Installation

To install MetalDock correctly, please follow the instructions below:

Step 1: Create Conda Environment

First, make sure you have Miniconda or Anaconda installed. If not, you can find installation instructions at Miniconda.

Once you have Conda installed, create a new Conda environment named "MetalDock" and use Python 3.8:

conda create -n MetalDock python=3.8

Activate the "MetalDock" environment:

conda activate MetalDock

Step 2: Install Required Packages

Next, install several required packages using Conda and Pip:

conda install -c conda-forge openbabel

pip install ase==3.22.1 networkx numpy pandas pdb2pqr plams typing_extensions

Step 3: Clone MetalDock repository

Clone the MetalDock respository to your desired location.

git clone https://github.com/MatthijsHak/MetalDock

Step 4: Setup QM environment variables

MetalDock can run on three different quantum chemistry software packages:

ADF

To run ADF as QM engine the following environment variables need to be exported:

export AMSHOME=/full/path/to/ams/ams2022
export AMSBIN=$AMSHOME/bin
export AMSRESOURCES=$AMSHOME/atomicdata
export SCMLICENSE=$AMSHOME/license.txt

Relativistic effects with ZORA. For more infromation see SCM site.

Gaussian

To run Gaussian as QM engine the following environment variables need to be exported.

export g16root=/full/path/to/gaussian/g16

Relativistic effects with DKH. For more information see Gaussian site.

ORCA (free)

Currently, the latest ORCA 6.0.0 version is not supported, install ORCA 5.0.4 or lower to use MetalDock. To run ORCA as QM engine with correct parralelization the full path to the orca binary has to be exported with the following command:

export ASE_ORCA_COMMAND='/full/path/to/orca/orca PREFIX.inp > PREFIX.out'

Relativistic effects can be selected with input. For more infromation see ORCA site.

Step 5: Add MetalDock to PATH

If you want to use MetalDock conventiely from any directory, you can add its executable to your PATH. Replace /user/directory/MetalDock with the actual path to your MetalDock installation directory:

export PATH=$PATH:/user/defined/path/MetalDock

This completes the installation process for MetalDock. You can now run metaldock by:

metaldock -i input.ini