1. 130120 ver. 2.0
AutoDock Vina & MGLTools
on Mac OSX 10.6
AutoDock 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。
Provided by Satoshi Kume
Osaka Prefecture University
2. 1. AutoDockToolsの起動
2. Proteinの設定
2-1. File → Read Molecule → Open PDB file (表示設定 → Ribbonが見易い)
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) → 必ず 1.000 angstrom number of points in z-dimension: 28
3-3. xyz-dimensions → 20-30 (覚えておくこと!!!) 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 → Output → Save PDBQT (※ Protein fileと同じフォルダに保存)
4-4. AutoDockToolsを終了する
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
--flex arg
rigid part of the receptor (PDBQT)
flexible side chains, if any (PDBQT) ※ パス設定をしても良い!
--ligand arg ligand (PDBQT)
Search space (required):
--center_x arg X coordinate of the center
--center_y arg
--center_z arg
Y coordinate of the center
Z coordinate of the center
6-3. 設定オプションが出力される
--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. 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 & Log fileが新規に # 455-461 #
# #
作製される # DOI 10.1002/jcc.21334
#
#
#
# Please see http://vina.scripps.edu for more information. #
(BBBは任意のリガンドファイル名) #################################################
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.
(※ PyMOL → File → Open...ではダメ!) Refining results ... done.
mode | affinity | dist from best mode
8-2. 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 9.201
8-3. 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が低い順に表示される 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.