Running AutoDock Vina - Alicecomma/VinaCarbResults GitHub Wiki

AutoDock Vina takes .pdbqt files and can be downloaded for all platforms. GPU-accelerated versions of AutoDock Vina exist for Linux/iOS. It ignores glycosidic torsions. If you don't care about carbohydrate torsions, I would suggest using ADV - if you do care about them, the rest of this text summarizes the complexities surrounding VinaCarb.

Running VinaCarb on Linux: Least time input / Least convenient (for Windows user)

VinaCarb takes into account some glycosidic torsions through its GlyLib. If you want to run this on Linux, it works fine:

  1. Download VinaCarb (vina-carb_1.0.tgz).
  2. Copy VinaCarb\build\linux\release\vina-carb (the authors have left a compiled Linux application here).
  3. Run it on Linux as you would run AutoDock Vina.

Running VinaCarb on Windows through WSL: More time input / More convenient

If you want to run it on Windows, I highly recommend the following. Although there are many steps, I can virtually guarantee it works:

  1. Follow all steps to install Windows Subsystem for Linux. WSL and WSL2 both work, it doesn't matter much which you choose, although WSL is apparently faster for native Linux applications.

  2. Execute from .bat as follows: cmd /c wsl export VINA_CARB=/mnt/[location of vina-carb]; [location of vina-carb] --[parameters]

    • In .bat files you can call cmd /c wsl to run Linux applications.
    • To run vina-carb through WSL, you have to set VINA_CARB (export VINA_CARB=/mnt/*), as for some reason WSL when called through cmd /c wsl doesn't load any of ~/.bashrc, ~/.profile, /etc/environment unless logged in through say cmd /c bash -lc, however this method stopped working for me before.
    • The location of vina-carb relative to ~ and the location of the .bat file need to both be specified. For my computer, these values are set to: /mnt/e/Users/[user]/Desktop/Docking; ../Docking/vina-carb. Depending on your setup, this will greatly differ.
    • The further parameters vary greatly depending on your preferences. In an integrated .bat I call as: --ligand "%~n2/%~n3.pdbqt" !npar! --out !nw!.pdbqt --log !nw!.log --num_modes 120 --exhaustiveness 20 --energy_range 10. Here !npar! puts further contents of *.enzyme.

Recompiling VinaCarb: Most time input / Least convenient

This consists of several parts, namely compiling of Boost, AutoDock Vina and GlyLib.

AutoDock Vina allows both Windows and Linux compilation, originally using Boost libraries 1.41.0. This approach has multiple hurdles:

  • Boost 1.41.0 libraries are difficult to compile out of the box. mkoohim wrote an in-depth guide on it, which does work for AutoDock Vina.
  • Newer Boost comes pre-compiled, but with feature changes, so AutoDock Vina source code needs to be altered. Navan Chauhan has your back for Boost 1.68.0 on iOS.

Sadly some Linux functions in GlyLib have no direct Windows analogue. Eric Boittier seems to circumvent some of these problems, but it seems this comes at the cost of some functionality.

  • GlycoTorch-Vina by Eric Boittier is pre-compiled and includes terms to handle other kinds of torsions. It's ported to Windows, but in doing so several functionalities have been removed and altered.
  • Another pre-compiled using Boost 1.67.0 by Eric Boittier.