Installation

Prior to installing Dockey, you should first install a docking engine, any of AutoDock4, AutoDock Vina and QuickVina-W.

Dockey download: https://github.com/lmdu/dockey/releases

中国镜像下载地址: https://big.cdu.edu.cn/software/dockey

We have tested Dockey on these systems:

System

Versions

windows

Windows

10, 11

linux

Ubuntu

20.04, 22.04

macos

MacOS

Big Sur 11.7

On Windows

Install AutoDock4:

Go to https://autodock.scripps.edu/download-autodock4/ page, click on AutoDock4 Windows to download autodocksuite-4.2.6.i86Windows.exe installer, and then double click installer to install AutoDock4.

Or install AutoDock Vina:

Go to https://github.com/ccsb-scripps/AutoDock-Vina/releases page, click on vina_1.2.5_win.exe to download it, and put it any where.

Or install QuickVina-W:

The QuickVina homepage only provide linux executable. For Windows, you can install QuickVina-W by anaconda.

Install Dockey:

  1. Go to https://github.com/lmdu/dockey/releases page, click on Dockey-version-win64.exe to download it. Then double click the downloaded installer to install the program following the on-screen instructions.

  2. Or, you can click on Dockey-version-win64.7z to download it. Then uncompress the 7z file using 7-zip and double click the Dockey.exe to run it.

On Linux

Install AutoDock4:

Go to https://autodock.scripps.edu/download-autodock4/ page, click on AutoDock v4.2.6 (Linux 64bit) to download autodocksuite-4.2.6-x86_64Linux2.tar package, Then uncompress the package:

tar xvf autodocksuite-4.2.6-x86_64Linux2.tar

After uncompress, you will get a folder named x86_64Linux2 which contains autogrid4 and autodock4 executables. You can move these two executables to any where, for example, move to /usr/local/bin:

cd x86_64Linux2
sudo mv autogrid4 autodock4 /usr/local/bin

Or install AutoDock Vina:

Go to https://github.com/ccsb-scripps/AutoDock-Vina/releases page, click on vina_1.2.5_linux_x86_64 to download it, and put it any where.

Or install QuickVina-W:

Go to https://qvina.github.io/ page, and then click Download binary QuickVina-W button on the right side of page to download qvina-w executable, and put it any where.

Install Dockey:

Note

Currently, we only tested Dockey on Ubuntu systems. It may also support other Linux systems based on Debian, for example, Deepin.

  1. Go to https://github.com/lmdu/dockey/releases page, click on Dockey-version-ubuntu.deb to download it. Then double click the downloaded installer to install the program following the on-screen instructions.

  2. You can also install Dockey using command line tool like this:

    sudo dpkg -i Dockey-version-ubuntu.deb

  3. Or, you can click on Dockey-version-ubuntu.AppImage to download it and run it like this:

    chmod +x Dockey-version-ubuntu.AppImage
./Dockey-version-ubuntu.AppImage

    You can also double click the .AppImage file to run it.

  4. Or, you can click on Dockey-version-ubuntu.tar.gz to download the compressed package, and then uncompress it to run Dockey:

tar xzvf Dockey-version-ubuntu.tar.gz
cd Dockey
./Dockey

Note

The installation file with -ubuntu20.04 can only run on Ubuntu 20.04, while file with -ubuntu22.04 can run on Ubuntu >= 22.04

MacOS

Because the docking engines and Dockey are unsigned applications which can not be installed from apple store, the gatekeeper of MacOS will prevent the installation and running of Dockey and AutoDock. So, before installation, you should disable gatekeeper from command line in MacOS.

To disable gatekeeper, follow these steps:

  1. Launch Terminal from Applications > Utilities.

  2. Enter the following command:

    sudo spctl --master-disable

  3. Press Enter and type your admin password.

  4. Press Enter again.

Now, the Anywhere option should be available under the Allow apps downloaded from section of System Preferences > Security & Privacy > General.

Note

If you want to re-enable gatekeeper, you can do with a simple command:

sudo spclt --master-enable

Install AutoDock4:

Go to https://autodock.scripps.edu/download-autodock4/ page, click on AutoDock4 (Mac OS X) to download autodocksuite-4.2.6-MacOSX.tar package, then uncompress the package:

tar xvf autodocksuite-4.2.6-MacOSX.tar

After uncompress, you will get a folder named MacOSX which contains autogrid4 and autodock4 executables. You can move these two executables to any where, for example, move to /usr/local/bin:

cd MacOSX
sudo mv autogrid4 autodock4 /usr/local/bin

After installation, you should set the permissions so they can work following these commands:

sudo xattr -r -d com.apple.quarantine /usr/local/bin/autogrid4
sudo xattr -r -d com.apple.quarantine /usr/local/bin/autodock4

Or install AutoDock Vina:

Go to https://github.com/ccsb-scripps/AutoDock-Vina/releases page, click on vina_1.2.3_mac_x86_64 to download it, and put it any where. And then set the permissions following:

sudo xattr -r -d com.apple.quarantine vina_1.2.5_mac_x86_64

Or install QuickVina-W:

The QuickVina homepage only provide linux executable. For MacOS, you can install QuickVina-W by anaconda.

Install Dockey:

Go to https://github.com/lmdu/dockey/releases page, click on Dockey-version-macos.dmg to download it. Then double click the downloaded installer to install the program following the on-screen instructions.

After installation, you should set the permissions following:

sudo xattr -r -d com.apple.quarantine /Applications/Dockey.app