Tutorial for Autodock and Autodock Tools I. Establishing Access to the Programs A. Autodock is in /usr/local/Autodock.

The executables are autodock4 and autogrid4. Set up aliases in your .bashrc file: alias autodock3=”/usr/local/Autodock/autodock4” alias autogrid3=”/usr/local/Autodock/autogrid4” B. Autodock tools are in /usr/local/MGLTools-1.5.4. Add to your .bashrc:: alias pmv=’/usr/local/MGLTools-1.5.4/bin/pmv’ alias adt=’/usr/local/MGLTools-1.5.4/bin/adt’ source /usr/local/MGLTools-1.5.4/bin/mglenv.sh The aliases access the main parts of the tools; the last line sets up the Python environment for the tools. II. Preparing the Files A. Two files in Protein DataBank (pdb) format are required for a docking experiment: a structure for the protein and a structure for the ligand. B. In general, the protein structure will be downloaded from the Protein DataBank (www.rcsb.org), and the ligand structure will be created with one of our modeling applications. You should inspect both files using less or a text editor. In the file from the PDB you want to identify any non-protein species that will be removed later. This includes water (HOH) or other solvents, sugars, and so on. Make a list of the types and their abbreviations. Make sure you have a single copy of the protein in the file. Many proteins crystallize as dimers or trimers, with each copy of the protein containing a catalytic site. You must delete all extra chains. There are a few proteins – the HIV protease is one – in which the catalytic site is formed by the interaction of the chains. In this case, keep both chains. In the ligand file, check the column that lists the residue or other structure of which each atom is a part, and make sure that you have the three-letter code for the amino acids (if the ligand is a peptide), or a code of your choice for other ligands. PCModel puts UNK in this column when writing a pdb file. Change this to a three-letter acronym for your ligand so that the ligand can be selected properly for display in a program like JMol.

This will create your two pdb files and a subdirectory containing the results from the docking for analysis. for manipulating the molecule display. Start the ADT by typing ‘adt’ in a shell window in the directory where you have placed your PDB files. “Using AutoDock with AutoDock Tools”. right click on PMV Molecules at the bottom of the window and choose the protein pdb file. For the tutorial.tar. III. Before beginning this section. As displayed. select hsg1. highlight the PDB file for your protein. Or.gz).These files should be in the directory in which you choose to start. You must extract these by typing in a shell window “tar –zxvf filename. creating images. If you are working with the tutorial from the AutoDock web site. this means that multiple files have been combined into one (tar) and compressed (gz). choose Read Molecule. You can color it according to any of several schemes by selecting Color from the main menu bar. the Python molecular viewer. inspect the PDB file to learn what such structures may be present. such as missing bonds or atoms. Load the protein From the File menu. and modifying coordinates (2) A row of buttons for quick access the PMV functions (3) Menus to access AutoDock Tools functions. Figure 1 showsthe ADT interface. Editing the Protein PDB File with AutoDock Tools (ADT) We are going to fix any problems with the PDB files. B. A. C.pdb (1). (4) The molecule viewer window (5) The Dashboard. and click Open. We want to keep only the protein and such cofactors as may be bound to it naturally.gz” (without the quotes. including reading and writing coordinates. and remove extraneous structures such as water molecules. The ADT window has several parts: (1) At the top are menus that access the functionality of PMV. of course). and . the protein appears white.tar. the file as downloaded is both tarred and gzipped (extensions .

Alternatively. choose Select. and then on OK. click on the diamond under “atom” on the dashboard to color by atom type. we remove the waters (those little red dots all over the display). click on All Geometries.choosing any of the schemes listed there. The asterisk is a “wild card”. You now have a pretty picture. It means accept any characters at . (Figure 2) Figure 1 The AutoDock Tools Window C. On the main menu bar. In the widget that pops up. Select From String. A widget pops up (Figure 3): In the Residue entry box. used in case the waters are numbered. Next. type HOH*.

this time meaning “any atom”. again the * is a wild card. you will get a message asking if setting it there is OK. choose Edit. Then type * in the Atom entry box. Then click Dismiss. If the PCOM level is not already set to Atom (yellow button).all following the H. The selected waters will disappear. Click select. Click Continue. Delete AtomSet. Delete. Figure 2. You should now see all of the waters marked with small yellow crosses (Figure 4). Click Yes. . Protein hsg1 Loaded and Colored On the main menu bar. ADT will ask if you really want to do this.

