AutoDock_vina_japanese_ver.1.0

2,385 views

Published on

This is a japanese manual of AutoDock vina.

Published in: Education
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
2,385
On SlideShare
0
From Embeds
0
Number of Embeds
8
Actions
Shares
0
Downloads
17
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

AutoDock_vina_japanese_ver.1.0

  1. 1. 121118 version 1.0AutoDock Vina & MGLTools on Mac OSX 10.6AutoDock Vinaは、Oleg Trott 博士 (The Scripps Research Institute)により提供されるAutoDock4の改良型ドッキングツールである。計算速度、ドッキング精度ともに大幅に改善されている。ただ、結合プロファイルがFree energyしかログに残らないのが問題である。 Provided by Satoshi Kume Osaka Prefecture University
  2. 2. 1. AutodockToolsの起動2. Proteinの設定 2-1. File → Read Molecule → Open PDB file (表示設定: Ribbon.) 2-2. Edit → Hydrogens → add → Polar only → OK. 2-3. Grid → Macromolecule → Choose... → Select Molecule.. (同じファイル)   → Save PDBQT 例3. GridBoxの設定 number of points in x-dimension: 22 3-1. Grid → GridBox → Center Grid Boxの設定 number of points in y-dimension: 24 3-2. Spacing (angstrom) → 1.000 angstrom number of points in z-dimension: 28 3-3. xyz-dimensions → 20-30 (覚えておく!!!) Spacing (angstrom): 1.000 ※ Search space volumeを27000 Angstrom3以下に設定する4. Ligandの設定 4-1. Ligand → Input → Open → リガンドのPDB fileを選択 4-2. Ligand → Torsion Tree → Choose Torsions... → Rotatable bondsの設定   (基本的にDefault) → Done 4-3. Ligand → Ourput → Save PDBQT (※ Protein fileと同じフォルダに保存) 4-4. AutodockToolsを終了する
  3. 3. 設定の記入例5. Vinaの設定ファイル作製 receptor = AAA.pdbqt5-1. CotEditorあるいはテキストエディットで新規 ligand = BBB.pdbqt log = BBB.log  テキストファイルを作製する5-2. 右のような記入例に従って、設定ファイルを center_x = -3.889 center_y = -2.222  作製・保存する。 center_z = 0.000※ Protein & ligand filesと同じフォルダに保存 size_x = 24 size_y = 28 size_z = 30 < 27000 cpu = 1 seed = 1000 size_x num_modes = 100 size_y energy_range = 3 size_z 各設定の簡易説明 receptor = : Protein file name, ligand = : Liandcenter_x file name, log = : Output log name, cpu = : コアcenter_y 使用数, Seed: 初期配座試行回数, num_modes:center_z 計算試行回数, energy_range: 計算内の自由エ ネルギー差(kcal/mol)
  4. 4. 6. AutoDock Vinaの起動6-1. ターミナルの起動 & 所定のディレクトリへの移動(vinaのディレクトリを確認する)(例えば、“/Users/AUTODOCK/ADvina_1_1_2_mac/bin/vina”の場合)6-2. % /Users/AUTODOCK/ADvina_1_1_2_mac/bin/vina --help # ヘルプの確認 Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) Search space (required): 6-3. 設定オプションが出力される --center_x arg X coordinate of the center --center_y arg Y coordinate of the center --center_z arg Z coordinate of the center --size_x arg size in the X dimension (Angstroms) --size_y arg size in the Y dimension (Angstroms) --size_z arg size in the Z dimension (Angstroms) Advanced options (see the manual): --score_only score only - search space Output (optional): --out arg output models (PDBQT), the default is chosen based on can be omitted the ligand file name --local_only do local search only --log arg optionally, write log file --randomize_only randomize input, attempting to avoid clashes Misc (optional): --weight_gauss1 arg (=-0.035579) gauss_1 weight --cpu arg the number of CPUs to use (the default is to try to --weight_gauss2 arg (=-0.005156) gauss_2 weight detect the number of CPUs or, failing that, use 1) --weight_repulsion arg (=0.84024500000000002) repulsion weight --seed arg explicit random seed --exhaustiveness arg (=8) exhaustiveness of the global search (roughly --weight_hydrophobic arg (=-0.035069000000000003) hydrophobic weight proportional to time): 1+ --weight_hydrogen arg (=-0.58743900000000004) Hydrogen bond weight --num_modes arg (=9) maximum number of binding modes to generate --weight_rot arg (=0.058459999999999998) N_rot weight --energy_range arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) 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
  5. 5. 7. AutoDock Vinaを用いたドッキング計算7-1. % /Users/AUTODOCK/ADvina_1_1_2_mac/bin/vina --config conf.txt(confは任意のファイル名) ################################################# # If you used AutoDock Vina in your work, please cite: #7-2. 右のようなログが出力される # # # O. Trott, A. J. Olson, #7-3. Writing output ... done → 計算完了 # AutoDock Vina: improving the speed and accuracy of docking # with a new scoring function, efficient optimization and # # # multithreading, Journal of Computational Chemistry 31 (2010) #7-4. BBB_out.pdbqtが新規に作製される # 455-461 # # #(BBBは任意のリガンドファイル名) # DOI 10.1002/jcc.21334 # # # # Please see http://vina.scripps.edu for more information. # ################################################# Output will be LA1_out.pdbqt Reading input ... done.8. PyoMOLによる可視化 Setting up the scoring function ... done. Analyzing the binding site ... done. Using random seed: 1000 Performing search ...8-1. BBB_out.pdbqtをPyMOLにドラッグし 0% 10 20 30 40 50 60 70 80 90 100% | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- |  て開く! *************************************************** done. Refining results ... done.(※ PyMOL → File → Open...ではダメ!) mode | affinity | dist from best mode8-2. PyMOL → File → Open... → Protein PDB | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+----------  fileを開く 1 -5.5 0.000 0.000 2 -5.3 4.700 9.2018-3. 結合部位を確認する 3 -5.3 1.272 2.895 4 -5.3 1.150 1.838 5 -5.3 4.682 8.772(Binding free energyが低い順) 6 -5.3 1.420 2.117 7 -5.3 4.218 8.038 8 -5.3 4.373 8.487 9 -5.2 1.390 2.106 10 -5.2 4.939 9.404 Writing output ... done.

×