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Autodock
2016-08-30 01:05:14 -0700
CompCB
CADD Docking

Autodock是由Arthur J. Olson组Molecular Graphics Laboratory所开发的, 有两个版本: Autodock 和Autodock Vina, 以及一个可视化程序MGLTools.

Autodock

下载可以下载相应版本的已编译文件, 只有两个执行文件: autodock4autogrid4

Autodock Vina

下载 可以下载相应版本的已编译文件, 只有两个文件:

MGLTools

下载

安装很简单, ./install -d install_folder -c 1, -d 指定安装目录, -c 为0:不优化, 或者 1: 优化

其主要包含

  • ADT: AutoDockTools, 就是可视化对接的前端
  • PMV: Python Molecular Viewer, 就是显示的一个程序
  • Vision: 类似于Pipeline Pilot的东东, 可以交互地搭建各种流程来处理数据而不用写代码.

运行下述脚本 ./make_autodock.sh来创建一个autodock的软链接到MGLTools, 并使MGLTools包含autodock和vina的主程序链接.

#! /bin/bash                                                                                         
totaldir="`dirname $(readlink -f $0)`"

autodock_dir=autodock_4_2_6_x86_64Linux2
vina_dir=autodock_vina_1_1_2_linux_x86
mgl_dir=MGLTools

[ -L $mgl_dir/bin/autodock4 ] && rm $mgl_dir/bin/autodock4
[ -L $mgl_dir/bin/autogrid4 ] && rm $mgl_dir/bin/autogrid4
[ -L $mgl_dir/bin/vina ] && rm $mgl_dir/bin/vina
[ -L $mgl_dir/bin/vina_split ] && rm $mgl_dir/bin/vina_split

if [ -f "$totaldir/$autodock_dir/autodock4" -a -f "$totaldir/$autodock_dir/autogrid4" ];then
    ln -s "$totaldir/$autodock_dir/autodock4" "$mgl_dir/bin/autodock4"
    ln -s "$totaldir/$autodock_dir/autogrid4" "$mgl_dir/bin/autogrid4"
else
    echo "Autodock programs can't be found!"
fi
if [ -f "$totaldir/$vina_dir/vina" -a -f "$totaldir/$vina_dir/vina_split" ];then
    ln -s "$totaldir/$vina_dir/vina" "$mgl_dir/bin/vina"
    ln -s "$totaldir/$vina_dir/vina_split" "$mgl_dir/bin/vina_split"
else
    echo "Autodock Vina programs can't be found!"
fi

[ -L autodock ] && rm autodock
ln -s $mgl_dir autodock

可以将下述的写到initAutoDock.sh脚本, 用于加载

source ~/initAutoDock.sh

alias autodock4="$SWSROOT/Autodock/autodock/bin/autodock4"
alias autogrid4="$SWSROOT/Autodock/autodock/bin/autogrid4"
alias vina='$SWSROOT/Autodock/autodock/bin/vina'
alias vina_split='$SWSROOT/Autodock/autodock/bin/vina_split'                                                                                
alias pmv='$SWSROOT/Autodock/autodock/bin/pmv'
alias adt='$SWSROOT/Autodock/autodock/bin/adt'
alias vision='$SWSROOT/Autodock/autodock/bin/vision'
alias pythonsh='$SWSROOT/Autodock/autodock/bin/pythonsh'

# or export to PATH
# export PATH="$PATH:$SWSROOT/Autodock/autodock/bin"

使用Autodock和ADT参考官方的Using AutoDock 4 and AutoDock Vina with AutoDockTools: A Tutorial