This plugin should help to set up docking runs with Autodock and view docking results. It has two features:
- Setup of a docking grid for Autodock with PyMOL.
- View the docking results.
you can download it manually
Watch Dan Seeliger's autodock plugin tutorial.
- The Autodock tools, does not like funny atoms names like "C1, N13, O28" and so on. Rename them! See example 1.
- 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/you/another/pymol/Pymol-script-repo/modules/autodock_tools/AutoDockTools/Utilities24 autogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_42/autogrid4 autogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_42/autodock4 vina executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_vina/vina Working Directory: /home/you/another/pymol/workingdir
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
Ligands can not be in alternative configuration. Create by: create ROC_A, 1HXB and resn ROC and alt a .
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 (firstname.lastname@example.org) 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 email@example.com 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.
|This code has been put under version control in the project Pymol-script-repo|