Autodock plugin

Description

This plugin should help to set up docking runs with Autodock and view docking results. It has two features:

1. Setup of a docking grid for Autodock with PyMOL.
2. View the docking results.

Installation

you can download it manually

1. Download plugin
2. PyMOL > Plugin > Install Plugin
3. MGLTools/AutoDockTools
4. AutoDock4.2
5. AutoDock Vina

Tutorial Video

Watch Dan Seeliger's autodock plugin tutorial.

Author

Daniel Seeliger

Important

1. The Autodock tools, does not like funny atoms names like "C1, N13, O28" and so on. Rename them! See example 1.
2. Ligands can not be in alternative configuration. Create by: create ROC_A, 1HXB and resn ROC and alt a . See example 2.

Example 1 - Rename of funny atom names

Read about the protein here: http://www.proteopedia.org/wiki/index.php/3ig7
The example of video http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html
Note, that the module "prepare_ligand4.py" does not like funny names of atoms, so we have to rename them

reinitialize 
fetch 3IG7, async=0
#load 3ig7.pdb, 3IG7
create cdk2, 3IG7 and polymer
create EFP, 3IG7 and organic and not resn ACE
delete 3IG7
 
hide everything, all
#h_add cdk2
#h_add EFP
show_as cartoon, cdk2
show_as sticks, EFP
util.cbay EFP
 
python
# The module "prepare_ligand4.py" does not like funny names of atoms, so we have to rename them
Ligand_prop = []
cmd.iterate("EFP", "Ligand_prop.append((resi, resn, name, elem, ID))")
for resi, resn, name, elem, ID in Ligand_prop:
    print("resi %s, resn %s, name %s, elem %s, ID %s"%(resi, resn, name, elem, ID))
    cmd.alter('%s and id %s'%(resn,ID),'name=%s%s%s'%('"',elem,'"'))
# To see the change, we rewrite the list.
Ligand_prop = []
cmd.iterate("EFP", "Ligand_prop.append((resi, resn, name, elem, ID))")
for resi, resn, name, elem, ID in Ligand_prop:
    print("resi %s, resn %s, name %s, elem %s, ID %s"%(resi, resn, name, elem, ID))
python end
select flexible, byres cdk2 within 3.5 of EFP
show sticks, flexible
util.cbag flexible
disable flexible

Open the Autodock/Vina plugin. Set executable to folders:

Autodock Tools: /home/tlinnet/Software/pymol/Pymol-script-repo/modules/autodock_tools/AutoDockTools/Utilities24
autogrid4 executable: /home/tlinnet/Software/pymol/Pymol-script-repo/modules/autodock_42/autogrid4
autogrid4 executable: /home/tlinnet/Software/pymol/Pymol-script-repo/modules/autodock_42/autodock4
vina executable: /home/tlinnet/Software/pymol/Pymol-script-repo/modules/autodock_vina/vina
Working Directory: /home/tlinnet/pymol

Enlarge the window and click Save Plugin Configuration file.

Click tab Grid settings. In Calculate Grid Center by Selection, write EFP.
Try clicking Wired Box in top right, and then Show Box, Hide Box, Cylindric Box, Show Box.
Then push Select binding site. In PyMOL, write

show sticks, binding_site
cmd.disable("binding_site")
hide sticks, binding_site

Click tab Receptor. Mark cdk, and click Generate Receptor.
Click cdk2 to the "right", and see where the files are located.
Click tab Ligands. Mark EFP, and click EFP in the Ligand list. Here is the files stored. Click Generate Ligand
Click tab Docking, and click Run Vina. Wait 3-5 minutes, until Writing output ... done.
Click tab View poses, Browse to EFP.docked.pdbqt. Click Load, Show best 10. Experiment with "Display options, and click the candidates"
Congratulations, you did it!

Example 2 - Alternative configurations of a Ligand

Read about the protein here: http://www.proteopedia.org/wiki/index.php/1hxb

reinitialize 
fetch 1HXB, async=0
#load 1hxb.pdb, 1HXB
create HIV-1_PROTEINASE, 1HXB and polymer and not resn ROC
create ROC_A, 1HXB and resn ROC and alt a
create ROC_B, 1HXB and resn ROC and alt b
delete 1HXB

hide everything, all
#h_add cdk2
#h_add EFP
show_as cartoon, HIV-1_PROTEINASE
show_as sticks, ROC_A or ROC_B
util.cbay ROC_A
util.cbap ROC_B

select flexible_A, byres HIV-1_PROTEINASE within 3.5 of ROC_A
select flexible_B, byres HIV-1_PROTEINASE within 3.5 of ROC_B
show sticks, flexible_A or flexible_B
util.cbag flexible_A or flexible_B 
disable flexible_A or flexible_B

References and LICENSES

If you used AutoDock Vina in your work, please cite:
O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461

LICENSE of MGLTOOLS:

This software is copyrighted by Michel F. Sanner (sanner@scripps.edu) and TSRI.
The following terms apply to all files associated with the software 
unless explicitly disclaimed in individual files.

       MGLTOOLS SOFTWARE LICENSE AGREEMENT.

  1. Grant Of Limited License; Software Use Restrictions. The programs
     received by you will be used only for NON COMMERCIAL purposes.
     This license is issued to you as an individual.

     For COMMERCIAL use done with the software please contact Michel F. 
     Sanner for details about commercial usage license agreements.
     
     For any question regarding license agreements, please contact
             Michel Sanner:
	     TSRI, Molecular Biology Department, TCP 26,
	     10550 North Torrey Pines Road, La Jolla, CA 92037
	     sanner@scripps.edu
	     tel (858) 784-7742
	     fax (858) 784-2341

  2. COMMERCIAL USAGE is defined as revenues generating activities. These
     include using this software for consulting activities and selling
     applications built on top of, or using this software. Scientific 
     research in an academic environment and teaching are considered 
     NON COMMERCIAL.

  3. Copying Restrictions. You will not sell or otherwise distribute commercially 
     these programs or derivatives to any other party, whether with or without 
     consideration.

  4. Ownership of Software. You will not obtain, and will not attempt to 
     obtain copyright coverage thereon without the express purpose written 
     consent of The Scripps Research Institute and Dr. Sanner.

  5. IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY
     FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
     ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY
     DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE
     POSSIBILITY OF SUCH DAMAGE.

  6. THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES,
     INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY,
     FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT.  THIS SOFTWARE
     IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE
     NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
     MODIFICATIONS.