however.Repeat this process for any other small molecules you need to get rid of (check your pdb file!). are important in binding ligands. Hydrogens. such as other solvents like isopropyl alcohol (IPA). Figure 3 The Select from String Widget D. N-acetylglucosamine (NAG). (2) Hide the protein by clicking the little gray box under “Show/Hide”. you will choose Polar Only in the widget that pops up. hence most PDB files do not include them. Preparing the Ligand File with ADT In this section information is added to the ligand pdb file to select bonds about which segments of the ligand will be rotated. If you wanted to interrupt processing at this point. particularly those that can hydrogen bond. This set of selections will add hydrogens to backbone N. X-ray crystallography usually does not locate hydrogens. . IV. But hydrogens. we are going to add charges and AutoDock atom types. and renumbering OK. Add. You will see them appear. Charges are added. (1) Choose Edit. and other relics of the isolation and crystallization procedures. using Method noBondOrder. you could choose File -> Save -> Write PDB. Whole chains similarly can be deleted using the Chain entry box. using the Kollman scheme for peptide ligands and Gasteiger charges for other structures. Usually. and to amine and hydroxyl side side chains.

Before beginning. turn off display of the protein structure: click the Show/Hide Molecule button. Figure 4 Water Molecules Selected for Deletion A. and then click the button next to the name of your protein. Click the show/Hide button again to close the widget. Load the Ligand .

B. The widget offers you several general selections of rotatable and non-rotatable bonds. this is called the Rigid Root. (2) Next. A central benzene ring is a popular choice. marking the choice. making sure all hydrogens are present. In the tutorial. this is ind. normally this is a poor choice . select Ligand -> Torsion Tree -> Choose Torsions. Open Molecule.(1) From the tan menubar just above the view window select: Ligand. ADT tries to select a Root with the minimum number of rotatable branches. Summary of Actions on Ligand: ADT has done its job of assigning charges.pdb After a pause. (1) On the tan menubar. select Ligand -> Torsion Tree -> Detect Root. Then choose the file containing your ligand. and click Open. (a) making peptide backbone bonds non-rotatable locks in the secondary structure of the peptide. A small green dot will appear. a message will pop up. TORSDOF is torsional degrees of freedom. The Torsion Count widget appears (Figure 6). Selecting Rotatable Segments The initial step is selecting a set of atoms with respect to which other groups of atoms will be rotated. looking something like this (Figure 5) Figure 5. Click the file types button on the widget that appears and select PDB files. and detecting planar carbons in rings. Input Molecule.

Figure 6.(b) At laboratory temperatures. The Torsion Count Widget Rotatable bonds also may be selected individually. or the largest possible number. If you do this. Setting Number of Torsions in Ligand . to select rotatable bonds that move the fewest possible atoms. click this button. be careful! Bonds within ring MUST be non-rotatable. (3) It is possible. the barrier to rotation around the CO-N bond of an amide is too high to permit free rotation. but optional. Figure 7. if the ligand has amide functions. and no more than 32 rotatable bonds may be selected. If you wish to do this. Select Ligand -> Torsion Tree -> Set Number of Torsions (Figure 7).

select Ligand -> Output -> Write PDBQT. (For the tutorial.pdbqt. and the T that torsions have been selected.pdbqt.You can see how this works by entering different numbers in the data window and alternately clicking the fewest/most buttons while watching the molecule in the display window. When finished manipulating the torsions. Click Save. Enter a the name using the extension . . click Done.) The Q signifies that charges have been added. this will be ind. Then hide the root marker and ligand: click on its gray Show/Hide marker. Ligand with Torsions Selected (4) To save the modified file. The display now looks like this (Figure 8): Figure 8.

) Six bonds are now rotatable. the Selected box should show “2 Residues” (3) Now define the rotatable bonds in the selected residues: Flexible Residues > Choose Torsions in Currently Selected Residues. Select Flexible Residues -> Input -> Choose Macromolecule. Flexible Residues in the Protein Beginning with AutoDock 4. Torsion Count Widget for Flexible Residues in Protein In the display.V. Clear the Selected box by clicking on the red dots. (You may have to rotate the display in order to see both residues. You will get a message that Gasteiger charges and AutoDock atom types have been added. . click OK. B. and the Torsion Count widget appears (Figure 9): Figure 9. Select the residues to be flexible: Select -> Select from String. (2) At the bottom of the Dashboard. type ARG8 in the Residue box. A. Redisplay hsg1 by clicking its gray Show/Hide marker. and then Dismiss. Working on the tutorial. (1) If you are asked whether you want to merge the non-polar hydrogens. click on the bond between CA and CB in each residue to inactivate it. Then click on sg1 in the widget that appears and click on Select Molecule. Click Close. (1) Click Clear Form to remove the waters. rather than treating it entirely as a rigid shape. support was added for making a portion of the protein flexible. Click Add. Everything except the selected residues disappears.

