AutoDock Vinaは、
Oleg Trott 博士 (The Scripps Research Institute)らによって提供された、
AutoDock4の改良型ドッキングツール（AutoDockの後継）です。
Vinaの登場によって、計算の速度、ドッキング精度ともに大幅に改善されました。
原著論文 - AutoDock Vina -
AutoDock Vinaに関する原著論文は以下の2報となります。
"J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli. (2021). AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. Journal of Chemical Information and Modeling."
"O. Trott and A. J. Olson. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455-461."
#ヘルプ表示
vina -help#AutoDock Vina v1.2.2-22-gb5f8dc1-mod#Command line parse error: unrecognised option '-help'##Correct usage:##Input:# --receptor arg rigid part of the receptor (PDBQT)# --flex arg flexible side chains, if any (PDBQT)# --ligand arg ligand (PDBQT)# --batch arg batch ligand (PDBQT)# --scoring arg (=vina) scoring function (ad4, vina or vinardo)##Search space (required):# --maps arg affinity maps for the autodock4.2 (ad4) or vina # scoring function# --center_x arg X coordinate of the center (Angstrom)# --center_y arg Y coordinate of the center (Angstrom)# --center_z arg Z coordinate of the center (Angstrom)# --size_x arg size in the X dimension (Angstrom)# --size_y arg size in the Y dimension (Angstrom)# --size_z arg size in the Z dimension (Angstrom)# --autobox set maps dimensions based on input ligand(s) (for # --score_only and --local_only)##Output (optional):# --out arg output models (PDBQT), the default is chosen based# on the ligand file name# --dir arg output directory for batch mode# --write_maps arg output filename (directory + prefix name) for # maps. Option --force_even_voxels may be needed to # comply with .map format##Misc (optional):# --cpu arg (=0) the number of CPUs to use (the default is to try # to detect the number of CPUs or, failing that, use# 1)# --seed arg (=0) explicit random seed# --exhaustiveness arg (=8) exhaustiveness of the global search (roughly # proportional to time): 1+# --max_evals arg (=0) number of evaluations in each MC run (if zero, # which is the default, the number of MC steps is # based on heuristics)# --num_modes arg (=9) maximum number of binding modes to generate# --min_rmsd arg (=1) minimum RMSD between output poses# --energy_range arg (=3) maximum energy difference between the best binding# mode and the worst one displayed (kcal/mol)# --spacing arg (=0.375) grid spacing (Angstrom)# --verbosity arg (=1) verbosity (0=no output, 1=normal, 2=verbose)##Configuration file (optional):# --config arg the above options can be put here##Information (optional):# --help display usage summary# --help_advanced display usage summary with advanced options# --version display program version
AutoDock Vina v1.2.2-22-gb5f8dc1-mod
################################################################## If you used AutoDock Vina in your work, please cite: ## ## J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli ## AutoDock Vina 1.2.0: New Docking Methods, Expanded Force ## Field, and Python Bindings, J. Chem. Inf. Model. (2021) ## DOI 10.1021/acs.jcim.1c00203 ## ## O. Trott, A. J. Olson, ## AutoDock Vina: improving the speed and accuracy of docking ## with a new scoring function, efficient optimization and ## multithreading, J. Comp. Chem. (2010) ## DOI 10.1002/jcc.21334 ## ## Please see https://github.com/ccsb-scripps/AutoDock-Vina for ## more information. ##################################################################
Scoring function : vina
Rigid receptor: 1iep_receptor.pdbqt
Ligand: 1iep_ligand.pdbqt
Grid center: X 15.19 Y 53.903 Z 16.917
Grid size : X 20 Y 20 Z 20
Grid space : 0.375
Exhaustiveness: 32
CPU: 0
Verbosity: 1
Computing Vina grid ... done.
Performing docking (random seed: -885801442) ...
0% 102030405060708090100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1-13.38002-11.42.99312.413-11.41.6582.0534-11.153.86912.315-10.762.54412.646-10.11.98813.737-9.7741.70613.638-9.6952.68312.649-9.4942.83412.4
#PyMolのインストール: 5-10分くらいかかる
brew install brewsci/bio/pymol
#パス確認
which pymol
#/opt/homebrew/bin/pymol#pymol実行
pymol
# PyMOL(TM) Molecular Graphics System, Version 2.5.0.# Copyright (c) Schrodinger, LLC.# All Rights Reserved.# # Created by Warren L. DeLano, Ph.D. # # PyMOL is user-supported open-source software. Although some versions# are freely available, PyMOL is not in the public domain.# # If PyMOL is helpful in your work or study, then please volunteer # support for our ongoing efforts to create open and affordable scientific# software by purchasing a PyMOL Maintenance and/or Support subscription.## More information can be found at "http://www.pymol.org".# # Enter "help" for a list of commands.# Enter "help <command-name>" for information on a specific command.## Hit ESC anytime to toggle between text and graphics.## Detected OpenGL version 2.1. Shaders available.# Detected GLSL version 1.20.# OpenGL graphics engine:# GL_VENDOR: Apple# GL_RENDERER: Apple M1# GL_VERSION: 2.1 Metal - 71.7.1# Detected 8 CPU cores. Enabled multithreaded rendering.
