總結(jié)：
step1. MGLtools
蛋白質(zhì)Edit——加polar H峭梳，加Kollman電荷后穷躁，Grid——Macromolecule——choose，自動保存pro1.pdbqt
配體 Ligand——Input——QuickSetup逼友，自動保存.out.pdbqt
step2. Autodock Vina
寫參數(shù)文件config1.txt
receptor = clusters_0001_model1.pdbqt
ligand = hypericin.out.pdbqt
center_x = 2.148 （第一個文件可以由Docking——output——Vina生成）
center_y = 3.704
center_z = -2.81
size_x = 74.55 ? （大于30*30*30拇惋，要增加exhaustiveness）
size_y = 74.55
size_z = 74.55
out = cluster1_hypericin_out.pdbqt
log =?cluster1_hypericin_out.log
exhaustiveness=24（可以多少個CPU設(shè)置多少個，并行計算震糖，exhaustiveness控制一個docking過程重復(fù)計算多少次录肯，越高花時間越長，但也不要設(shè)置特別大吊说，也沒有意義论咏，要在效率和準確度找一個平衡點）
num_modes=30 （不一定輸出30個优炬，可能只找到<30構(gòu)象，也有可能被energy_range限制?）
energy_range=6 (kcal/mol)
（柔性殘基信息：flex=side_chains.pdbqt）
運行：
vina --config config1.txt
結(jié)果分析：
用pymol打開cluster1_hypericin_out.pdbqt看結(jié)果
以下為詳細設(shè)置和操作：
1. 首先用MGLtools準備蛋白和小分子的坐標文件（pdbqt）
蛋白質(zhì):?加氫（Add all hydrogens or just non-polar hydrogens. Merge non-polar hydrogens and their charges with their parent carbon atom）厅贪、計算電荷（Assign partial atomic charges to the ligand and the macromolecule (Gasteiger or Kollman United Atom charges))蠢护、添加原子類型、柔性殘基信息
1. Edit——加polar H养涮，merge nonpolar（自動）后葵硕，pdbqt中的原子數(shù)會改變，加H的時候贯吓，可能會重新編號
2.Edit——加Kollman United Atom charges電荷（只能加這個，還可以計算Gasteiger 電荷悄谐，其值更負）介评，加電荷后，pdbqt中的電荷會改變
配體分子:?加氫爬舰、計算電荷们陆、確定root（扭矩中心），選擇可旋轉(zhuǎn)的鍵 (Set up rotatable bonds in the ligand using a graphical version of AutoTors)。我直接使用的quick setup。
Tips：?H的位置是任意的栏笆，僅取決于輸入文件；電荷AutoDock Vina ignores the user-supplied partial charges. It has its own way of dealing with the electrostatic interactions through the hydrophobic and the hydrogen bonding terms.?
保存pdbqt文件：pro1.pdbqt椅文，pro2.pdbqt，pro3.pdbqt惜颇，lig1.pdbqt雾袱，lig2.pdbqt，lig3.pdbqt
2. 寫參數(shù)文件 config.txt
eg. config.txt
receptor = clusters_0001_model1.pdbqt
ligand = hypericin.out.pdbqt
center_x = 2.148
center_y = 3.704
center_z = -2.81
size_x = 74.55 ? （大于30*30*30望伦，要增加exhaustiveness）
size_y = 74.55
size_z = 74.55
out = cluster1_hypericin_out.pdbqt
log =?cluster1_hypericin_out.log
exhaustiveness=15
num_modes=30 （不一定輸出30個，可能只找到<30構(gòu)象煎殷，也有可能被energy_range限制?）
energy_range=6
Details：
Input:
? --receptor arg? ? ? ? rigid part of the receptor (PDBQT)
? --flex arg? ? ? ? ? ? flexible side chains, if any (PDBQT)
? --ligand arg? ? ? ? ? ligand (PDBQT)
Search space (required):?搜索空間有效地限制了包括柔性側(cè)鏈在內(nèi)的可移動原子的位置劣摇。
（How big should the search space be?
