** Requires installing AutoDock Vina locally **
As of 4/30/2020, the AutoDock Vina web service from the National Biomedical Computation Resource (NBCR) has been discontinued. This Chimera tool will no longer work unless you download and install the AutoDock Vina program on your own computer and then in this tool, change the Executable location to Local and enter its location.
|However, this tool only allows docking a single ligand with very limited sampling. For a more intensive sampling of space, as needed for most research applications, or access to other options such as ligand database search, we recommend running the locally installed copy of AutoDock Vina directly (not using Chimera). Chimera can still be used to view the output. Other limitations are given below.|
The AutoDock Vina tool allows running ligand-receptor docking calculations with AutoDock Vina. The results are shown automatically in ViewDock. See also: AddH, Dock Prep
Users should cite:
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Trott O, Olson AJ. J Comput Chem. 2010 Jan 30;31(2):455-61.
There are several ways to start AutoDock Vina, a tool in the Surface/Binding Analysis category. It is also implemented as the command vina.
The receptor and ligand structures should be opened as separate models in Chimera. If the receptor structure contains MSE (selenomethionine) residues, incomplete side chains, or atoms with alternate locations, running Dock Prep beforehand to correct those issues is recommended. The AutoDock Vina tool runs AutoDock accessory scripts locally to (further) prepare the structures, such as to add hydrogens if they have not been added already with Chimera.
Output file - location and filename prefix for output files. If the prefix is name, the files generated by a successful run will be:
Ligand - the model to use as the ligand (choose from pulldown menu)
Receptor search volume options - definition of the box in which to sample ligand positions
Center: [x][y][z] - box center in the receptor coordinate system; can be edited directly
Size: [x][y][z] - box dimensions along X, Y, and Z in the receptor coordinate system; can be edited directly
Receptor options - settings for the receptor preparation script:
Ligand options - settings for the ligand preparation script (see limitations):
The ligand prep script will check for hydrogens and add them if they are missing. AutoDock Vina needs the polar (potentially H-bonding) hydrogens to identify atom types for scoring purposes.
Advanced options - docking parameters
The docking results will be opened as a new model (with multiple submodels) and shown automatically using ViewDock. Please see the AutoDock Vina manual for a description of the output values.
Docked peptides and other multiresidue ligands appear fragmented. AutoDock Vina changes the order of the atomic coordinates based on the branching of rotatable groups, and this scrambles multiresidue ligands such as peptides. The misordering of the atoms leads to an incorrect bonding pattern in Chimera. For all-atom representations (stick or ball-and-stick but not ribbons), there is a workaround: deleting all the bonds and adding them back based on distances. For example, if the docking results are opened as model #5, commands:
~ribbon #5...and then adding all reasonable bonds among selected atoms using the Adjust Bonds section of Build Structure. Another workaround is to make the ligand a single residue before docking, but that would not allow display as a ribbon either.
Rings in ligand broken by misidentification of rotatable bonds. The ligand preparation script may identify bonds in rings as rotatable, resulting in impossible (“broken”) ring conformations. Because the workflow of the Chimera interface does not allow intervention between ligand preparation and docking, and there is no option to keep the ligand rigid, there is no workaround other than to prepare input files and run AutoDock Vina directly (not using Chimera). This ring-opening problem has been observed with prolines and may occur with other rings as well.