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linux命令行并行 linuxshell并行执行( 四 )

IT技术命令


--ligand argligand (PDBQT)
Search space (required):搜索空间有效地限制linux命令行并行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 probablyavoid search spaces bigger than 30 x 30 x 30 Angstrom, unless you also increase "--exhaustiveness" .）
--center_x argX coordinate of the center
--center_y argY coordinate of the center
--center_z argZ coordinate of the center
--size_x argsize in the X dimension (Angstroms)
--size_y argsize in the Y dimension (Angstroms)
--size_z argsize in the Z dimension (Angstroms)
Output (optional):
--out argoutput models (PDBQT), the default is chosen based on
the ligand file name
--log argoptionally, write log file
Misc (optional):
--cpu argthe number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)
--seed argexplicit 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 argthe above options can be put here
Information (optional):
--helpdisplay usage summary
--help_advanceddisplay usage summary with advanced options
--versiondisplay 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, aredegenerate.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 intoone multimodel PDBQT file specified by the "out" parameteror 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

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