The Michaelis-Complex Molecular dynamic simulation was obtained using amber, for detailed explaination please refers to:
-Ramos-Guzmán, Carlos A.; Ruiz-Pernía, J. Javier; Tuñón, Iñaki (2020): A Microscopic Description of SARS-CoV-2 Main Protease Inhibition with Michael Acceptors. Strategies for Improving Inhibitors Design. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.12895064.v1
The Transition State trajectory was obtained using the string methodology:
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Zinovjev, K.; Tuñón, I. Adaptive Finite Temperature String Method in Collective Variables. J. Phys. Chem. A 2017, 121 (51), 9764–9772.
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Zinovjev, K. String-Amber https://github.com/kzinovjev/string-amber
Use the next atom selection in VMD to visualize the QM region in the transition state trayectory:
index 608 to 619 2238 to 2241 4663 to 4673 4685 to 4688 4704 53383 to 53385