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 Mamba environment for qmrebind calculations:

  mamba create --name QMMM

Installing ORCA

---

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

Installing SEEKR2 (optional)

---

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 Mamba environment:

mamba activate QMMM # activate the mamba environment
mamba install 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 -m pip install .
pytest # optional

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

Input PDB file Requirements.

---

qmrebind accepts the PDB input file with the following requirements:

• PDB file typically should have the box vector information (In a CRYST1 line).

• 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:

• Ojha AA, Votapka LW, Amaro RE. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chem Sci. 2023 Oct 24;14(45):13159-13175. doi: 10.1039/d3sc04195f. PMID: 38023523; PMCID: PMC10664576.

Copyright

Copyright (c) 2023, Anupam Anand Ojha

Acknowledgements

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