and choose ind. (2) Use the thumbwheels to set the numbers of points to 60. but save the Rigid PDBQT as hsg1_rigid. click Yes. You can use the View menu on the Grid Options widget to control the display of the blue box. will vary from enzyme to enzyme. of course. use Grid -> Set Map Types -> Directly to check that all atom types in your ligand are represented. You can do this by clicking and dragging on the wheel. click OK. B. It looks like this (Figure 10) You will also notice that a blue and red box has appeared on the main display. 60. Before going on. or by right-clicking and entering the number in the box that appears. Further Preparation of the Protein Files The next step is to prepare the grid files. Locate and click on hsg1_rigid. A. If your ligand file is still open. If you rotate the display. Load the first protein file: Grid ->. you can see that the box is 3-dimensional (Figure 11). for example.pdbqt. . Remove the original version of hsg1: Edit -> Delete -> Delete Molecule. These numbers.pdbqt. (5) Repeat. ADT checks the charges. If it asks if you want to retain the existing charges. If not add the ones that are missing and close the widget. Dismiss any other messages that may appear. If it is not open use: Grid -> Set Map types -> Open Ligand. changing it to display as lines. and click Dismiss. C.(4) Save the flexible residues: Flexible Residues -> Output -> Save Flexible PDBQT. If you get a warning about non-integer charges. (1) Open the Grid Options widget: Grid -> Grid Box. NOTE: The official tutorial at this point suggests that the AutoGpf Ligand widget will open when you select the ligand. select the ligand: Grid -> Set Map Types -> Choose Ligand. and 66. VI. They are derived by inspecting the pdb file and locating the coordinates of the active site residue(s).pdbqt in the File Browser window and Slick Save. click on Delete Molecule. Select ind. This is the box within which we are going to search.pdbqt. Type hsg1_flex. Choose hsg1. Macromolecule -> Open.. the Grid Box widget allows you to set the size of the box. its location. (3) This will center the grid box on the active site of the HIV-1 protease. and the number and spacing of the points within it that will be tested. Both your protein and your ligand are now displayed. It does not.

Figure 10. You are now ready to run AutoGrid. Parameter filename should be displayed automatically. The Grid Options Widget Use the Browse button to navigate to /usr/local/AutoDock/autogrid4. (1) Autogrid can be run from within AutoDock Tools. Choose Run -> AutoGrid from the tan menu. . Then write the grid point file: Grid -> Output -> Save GPF.(4) Use the File menu on the box to Close Saving Current.gpf”. Browse to it if it is not. Name the file “hsg1. The log filename will be generated from the parameter filename. and the run command in the last box will be displayed. The widget (Figure 12) appears. C.

we prepare the Docking Parameter file. and allow you to terminate it if desired. as seen in the directory listing below (Figure 13). Figure 11. AutoGrid will generate a series of Grid Parameter Map files. A small process manager widget will appear that will show you that AutoGrid is running. Next. . The Grid Box D.(2) Run the program by pressing Launch.

Directory Listing Showing Maps Created by AutoGrid. which gives 250. click Open. (2) Next.(1) From the tan menu. and select “hsg1_rigid. choose Docking -> Macromolecule -> Set Rigid Filename. simply click Accept. choose Docking -> Search Parameters -> Genetic Algorithm.pdbqt”. Figure 12. Select the Short setting. (3) Set the Flexible Residues file: Docking -> Macromolecule -> Set Flexible Residues Filename. The Run AutoGrid Widget (3) To set the search parameters.000 energy evaluations. and select “ind” A panel appears (below) that allows you to set the initial position of the ligand and initial values for the dihedrals. Another widget appears (below). Click Accept. and choose “hsg1_flex. For the tutorial.pdbqt”. . Figure 13. choose Docking -> Ligand -> Choose.

The dpf File Widget .Figure 14.

it printed the message: “/usr/local/Autodock/autodock4 Successful Completion on “karplus” If you used an alias other than “autodock” for the AutoDock executable. gpf. (Figure 15) (5) Set the output filename and the choice of genetic algorithm. So then I opened a shell window. E.glg & And the program ran properly. Docking -> Docking Parameters. Type in “ind. When it finished. dpf. In principle. Docking -> Output -> Lamarckian GA. ligand. . AutoDock ran long enough to write the starting conditions into the log file. moving into the directory with the necessary files. and typed at the command line: autodock –p ind.dpf –l ind. Running AutoDock AutoDock must be run in the directory where the macromolecule. and map files are located. and quit.(4) Choose the random number generator.dlg” and click save. When I did this. replace “autodock” in the above command with whatever alias you used. Just go with the defaults in this tutorial. AutoDock can be started from the Run menu in ADT just the way you started AutoGrid.

The Genetic Algorithm Widget Figure 16. Choosing the Random Number Generator. .Figure 15.

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