Autodock vina 和MGL tools linux版本操作（命令行操作）

蛋白质Edit——加polar H，加Kollman电荷后，Grid——Macromolecule——choose，自动保存pro1pdbqt

配体 Ligand——Input——QuickSetup，自动保存outpdbqt

receptor = clusters_0001_model1pdbqt

ligand = hypericinoutpdbqt

center_x = 2148 （第一个文件可以由Docking——output——Vina生成）

center_y = 3704

center_z = -281

size_x = 7455   （大于303030，要增加exhaustiveness）

size_y = 7455

size_z = 7455

out = cluster1_hypericin_outpdbqt

log = cluster1_hypericin_outlog

exhaustiveness=24（可以多少个CPU设置多少个，并行计算，exhaustiveness控制一个docking过程重复计算多少次，越高花时间越长，但也不要设置特别大，也没有意义，要在效率和准确度找一个平衡点）

num_modes=30 （不一定输出30个，可能只找到<30构象，也有可能被energy_range限制 ）

energy_range=6 (kcal/mol)

（柔性残基信息：flex=side_chainspdbqt）

vina --config config1txt

用pymol打开cluster1_hypericin_outpdbqt看结果

以下为详细设置和操作：

1 首先用MGLtools准备蛋白和小分子的坐标文件（pdbqt）

蛋白质:  加氢（Add all hydrogens or just non-polar hydrogens Merge non-polar hydrogens and their charges with their parent carbon atom）、计算电荷（Assign partial atomic charges to the ligand and the macromolecule (Gasteiger or Kollman United Atom charges))、添加原子类型、柔性残基信息

1 Edit——加polar H，merge nonpolar（自动）后 ，pdbqt中的原子数会改变，加H的时候，可能会重新编号

2Edit——加Kollman United Atom charges电荷（只能加这个，还可以计算Gasteiger 电荷，其值更负），加电荷后，pdbqt中的电荷会改变

配体分子:  加氢、计算电荷、确定root（扭矩中心），选择可旋转的键 (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，仅取决于输入文件；电荷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：pro1pdbqt，pro2pdbqt，pro3pdbqt，lig1pdbqt，lig2pdbqt，lig3pdbqt

2 写参数文件 configtxt

eg configtxt

receptor = clusters_0001_model1pdbqt

ligand = hypericinoutpdbqt

center_x = 2148

center_y = 3704

center_z = -281

size_x = 7455   （大于303030，要增加exhaustiveness）

size_y = 7455

size_z = 7455

out = cluster1_hypericin_outpdbqt

log = cluster1_hypericin_outlog

exhaustiveness=15

num_modes=30 （不一定输出30个，可能只找到<30构象，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):  搜索空间有效地限制了包括柔性侧链在内的可移动原子的位置。

（ 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+  //使用默认的(或任何给定的)穷尽性设置，用于搜索的时间已经根据原子的数量、flexibility等自发变化。通常情况下，花费额外的时间搜索来降低找不到评分函数的全局最小值的概率是没有意义的，这个概率远远低于该最小值远离本机构象的概率。然而，如果你觉得在exhaustiveness和时间之间的自动平衡是不够的，你可以提高exhaustiveness的数值。这将线性地增加时间，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分割成多个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来实现，找到vina_split所在的目录，运行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" (0375 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, ie 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为the number of runs，并行，可以设为cpu数，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" (0375 Angstrom), instead of Angstroms

Your ligand or receptor might not have been correctly protonated （初始结构没有优化好）

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 （搜索算法没有找到最优结构，可以增大exhaustiveness或减小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, ie 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（换受体结构）

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 -12

doubles the strenth of all hydrogen bonds

我如何调整评分功能

通过在配置文件或命令行中指定权重，可以轻松地更改权重。例如

vina—weight_hydrogen -12…

所有氢键强度的两倍。

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 AutoDock42 User Guide (page 14) for how to do this in AutoDock Tools Then, you can issue this command: vina --config conf --receptor rigidpdbqt --flex side_chainspdbqt --ligand ligandpdbqt Also see this write-up on this subject

Vina源于拉丁文：从葡萄园来的姑娘

Vivienne 法语：Alive

Vienna 拉丁：From Wine Country - Cities in Austria and the US State of Virginia

前面几个内容是指蛋白和小分子的处理过程，接下来一个非常重要的步骤是如何确定对接的位点，这也是整个分子对接过程中的重点。如果你能够找到原结晶的配体，那么最方便的方法就是按照共结晶配体的位置确定对接位点，如果没有，那就需要查阅文献或者根据自身的经验来确定这个对接位点。当然，目前也有很多的关于位点选择的预测方法，供大家参考。下面我们结合共结晶配体来对对接位置进行设置。

1 首先确定共结晶配体的三维结构的位置，这里面介绍个比较繁琐但是会保险一点的方法，就是根据PDB文件中的XYZ轴的数据计算下配体的在每个坐标轴的平均值，这样就大致属于配体的中心结构；由此便可以大致确定下对接位置的中心坐标

2 打开AutoDockTools，依次点击Grid-Macromolecule-Open，打开已经预处理好的蛋白文件，可以设置为卡通格式；

3 点击Grid Box，然后生成格点空间，下面开始对格点中心坐标，距离中间点的位置和格点间隔进行设置，其中格点间隔在Vina默认设置为1；

4 对格点文件进行保存；

5 将格点文件GPF保存在默认文件夹中；

好了，以上就是对接位置的设置，这是非常重要的步骤；但是大部分时候要根据自己的具体情况设置数据，但是设置的步骤就是这样的。好了，如果有问题可以关注木初专栏，互相交流。

vina4101有圆角缺角之分

额 这款吉他现在便宜了，不到500就可以买到，

这款琴确实是一款性价比不错的琴，我自己上段时间帮朋友买了一把

vina4101分圆角和缺角-------

 缺角琴体，方便个人solo，边弹边唱，并且不会妨碍对各品位的联系，高品位演奏没问题。

圆角琴体共鸣好，声音饱满圆润，穿透力强。弹唱，合奏，都是它的强项。

Vina 4101以其良好的木材，理性的设计，细腻的做工，在其价格区间内，成为市场上性价比非常高的一把吉他。精妙绝伦的音色，会让你瞬间迷上它。

面板是声音共鸣的发源地，vina 4101采用A级云杉木，增强了其音色的中高频成分，而且随着弹奏时间的增长，其音色会越来越好。表面采用静电烤喷工艺且不会掩盖吉他本身的用料材质，让您清晰地看的到。

精选沙比利材质作为背侧板，更增加了吉他音色的中频成分和整体的音色力度。而市场同品质吉他一般都是选用的楸木材料，这也是vina 优于同档次其他产品的一个原因。且琴身设计为D型筒，这种形状的吉他箱体大，共鸣优，低音浑厚清晰，整体音色饱满，圆润，明亮。

个人觉得，vina在国产琴这个价位里，是性价比很高的一把琴，是吉他初学者的必备选择。

有朋友问我们为什么说VINA41寸民谣吉他比市面上别的同价位的吉他要好很多呢，吉他爱好者都清楚一个真理：“决定吉他音色一个最重要的因素是琴体！”而琴体的质量好坏（也是好琴坏琴的重要区分标准）又主要靠三个因素来决定：1木材2形状3做工。这三者都会影响琴的共鸣进而影响到音色，而在这三者中木材又显得比较重要一点。

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