This page was last updated on January 13th, 2022 at 03:51 am

Running AutoDock CrankPep on Windows 10 or above using WSL

Starting with Windows 10, it has become possible to run a Linux subsystem  on windows (Windows Subsystem for Linux). Once enabled, it is possible to install the Linux 64 bit build of ADFRsuite to run ADCP on windows.

This page provides information on how to enable WSL, install Ubuntu 20.04, install ADFRsuite1.0 to run ADCP.

NOTE: this installation currently only allows to run command line programs. Graphical User Interfaces such as AGFRGUI will not work as they require a X server for windows.

Follow the instructions on this page to install enable WSL and install Ubuntu.

in summary:

  1. Control Panel > Programs > Turn Windows Features On Or Off. Enable the “Windows Subsystem for Linux” option in the list, and then click the “OK” button.
  2. Click “Restart” now to reboot windows
  3. open the Microsoft Store (Start menu, type store) and search for “Ubuntu”. get Ubuntu 20.04
  4. Launch Ubuntu: (Start -> Ubuntu). The first time you launch the Linux environment, you’re be prompted to enter a UNIX username and password.

At this point you have a working Ubuntu subsystem.

NOTE: you can access files from the Windows OS through /mnt/c. So if you download software with the webrowser under windows you can copy it over from /mnt/c/Users/yourname/Downloads

Now we can download and install ADFRsuite1.0 for Linux

in summary:

  1. Obtain the tarball installer for linux 64 bits here
  2. in the Ubuntu shell:
    • mv /mnt/c/Users/myUserName/Downloads/ADFRsuite_x86_64Linux_1.0.tar.gz .
    • tar zxvf ADFRsuite_x86_64Linux_1.0.tar.gz
    •  cd ADFRsuite_x86_64Linux_1.0
    • bash ./install.sh -d ../ADFR10 -c 0 # NOTE you have to type “bash” for this to work
    • cd ..
    • sudo apt-get install libgomp1
    • sudo apt-get install unzip
    • repalce reduce with a 64 bit version

At this point you can download tutorial files for ADFR and ADCP and try to run dockings

from https://ccsb.scripps.edu/adfr/tutorial-redocking/

  1. download data here

  2. mv /mnt/c/Users/myUserName/Downloads/ADFRsuite-1.0_tutorial_data.zip .

  3. unzip ADFRsuite-1.0_tutorial_data.zip

  4. ./ADFR10/bin/agfr -r data/4EK3_rec.pdbqt -l data/4EK4_lig.pdbqt -o ligPocket -ng

  5. ./ADFR10/bin/adfr -l data/4EK4_random.pdbqt -t ligPocket.trg -J rigid -n 8 -e 20000 -O -s 1

  1. The version of reduce provided by the installer is 32 bit and will fail.
    1. download this 64 bit version for Linux.

    2. mv /mnt/c/Users/myUserName/Downloads/reduce64Bit.exe ADFR10/bin/reduce

  2. download the tutorial data

  3. mv /mnt/c/Users/myUserName/Downloads/ADCP_tutorial_data.zip .

  4. from https://ccsb.scripps.edu/adcp/tutorial-redocking/

    1. unzip ADCP_tutorial_data.zip

    2. cd ADCP_tutorial_data/3Q47

    3. ../../ADFR10/bin/reduce 3Q47_rec.pdb > 3Q47_recH.pdb

    4. ../../ADFR10/bin/reduce 3Q47_pep.pdb > 3Q47_pepH.pdb

    5. ../../ADFR10/bin/prepare_receptor -r 3Q47_recH.pdb

    6. ../../ADFR10/bin/prepare_ligand -l 3Q47_pepH.pdb

    7. ../../ADFR10/bin/agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47 -ng

    8. ../../ADFR10/bin/adcp -t 3Q47.trg -s npisdvd -N 20 -n 1000000 -o 3Q47_redocking -ref 3Q47_pepH.pdb