ADCP 1.0 on Windows 10 and later (WSL)

WarningYou are viewing ADCP 1.0 (deprecated)

These pages describe version 1.0, distributed with ADFRsuite 1.0. For new work use ADCP 1.1.

Since Windows 10 you can run a Linux subsystem on Windows (Windows Subsystem for Linux, WSL). With it enabled, you can install the Linux 64-bit build of ADFRsuite and run ADCP.

This page shows how to enable WSL, install Ubuntu 20.04 and install ADFRsuite 1.0 to run ADCP.

Note

This setup runs command-line programs only. Graphical interfaces such as AGFRGUI need an X server for Windows and will not work.

Enable WSL and install Ubuntu

  1. Control Panel → Programs → Turn Windows Features On Or Off. Enable “Windows Subsystem for Linux” and click OK.
  2. Click “Restart now” to reboot Windows.
  3. Open the Microsoft Store (Start menu, type store), search for Ubuntu and get Ubuntu 20.04.
  4. Launch Ubuntu (Start → Ubuntu). The first time, you are asked for a UNIX user name and password.

You now have a working Ubuntu subsystem.

Tip

Windows files are visible under /mnt/c. Files downloaded with a Windows browser are in /mnt/c/Users/yourname/Downloads.

Install ADFRsuite (Linux 64-bit)

  1. Get the Linux 64-bit tarball.
  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   # you must type "bash" for this to work
cd ..
sudo apt-get install libgomp1
sudo apt-get install unzip
  1. Replace reduce with a 64-bit version: download reduce64Bit.exe and move it into place. The reduce shipped with the installer is 32-bit and fails under WSL.
mv /mnt/c/Users/myUserName/Downloads/reduce64Bit.exe ADFR10/bin/reduce

You can now download the tutorial files and run dockings.

Dock with ADCP

Download the tutorial data, then follow the re-docking tutorial:

mv /mnt/c/Users/myUserName/Downloads/ADCP_tutorial_data.zip .
unzip ADCP_tutorial_data.zip
cd ADCP_tutorial_data/3Q47
../../ADFR10/bin/reduce 3Q47_rec.pdb > 3Q47_recH.pdb
../../ADFR10/bin/reduce 3Q47_pep.pdb > 3Q47_pepH.pdb
../../ADFR10/bin/prepare_receptor -r 3Q47_recH.pdb
../../ADFR10/bin/prepare_ligand -l 3Q47_pepH.pdb
../../ADFR10/bin/agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47 -ng
../../ADFR10/bin/adcp -t 3Q47.trg -s npisdvd -N 20 -n 1000000 -o 3Q47_redocking -ref 3Q47_pepH.pdb

Dock with ADFR

From the ADFR re-docking tutorial. Download the ADFR tutorial data (see ADFR tutorials), then:

mv /mnt/c/Users/myUserName/Downloads/ADFRsuite-1.0_tutorial_data.zip .
unzip ADFRsuite-1.0_tutorial_data.zip
./ADFR10/bin/agfr -r data/4EK3_rec.pdbqt -l data/4EK4_lig.pdbqt -o ligPocket -ng
./ADFR10/bin/adfr -l data/4EK4_random.pdbqt -t ligPocket.trg -J rigid -n 8 -e 20000 -O -s 1
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