6.7. How to install AutoDock-GPU on Apple silicon#

Note: The binary used here is from the Scripps AutoDock-GPU release, not the separate AutoDock Vina codebase. This guide follows the working installation path for the Apple Silicon OpenCL/OpenMP binary:

adgpu-v1.6_omp_macos_aarch64_ocl_128wi

This guide assumes you are installing on an Apple Silicon Mac, such as an M1, M2, M3, or newer Mac. The example below was tested on an M2 Pro Mac.

6.7.1. 1. Install Homebrew if needed#

If Homebrew is not already installed, install it from the command line:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

After installation, make sure Homebrew is available in your shell. On Apple Silicon Macs, Homebrew is usually installed under /opt/homebrew.

You can test it with:

brew --version

6.7.2. 2. Install the required OpenMP runtime#

The omp_macos AutoDock-GPU binary expects libomp.dylib to be available from Homebrew LLVM.

Install LLVM with:

brew install llvm

Install OpenMP:

brew install libomp

Verify that the OpenMP library exists:

ls -l /opt/homebrew/opt/llvm/lib/libomp.dylib

If this file exists, the required runtime dependency is installed.

6.7.3. 3. Download the Apple Silicon AutoDock-GPU binary#

Download the Apple Silicon OpenCL/OpenMP binary from the official AutoDock-GPU GitHub releases page:

adgpu-v1.6_omp_macos_aarch64_ocl_128wi

For example, the downloaded file may initially be in:

$HOME/Downloads/adgpu-v1.6_omp_macos_aarch64_ocl_128wi

6.7.4. 4. Create a program directory for AutoDock-GPU#

Create a dedicated directory under $HOME/Programs:

mkdir -p $HOME/Programs/autodock
mkdir -p $HOME/Programs/bin

6.7.5. 5. Move the downloaded binary into place#

Move the downloaded file into the AutoDock program directory:

mv $HOME/Downloads/adgpu-v1.6_omp_macos_aarch64_ocl_128wi \
   $HOME/Programs/autodock/adgpu-v1.6_omp_macos_aarch64_ocl_128wi

Make the binary executable:

chmod +x $HOME/Programs/autodock/adgpu-v1.6_omp_macos_aarch64_ocl_128wi

Remove the macOS quarantine attribute if the file was downloaded through a browser:

xattr -d com.apple.quarantine \
  $HOME/Programs/autodock/adgpu-v1.6_omp_macos_aarch64_ocl_128wi 2>/dev/null || true

6.7.7. 7. Add $HOME/Programs/bin to your PATH#

If $HOME/Programs/bin is not already in your PATH, add it to your shell startup file.

For the default macOS zsh shell:

echo 'export PATH="$HOME/Programs/bin:$PATH"' >> $HOME/.zshrc
source $HOME/.zshrc

Confirm that the command is found:

which vina_gpu

The output should be similar to:

/Users/YOUR_USERNAME/Programs/bin/vina_gpu

6.7.8. 8. Test the installation#

Run:

vina_gpu --help

or:

vina_gpu

If the installation worked, AutoDock-GPU should print its usage information or command-line options.

6.7.9. 9. Example run command#

A typical AutoDock-GPU command uses an AutoDock grid map descriptor file and a ligand PDBQT file:

vina_gpu \
  --ffile receptor.maps.fld \
  --lfile ligand.pdbqt \
  --nrun 20

The key required inputs are:

  • --ffile or -M: the AutoDock grid map field file, usually ending in .maps.fld

  • --lfile or -L: the ligand file in .pdbqt format

  • --nrun: the number of docking runs to perform

6.7.10. 10. Troubleshooting#

6.7.10.1. Error: Library not loaded: /opt/homebrew/opt/llvm/lib/libomp.dylib#

Install LLVM with Homebrew:

brew install llvm

Then verify:

ls -l /opt/homebrew/opt/llvm/lib/libomp.dylib

Try again:

vina_gpu --help

6.7.10.2. Error: permission denied#

Make sure the binary is executable:

chmod +x $HOME/Programs/autodock/adgpu-v1.6_omp_macos_aarch64_ocl_128wi

6.7.10.3. Error: macOS says the file cannot be opened#

Remove the quarantine attribute:

xattr -d com.apple.quarantine \
  $HOME/Programs/autodock/adgpu-v1.6_omp_macos_aarch64_ocl_128wi 2>/dev/null || true

6.7.10.4. Check what libraries the binary needs#

Use otool:

otool -L $HOME/Programs/autodock/adgpu-v1.6_omp_macos_aarch64_ocl_128wi

To specifically check OpenMP linkage:

otool -L $HOME/Programs/autodock/adgpu-v1.6_omp_macos_aarch64_ocl_128wi | grep omp

6.7.11. Final installed layout#

After following this guide, the installation should look like this:

$HOME/Programs/
├── autodock/
│   └── adgpu-v1.6_omp_macos_aarch64_ocl_128wi
└── bin/
    └── vina_gpu -> ../autodock/adgpu-v1.6_omp_macos_aarch64_ocl_128wi

You can then run AutoDock-GPU from anywhere using:

vina_gpu