boinc-autodock-vina

This application works with ZIP archive that contains data to be calculated. Input ZIP archive must contain JSON file that describes the input data and other files that are used in docking process and described in the input JSON file.

JSON schema

This file supports next parameters:

• receptor - paths to receptor to be processed. This is a optional strings parameter. Only PDBQT format is supported. This file should not have absolute path. Can't be used together with maps parameter. Either receptor or maps should be specified for vina and vinardo scoring function. This parameter is not allowed for ad4 scoring function.
• ligand - list of paths to ligands to be processed. This is an optional list of strings parameter. Either ligand or batch parameter should be specified.
• flex - path to PDBQT file with flexible side chains, if any. This file should not have absolute path. This is an optional string parameter for vina and vinardo scoring functions. This parameter is required for ad4 scoring function.
• batch - paths to PDBQT files with batch ligands. This file should not have absolute path. This is an optional list of string parameters. Either ligand or batch parameter should be specified.
• scoring - scoring function (ad4, vina or vinardo). This is an optional string parameter. Default function is vina.
• maps - path to the folder with affinity maps including prefix. This is an optional string parameter. E.g. for the folder with maps .\maps\1iep_receptor.A.map and .\maps\1iep_receptor.C.map should be provided as maps\1iep_receptor. If this parameter is not specified, then center_x, center_y, center_z and size_x, size_y, size_x parameters should be specified to generate affinity maps. Can't be used together with receptor parameter. Either receptor or maps should be specified for vina and vinardo scoring function. This parameter is required for ad4 scoring function.
• center_x - X coordinate of the center (Angstrom). This double parameter is ignored when maps parameter is specified.
• center_y - Y coordinate of the center (Angstrom). This double parameter is ignored when maps parameter is specified.
• center_z - Z coordinate of the center (Angstrom). This double parameter is ignored when maps parameter is specified.
• size_x - size in the X dimension (Angstrom). This double parameter is ignored when maps parameter is specified.
• size_y - size in the Y dimension (Angstrom). This double parameter is ignored when maps parameter is specified.
• size_z - size in the Z dimension (Angstrom). This double parameter is ignored when maps parameter is specified.
• out - path to output model file (PDBQT). This file should not have absolute path. This is an optional parameter.
• dir - path to output directory when: (1) in batch mode, (2) ligand parameter is specified and contains more than 1 file. This directory should not have absolute path. This is an optional string parameter.
• write_maps - output filename (directory + prefix name) for maps. Parameter force_even_voxels may be needed to comply with map format. This is an optional string parameter. E.g. for the folder with maps .\maps\1iep_receptor.A.map and .\maps\1iep_receptor.C.map should be provided as maps\1iep_receptor.
• no_refine - when receptor is provided, do not use explicit receptor atoms (instead of precalculated grids) for local optimization and scoring after docking. This is an optional boolean parameter. Default value is false.
• force_even_voxels - calculated grid maps will have an even number of voxels (intervals) in each dimension (odd number of grid points). This is an optional boolean parameter. Default value is false.
• weight_glue - macrocycle glue weight. This is an optional double parameter. Default value is 50.000000.
• seed - explicit random seed. This is a required integer parameter.
• exhaustiveness - exhaustiveness of the global search (roughly proportional to time): 1+. This is an optional integer parameter. Default value is 8.
• max_evals - number of evaluations in each MC run (if zero the number of MC steps is based on heuristics). This is an optional integer parameter. Default value is 0.
• num_modes - maximum number of binding modes to generate. This is an optional integer parameter. Default value is 9.
• min_rmsd - minimum RMSD between output poses. This is an optional double parameter. Default value is 1.0.
• energy_range - maximum energy difference between the best binding mode and the worst one displayed (kcal/mol). This is an optional double parameter. Default value is 3.0.
• spacing - grid spacing (Angstrom). This is an optional double parameter. Default value is 0.375.

vina scoring function specific parameters.

• weight_gauss1 - gauss_1 weight. This is an optional double parameter. Default value is -0.035579.
• weight_gauss2 - gauss_2 weight. This is an optional double parameter. Default value is -0.005156.
• weight_repulsion - repulsion weight. This is an optional double parameter. Default value is 0.840245.
• weight_hydrophobic - hydrophobic weight. This is an optional double parameter. Default value is -0.035069.
• weight_hydrogen - Hydrogen bond weight. This is an optional double parameter. Default value is -0.587439.
• weight_rot - N_rot weight. This is an optional double parameter. Default value is 0.05846.

vinardo scoring function specific parameters.

• weight_gauss1 - gauss_1 weight. This is an optional double parameter. Default value is -0.045.
• weight_repulsion - repulsion weight. This is an optional double parameter. Default value is 0.8.
• weight_hydrophobic - hydrophobic weight. This is an optional double parameter. Default value is -0.035.
• weight_hydrogen - Hydrogen bond weight. This is an optional double parameter. Default value is 0.600.
• weight_rot - N_rot weight. This is an optional double parameter. Default value is 0.05846.

ad4 scoring function specific parameters.

• weight_ad4_vdw - ad4_vdw weight. This is an optional double parameter. Default value is 0.1662.
• weight_ad4_hb - ad4_hb weight. This is an optional double parameter. Default value is 0.1209.
• weight_ad4_elec - ad4_elec weight. This is an optional double parameter. Default value is 0.1406.
• weight_ad4_dsolv - ad4_dsolv weight. This is an optional double parameter. Default value is 0.1322.
• weight_ad4_rot - ad4_rot weight. This is an optional double parameter. Default value is 0.2983.

More information about specified parameters could be found on the official documentation webpage of Autodock-Vina: https://autodock-vina.readthedocs.io/en/latest/index.html

Minimal JSON file example

{
    "receptor": "1iep_receptor.pdbqt",
    "ligand": "1iep_ligand.pdbqt",
    "center_x": 15.190,
    "center_y": 53.903,
    "center_z": 16.917,
    "size_x": 20.0,
    "size_y": 20.0,
    "size_z": 20.0,
    "seed": 123456,
    "out": "1iep_ligand_vina_out.pdbqt"
}