Installation

At this time, QMrebind has only been tested on Linux systems. Therefore, all installation instructions are for Linux only.

Install Conda

If you do not already have Conda, it can be easily installed by completing the following steps:

Download Conda, run the script, and fill out the prompts:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Make sure Conda is installed by running:

which conda

You will want to use Python 3.8, so you can see which version you are with the command:

python -V

If it says any other version besides Python 3.8, then enter:

conda install python=3.8

If you want you can create a conda environment,

conda create --name QMMM python=3.8

but you can also just install all packages straight to the base environment if you wish to. If using an environment, whenever you’re installing or running anything involving QMrebind, make sure that you have activated your environment by running conda activate QMMM.

Install Orca

Make sure to install ORCA before running QMrebind:

Follow the instructions below or visit this page to install ORCA: https://www.orcasoftware.de/tutorials_orca/first_steps/install.html

1. Go to https://orcaforum.kofo.mpg.de/ucp.php?mode=login. Create an account to log in with a username and a password.

  1. Go to Downloads.

  2. Select ORCA 5.0.3

4. The ORCA tar files will be downloaded in three parts: Download ORCA 5.0.3, Linux, x86-64, .tar.xz Archive, Part 1/3, ORCA 5.0.3, Linux, x86-64, .tar.xz Archive, Part 2/3 and ORCA 5.0.3, Linux, x86-64, .tar.xz Archive, Part 3/3. These are separate downloaded tar files.

5. Extract all three parts and copy all the contents into the folder named “orca”.

tar -xf orca_5_0_3_linux_x86-64_openmpi411_part1.tar.xz
tar -xf orca_5_0_3_linux_x86-64_openmpi411_part2.tar.xz
tar -xf orca_5_0_3_linux_x86-64_openmpi411_part3.tar.xz
mv orca_5_0_3_linux_x86-64_openmpi411_part1/* .
mv orca_5_0_3_linux_x86-64_openmpi411_part2/* .
mv orca_5_0_3_linux_x86-64_openmpi411_part3/* .

6. To assign the path variable and source it, open the bashrc file (vi ~/.bashrc) and add the following lines:

export PATH="$HOME/orca:$PATH"
export LD_LIBRARY_PATH="$HOME/orca:$LD_LIBRARY_PATH"

  1. Source the bashrc file:

source ~/.bashrc

The correct environment probably deactivated:

conda activate QMMM

8. Run ORCA using the following command by typing “orca” in the terminal. The expected outcome for a successful installation will be similar to the following:

This program requires the name of a parameter file as an argument
For example, ORCA TEST.INP

Install OpenMPI

  1. Go to https://www.open-mpi.org/ and select Downloads.

2. Download the openmpi-4.1.1 release with this link: https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.bz2 (It must be this version)

  1. Extract the file and rename the folder as “openmpi”. Enter this directory.

tar -xzf openmpi-4.1.1.tar.gz
mv openmpi-4.1.1 $HOME/openmpi
cd $HOME/openmpi

4. Go into to the openmpi folder. Open the terminal and execute the following command in the terminal:

./configure --prefix=$HOME/openmpi
make all
make install

  1. To assign the path variable and source it, open the bashrc file (vi ~/.bashrc) and add the following lines:

export PATH=$HOME/openmpi/bin:$PATH
export LD_LIBRARY_PATH="$HOME/openmpi/lib:$LD_LIBRARY_PATH"

  1. Source the bashrc file:

source ~/.bashrc

The correct environment probably deactivated:

conda activate QMMM

Install XTB

  1. Go to https://github.com/grimme-lab/xtb/releases

2. Select the xtb version 6.5.1 or go to https://github.com/grimme-lab/xtb/releases/tag/v6.5.1

3. Download the xtb tar file, xtb-6.5.1-linux-x86_64.tar.xz, and extract the file.

tar -xf xtb-6.5.1-linux-x86_64.tar.xz

4. Copy the xtb executable to the orca folder in HOME, and rename it as otool_xtb.

cp xtb-6.5.1/bin/xtb ~/orca/otool_xtb

Install QMrebind

  1. Activate the previously created conda environment:

conda activate QMMM # activate the conda environment
conda install -c conda-forge ambertools
conda install -c conda-forge openmm
pip install PyPDF2

  1. Clone the qmrebind repository :

git clone https://github.com/seekrcentral/qmrebind.git

3. Perform the following steps to get this package installed quickly on a local Linux machine (Installation in the home directory is recommended) :

cd qmrebind
python -m pip install .
pytest # optional