molecular modeling of non-covalent binding of homochiral (3S,3 ‘ S)-astaxanthin to matrix metalloproteinase-13 (MMP-13). Bioorganic & Medicinal Chemistry, 14(16): 5451-5458.
  4. Hazai, E., Bikadi, Z., Zsila, F., and Lockwood, S.F. (2006) Molecular modeling of the non-covalent binding of the dietary tomato carotenoids lycopene and lycophyll, and selected oxidative metabolites with 5-lipoxygenase. Bioorganic & Medicinal Chemistry, 14(20): 6859-6867.
  5. Hetenyi, C. and van der Spoel, D. (2006) Blind docking of drug-sized compounds to proteins with up to a thousand residues. FEBS Letters, 580(5): 1447-1450.
  6. Iorga, B., Herlem, D., Barre, E., and Guillou, C. (2006) Acetylcholine nicotinic receptors: finding the putative binding site of allosteric modulators using the “blind docking” approach. Journal of Molecular Modeling, 12(3): 366-372.
Is there a graphical user interface to AutoGrid and AutoDock?2019-03-18T21:18:47+00:00

ADT (also known as AutoDockTools) is a graphical user interface to help you set up AutoGrid map calculations, AutoDock dockings, and analysis of results.  ADT is available as part of MGLTools.
How do I join the AutoDock Mailing List?2019-03-18T21:21:16+00:00

You can subscribe to the ADL by going to the ADL Info Page; you will need to give a valid email address, create a password, and decide if you want your messages to be sent as a daily digest or not.

About the AutoDock mailing list

This list is intended for novice and expert users of the ligand-protein and protein-protein docking software AutoDock, AutoGrid and ADT (AutoDockTools). This list will provide a forum for users to share experience, to ask questions about things not covered in the documentation, and hopefully, to get answers to these questions. Questions may range from technical to scientific, but should be about docking molecules using AutoDock and its associated programs and utilities. Suggestions for new features are also welcome. Announcements of new software versions and functionalities will be made on this list. In general, bugs should not be reported here but entered into our Bugzilla database. Just go to http://mgldev.scripps.edu/bugs/ and click on the “Open a new Bugzilla account” link.

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