10.17632/7GGDTB8G2R.1
Sekijima, Masakazu
Masakazu
Sekijima
Trajectory data of molecular dynamics simulation of SARS-CoV-2 RNA-dependent RNA polymerase with/without template RNA and Remdesivir triphosphate
Mendeley
2020
Dataset
Antiviral Drug
Molecular Dynamics Study
Severe Acute Respiratory Syndrome Coronavirus 2
COVID-19
Yamamoto, Kazuki
Kazuki
Yamamoto
Yasuo, Nobuaki
Nobuaki
Yasuo
Yoshino, Ryunosuke
Ryunosuke
Yoshino
2020-06-04
10.17632/7ggdtb8g2r
Creative Commons Attribution 4.0 International
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.