Chimera Commands Index

Usage:
vina docking  receptor recmodel  ligand ligmodel  options

Like the Chimera AutoDock Vina tool, the vina command runs single-ligand docking calculations with AutoDock Vina. The process can use either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy of the program.

As a shared resource, the web service only allows docking a single ligand with very limited sampling, and the vina command does not include all program options. For access to other options like ligand database search, we recommend downloading the AutoDock Vina program and using it directly. (Other limitations...)

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.
The receptor and ligand structures should be opened as separate models in Chimera and specified with the receptor and ligand keywords, respectively. The entire models containing the specified atoms will be used.

If the receptor contains MSE (selenomethionine) residues, incomplete side chains, or atoms with alternate locations, running Dock Prep beforehand to correct those issues is recommended. The vina command runs AutoDock accessory scripts locally to (further) prepare the structures, such as to add hydrogens if they have not been added already with Chimera.

Docking results will be shown automatically in ViewDock. Please see the AutoDock Vina manual for a description of the output values.

Options

Option keywords for vina can be truncated to unique strings and their case does not matter. A vertical bar “|” designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.

output  name
Pathname (location and filename prefix) of output files. If the run is successful, the following files will be generated: If name is not specified, a temporary filename prefix and location will be used.
prep true | false
Whether to run only the preparation steps, not AutoDock Vina. If true, the output will not include the docking results file.
wait true | false
Whether to wait for the calculation to finish before exiting Chimera. Must be set to true for running vina with Chimera in nogui mode.
The default box in which to sample ligand positions will enclose the entire receptor, with extra space on all sides. If the region of interest is smaller, the desired box center and size should be specified to allow for a more efficient search. Both must be supplied; if only the center or only the box size is specified, it will be ignored.
search_center  x,y,z
In the receptor coordinate system, location of the center of the box in which to sample ligand positions.
search_size  xlen,ylen,zlen
In the receptor coordinate system, dimensions along X, Y, and Z of the box in which to sample ligand positions.
Settings for the receptor preparation script:
r_addh true | false
Whether to add hydrogens in Chimera (see addh) before calling the script. The receptor 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.
r_nphs true | false
Whether to merge charges and remove nonpolar hydrogens. Note AutoDock Vina does not use charges or nonpolar hydrogens, so this setting is not expected to affect results except for the presence or absence of nonpolar hydrogens in the processed receptor.
r_lps true | false
Whether to merge charges and remove lone pairs. Note AutoDock Vina does not use charges or lone pairs, so this setting is not expected to affect results except for the presence or absence of lone pairs in the processed receptor (and there may not have been any lone pairs to start with).
r_waters true | false
Whether to remove water residues.
r_nonstdres true | false
Whether to remove chains composed entirely of residues other than the 20 standard amino acids.
r_nonstd true | false
Whether to remove all residues other than the 20 standard amino acids.
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.
l_nphs true | false
Whether to merge charges and remove nonpolar hydrogens. Note AutoDock Vina does not use charges or nonpolar hydrogens, so this setting is not expected to affect results except for the presence or absence of nonpolar hydrogens in the ligand output files.
l_lps true | false
Whether to merge charges and remove lone pairs. Note AutoDock Vina does not use charges or lone pairs, so this setting is not expected to affect results except for the presence or absence of lone pairs in the ligand output files (and there may not have been any lone pairs to start with).
Docking parameters:
num_modes  N
Maximum number of binding modes to generate (default 9).
exhaustiveness  M
Thoroughness of search, roughly proportional to time (default 8).
energy_range  range
Maximum difference in score (default 3.0 kcal/mol); binding modes with scores not within range of the best score will be discarded.
Executable location:
backend  opal | local
Whether to use an Opal web service (default) or a locally installed executable.
location  opal-URL | local-path
Depending on the backend setting, the URL of the web service (default is the URL for the service provided by the NBCR) or the pathname of the local executable.