SIRAH-CoV2 initiative: Spike D614G mutation (introduced on PDB id:6XR8)

This dataset contains the raw data of a coarse-grained molecular dynamics simulation of the D614G mutant of Spike protein from SARS-CoV-2. The initial coordinates correspond to the PDB structure 6XR8, where the coordinates of the side chain of Aspartate 614 were deleted to produce a Glycine. Missing loops were introduced with Swiss-Model (swissmodel.expasy.org).

Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020 Glycan parameters correspond to those reported by Garay et at.2020. For further details, please contact Pablo Garay (pgaray@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).