Trajectory data of molecular dynamics simulation of SARS-CoV-2 RNA-dependent RNA polymerase with/without template RNA and Remdesivir triphosphate

Published: 4 June 2020| Version 1 | DOI: 10.17632/7ggdtb8g2r.1
Contributors:
Kazuki YAMAMOTO,
Nobuaki Yasuo,
Ryunosuke Yoshino,
Masakazu Sekijima

Description

MD simulations were performed using Desmond on supercomputer TSUBAME 3.0. SARS-CoV-2 RdRp (also named nsp12) with/without template RNA and Remdesivir triphosphate complex models were placed in the orthorhombic box with a buffer distance of 10 Å in order to create a hydration model. TIP3P water model was used for creation of the hydration model. We performed MD simulations under the NPT ensemble for 1 μs on three complex structures using OPLS3e force field.

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Categories

Antiviral Drug, Molecular Dynamics Study, Severe Acute Respiratory Syndrome Coronavirus 2, COVID-19

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