qmrebind

Quantum Mechanical - Molecular Mechanical reparameterization at the receptor-ligand Binding site (qmrebind) implemented in Simulation Enabled Estimation of Kinetic Rates (SEEKR) multiscale software package

Detailed installation and usage instructions can be found at https://qmrebind.readthedocs.io/en/latest/index.html.

Software Requirements :

Make sure to install these packages before running qmrebind:

• ORCA
• SEEKR2 (optional)

One is likely to want to create a unique conda environment for qmrebind calculations:

  conda create --name QMMM python=3.8

Section IA: Installing ORCA

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Follow the instructions on this page: https://qmrebind.readthedocs.io/en/latest

Alternatively, visit the official site for instructions to install ORCA: https://www.orcasoftware.de/tutorials_orca/first_steps/install.html

Section II: Installing SEEKR2 (optional)

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Use the instructions on this page to install SEEKR2, if desired: https://seekr2.readthedocs.io/en/latest/installation.html

Installation and Setup Instructions :

• Activate the previously created conda environment:

conda activate QMMM # activate the conda environment
conda install -c conda-forge ambertools biopandas pandas matplotlib parmed regex openmm
pip install PyPDF2

• Clone the qmrebind repository :

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

• 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 setup.py install
python setup.py test # optional

Detailed documentation can be found at https://qmrebind.readthedocs.io/en/latest/installation.html.

Input PDB file Requirements.

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qmrebind accepts the PDB input file with the following requirements:

• PDB file typically should have the box vector information.

• Ligand and the receptor must be assigned a residue name, with the ligand following the receptor.

Authors and Contributors

The following people have contributed directly to the coding and validation efforts of qmrebind (listed in alphabetical order of first name). The author would like to thank everyone who has helped or will help improve this project by providing feedback, bug reports, or other comments.

• Anupam Anand Ojha, UC San Diego (Author and Lead Developer)
• Eliseo Marin-Rimoldi, MoLSSI (Project Mentor and Collaborator)
• Lane W. Votapka, UC San Diego (Project Mentor and Developer)
• Rommie E. Amaro, UC San Diego (Principal Investigator)

Citing qmrebind

If you use qmrebind, please cite the following paper:

• ADD PAPER HERE

Copyright

Copyright (c) 2022, Anupam Anand Ojha

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.