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IT技术命令


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 -1.2…
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 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.
Linux 命令大全Linux运维人员必会的120个命令
来自《跟老男孩学Linux运维linux命令行并行：核心系统命令实战》一书
前言
第1章 Linux命令行简介 / 1
1.1Linux命令行概述 / 1
1.2在Linux命令行下查看命令帮助 / 4
1.3Linux shutdown reboot halt / 9
关机：
shutdown -h now
halt
init 0
第2章 文件和目录操作命令 / 13
2.1pwd：显示当前所在的位置 / 13
2.2cd：切换目录 / 16
2.3tree：以树形结构显示目录下的内容 / 18
2.4mkdir：创建目录 / 22
2.5touch：创建空文件或改变文件的时间戳属性 / 27
2.6ls：显示目录下的内容及相关属性信息 / 30
2.7cp：复制文件或目录 / 39
2.8mv：移动或重命名文件 / 42
2.9rm：删除文件或目录 / 45
2.10rmdir：删除空目录 / 48
2.11ln：硬链接与软链接 / 49
2.12readlink：查看符号链接文件的内容 / 54
2.13find：查找目录下的文件 / 55
2.14xargs：将标准输入转换成命令行参数 / 68
2.15rename：重命名文件 / 71
2.16basename：显示文件名或目录名 / 72
2.17dirname：显示文件或目录路径 / 72
2.18chattr：改变文件的扩展属性 / 73
2.19lsattr：查看文件扩展属性 / 75
2.20file：显示文件的类型 / 76
2.21md5sum：计算和校验文件的MD5值 / 77
2.22chown：改变文件或目录的用户和用户组 / 80
2.23chmod：改变文件或目录权限 / 81
2.24chgrp：更改文件用户组 / 85
2.25umask：显示或设置权限掩码 / 86
2.26老男孩从新手成为技术大牛的心法 / 90
第3章 文件过滤及内容编辑处理命令 / 91
3.1cat：合并文件或查看文件内容 / 91
3.2tac：反向显示文件内容 / 103
3.3more：分页显示文件内容 / 104
3.4less：分页显示文件内容 / 107
3.5head：显示文件内容头部 / 109

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