Scripts to perform a) GROMACS MM setup and MM simulations for a metalloprotein and b) subsequent Chemshell QM/MM calculations as used in our nitrogenase QM/MM studies:
- QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site Bardi Benediktsson and Ragnar Bjornsson, Inorg. Chem. 2017, 56, 13417-13429. http://pubs.acs.org/doi/full/10.1021/acs.inorgchem.7b02158
- QM/MM calculations reveal a bridging hydroxo group in a vanadium nitrogenase crystal structure Bardi Benediktsson, Albert T. Thorhallsson, Ragnar Bjornsson* Chem. Comm., 2018, 54, 7310-7313.
- Resolving the structure of the E1 state of Mo Nitrogenase through Mo and Fe K-edge EXAFS and QM/MM calculations C. Van Stappen, A. Th. Thorhallsson, L. Decamps, R. Bjornsson*, S. DeBeer*, Chem. Sci. 2019, 10, 9807-9821.
- A model for dinitrogen binding in the E4 state of nitrogenase Albert Th. Thorhallsson, Bardi Benediktsson, Ragnar Bjornsson*, Chem. Sci. 2019, 10, 11110-11124.
- Quantum Mechanics/Molecular Mechanics Study of Resting-State Vanadium Nitrogenase: Molecular and Electronic Structure of the Iron–Vanadium Cofactor Bardi Benediktsson and Ragnar Bjornsson, Inorg. Chem. 2020, 59, 11514–11527.
- The E2 state of FeMoco: hydride formation vs. Fe reduction and a mechanism for H2 evolution A. Th. Thorhallsson, R. Bjornsson, Chem. Eur. J. 2021, 27, 16788-16800.
- Carbon Monoxide Binding to the Iron-Molybdenum Cofactor of Nitrogenase: A Detailed Quantum Mechanics/Molecular Mechanics Investigation N. B. Spiller, R. Bjornsson, S. DeBeer, F. Neese, Inorg. Chem. 2021, 60, 18031-18047.
- Analysis of the geometric and electronic structure of spin-coupled iron-sulfur dimers with broken-symmetry DFT: implications for FeMoco B. Benediktsson, R. Bjornsson, J. Chem. Theory Comput. 2022, accepted.
See page: https://sites.google.com/site/ragnarbjornsson/mm-and-qm-mm-setup for detailed descriptions on using the scripts.
If you find these scripts useful, please consider citing the article:
- QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site Bardi Benediktsson and Ragnar Bjornsson, Inorg. Chem. 2017, 56, 13417-13429. http://pubs.acs.org/doi/full/10.1021/acs.inorgchem.7b02158
Our research group has now switched over to our own open-source QM/MM program ASH which is Python-based and more convenient: See https://github.com/RagnarB83/ash and https://ash.readthedocs.io
See QM/MM tutorials: https://ash.readthedocs.io/en/latest/QM-MM-protein.html and https://ash.readthedocs.io/en/latest/Metalloprotein-I.html