Trajectory data of molecular dynamics simulation of SARS-CoV-2 RNA dependent RNA polymerase (RdRp, also named nsp12) and inhibitor drug candidates

Published: 7 May 2020| Version 2 | DOI: 10.17632/jwk3yvryjs.2
, Masakazu Sekijima


MD simulations were performed using Desmond on supercomputer TSUBAME 3.0. The inhibitor-SARS-CoV-2 RdRp 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.



RNA Polymerase, Molecular Dynamics, Molecular Docking, Severe Acute Respiratory Syndrome Coronavirus 2, COVID-19