As small as possible, but not smaller. The smaller the search space, the easier it is for the docking algorithm to explore it. On the other hand, it will not explore ligand and flexible side chain atom positions outside the search space. You should probably avoid search spaces bigger than?30 x 30 x 30?Angstrom, unless you also increase "--exhaustiveness".）
? --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)
Output (optional):
? --out arg? ? ? ? ? ? output models (PDBQT), the default is chosen based on
? ? ? ? ? ? ? ? ? ? ? ? the ligand file name
? --log arg? ? ? ? ? ? optionally, write log file
Misc (optional):
? --cpu arg? ? ? ? ? ? ? ? the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)
? --seed arg? ? ? ? ? ? ? ? explicit random seed
? --exhaustiveness arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ ?//使用默認的(或任何給定的)窮盡性設(shè)置，用于搜索的時間已經(jīng)根據(jù)原子的數(shù)量弓乙、flexibility等自發(fā)變化末融。通常情況下钧惧，花費額外的時間搜索來降低找不到評分函數(shù)的全局最小值的概率是沒有意義的，這個概率遠遠低于該最小值遠離本機構(gòu)象的概率勾习。然而浓瞪，如果你覺得在exhaustiveness和時間之間的自動平衡是不夠的，你可以提高exhaustiveness的數(shù)值巧婶。這將線性地增加時間乾颁，并降低不找到最小值的概率。
? --num_modes arg (=9)? ? ? maximum number of binding modes to generate //改成30
? --energy_range arg (=3)? maximum energy difference between the best binding //改成 8
? ? ? ? ? ? ? ? ? ? ? ? ? ? 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
Output：
1. Energy
The predicted binding affinity is in?kcal/mol.
2. RMSD
RMSD values are calculated relative to the best mode and use only movable heavy atoms. Two variants of RMSD metrics are provided,?rmsd/lb?(RMSD lower bound) and?rmsd/ub?(RMSD upper bound), differing in how the atoms are matched in the distance calculation:
rmsd/ub?matches each atom in one conformation with itself in the other conformation, ignoring any symmetry
rmsd'?matches each atom in one conformation with the closest atom of the same element type in the other conformation (rmsd'?can not be used directly, because it is not symmetric)
rmsd/lb?is defined as follows:?rmsd/lb(c1, c2) = max(rmsd'(c1, c2), rmsd'(c2, c1))
3. Hydrogen positions
Vina uses a united-atom scoring function. As in AutoDock, polar hydrogens are needed in the input structures to correctly type heavy atoms as hydrogen bond donors. However, in Vina, the degrees of freedom that only move hydrogens, such as the hydroxyl group torsions, are degenerate. Therefore, in the output, some hydrogen atoms can be expected to be positioned randomly (but consistent with the covalent structure). For a united-atom treatment, this is essentially a cosmetic issue.
4. Separate models 用vina_split分割成多個pdbqt
All predicted binding modes, including the positions of the flexible side chains are placed into one multimodel PDBQT file specified by the "out" parameter or chosen by default, based on the ligand file name. If needed, this file can be split into individual models using a separate program called "vina_split", included in the distribution.
注意：vina_split 的Windows版本要用cmd來實現(xiàn)艺栈，找到vina_split所在的目錄英岭，運行vina_split --input **.pdbqt
1. Why am I seeing a warning about the search space volume being over 27000 Angstrom^3?
This is probably because you intended to specify the search space sizes in "grid points" (0.375 Angstrom), as in AutoDock 4.?The AutoDock Vina search space sizes are given in Angstroms instead.?If you really intended to use an unusually large search space, you can ignore this warning, but note that the search algorithm's job may be harder.?You may need to increase the value of the exhaustiveness to make up for it.?This will lead to longer run time.
2. The bound conformation looks reasonable, except for the hydrogens.?Why?
AutoDock Vina actually uses a united-atom scoring function, i.e. one that involves only the heavy atoms.?Therefore, the positions of the hydrogens in the output are arbitrary.?The hydrogens in the input file are used to decide which atoms can be hydrogen bond donors or acceptors though, so the correct protonation of the input structures is still important.
