Author: Maria Bzówka; Karolina Mitusinska; Agata Raczynska; Aleksandra Samol; Jack Tuszynski; Artur Góra
Title: Molecular Dynamics Simulations Indicate the SARS-CoV-2 Mpro Is Not a Viable Target for Small-Molecule Inhibitors Design Document date: 2020_3_2
ID: mp3a9c9u_29
Snippet: The Packmol software [53] was used to build the initial systems consisting of protein (protonated according to the previously described procedure), water, and particular cosolvent molecules. 4 and 3 Na + ions were added to the SARS-CoV-2 Mpro and the SARS-CoV Mpros, respectively. It was assumed that the percentage concentration of the cosolvent should not exceed 5% (in the case of ACN, DMSO, MEO, and URE), or should be about 1% in the case of BNZ.....
Document: The Packmol software [53] was used to build the initial systems consisting of protein (protonated according to the previously described procedure), water, and particular cosolvent molecules. 4 and 3 Na + ions were added to the SARS-CoV-2 Mpro and the SARS-CoV Mpros, respectively. It was assumed that the percentage concentration of the cosolvent should not exceed 5% (in the case of ACN, DMSO, MEO, and URE), or should be about 1% in the case of BNZ and PHN phenol (see Supplementary Table S4 ). The mixed-solvent MD simulation procedures (minimization, equilibration, and production) carried out using the AMBER 18 package were identical as for the classical MD simulations. Only the heating stage differed -it was extended up to 40 ps.
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