carlos-a-ramos-g / 3clpro-n3-simulations Goto Github PK

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:

• Zinovjev, K.; Tuñón, I. Adaptive Finite Temperature String Method in Collective Variables. J. Phys. Chem. A 2017, 121 (51), 9764–9772.

• 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