3. What does "exhaustiveness" really control, under the hood? （exhaustiveness為the number of runs，并行湿右，可以設(shè)為cpu數(shù)诅妹，可以充分利用）
In the current implementation, the docking calculation consists of a number of independent runs, starting from random conformations.?Each of these runs consists of a number of sequential steps.?Each step involves a random perturbation of the conformation followed by a local optimization (using the Broyden-Fletcher-Goldfarb-Shanno algorithm) and a selection in which the step is either accepted or not.?Each local optimization involves many evaluations of the scoring function as well as its derivatives in the position-orientation-torsions coordinates.?The number of evaluations in a local optimization is guided by convergence and other criteria.?The number of steps in a run is determined heuristically, depending on the size and flexibility of the ligand and the flexible side chains.?However, the number of runs is set by the exhaustiveness parameter.?Since the individual runs are executed in parallel, where appropriate, exhaustiveness also limits the parallelism.?Unlike in AutoDock 4, in AutoDock Vina, each run can produce several results: promising intermediate results are remembered.?These are merged, refined, clustered and sorted automatically to produce the final result.
4. Why do I not get the correct bound conformation?
It can be any of a number of things:
If you are coming from AutoDock 4, a very common mistake is to specify the search space in "points" (0.375 Angstrom), instead of Angstroms.
Your ligand or receptor might not have been correctly protonated. （初始結(jié)構(gòu)沒有優(yōu)化好）
Bad luck (the search algorithm could have found the correct conformation with good probability, but was simply unlucky).?Try again with a different seed.
The minimum of the scoring function correponds to the correct conformation, but the search algorithm has trouble finding it.?In this case, higher exhaustiveness or smaller search space should help. （搜索算法沒有找到最優(yōu)結(jié)構(gòu)，可以增大exhaustiveness或減小search space）
The minimum of the scoring function simply is not where the correct conformation is.?Trying over and over again will not help, but may occasionally give the right answer if two wrongs (inexact search and scoring) make a right.?Docking is an approximate approach.
Related to the above, the culprit may also be the quality of the X-ray or NMR receptor structure.
If you are not doing redocking, i.e. using the correct induced fit shape of the receptor, perhaps the induced fit effects are large enough to affect the outcome of the docking experiment.（換受體結(jié)構(gòu)）
The rings can only be rigid during docking.?Perhaps they have the wrong conformation, affecting the outcome.
You are using a 2D (flat) ligand as input.
The actual bound conformation of the ligand may occasionally be different from what the X-ray or NMR structure shows.
Other problems
5. How can I tweak the scoring function?
You can change the weights easily, by specifying them in the configuration file, or in the command line.?For example
vina --weight_hydrogen -1.2 ...
doubles the strenth of all hydrogen bonds.
我如何調(diào)整評分功能?
通過在配置文件或命令行中指定權(quán)重诅需，可以輕松地更改權(quán)重漾唉。例如
vina—weight_hydrogen -1.2…
所有氫鍵強度的兩倍。
Functionality that would allow the users to create new atom and pseudo-atom types, and specify their own interaction functions is planned for the future.
This should make it easier to adapt the scoring function to specific targets, model covalent docking and macro-cycle flexibility, experiment with new scoring functions, and, using pseudo-atoms, create directional interaction models.
6. Why don't I get as many binding modes as I specify with "--num_modes"?
This option specifies the maximum number of binding modes to output.?The docking algorithm may find fewer "interesting" binding modes internally.?The number of binding modes in the output is also limited by the "energy_range", which you may want to increase.
7. Why don't the results change when I change the partial charges?
AutoDock Vina ignores the user-supplied partial charges. It has its own way of dealing with the electrostatic interactions through the hydrophobic and the hydrogen bonding terms. See the original publication [*] for details of the scoring function.
8. How do I use flexible side chains?
You split the receptor into two parts: rigid and flexible, with the latter represented somewhat similarly to how the ligand is represented. See the section "Flexible Receptor PDBQT Files" of the AutoDock4.2 User Guide (page 14) for how to do this in AutoDock Tools. Then, you can issue this command: vina --config conf --receptor rigid.pdbqt --flex side_chains.pdbqt --ligand ligand.pdbqt. Also see this write-up on this subject.
