SIRAH-CoV2 initiative: RBD triple glycosylated at Asn331, 343, and 481 from PDB structure 6XEY

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of a Spike's RBD from SARS-CoV2 glycosylated at Asn331, 343, and 481 with Man9 glycosylation trees. The initial coordinates correspond to amino acids 327 to 532 taken from the PDB structure 6XEY. Missing loops and glycosylation trees were added with CHARMM-GUI (charmm-gui.org).

Simulations have been 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 al For further details, please contact Pablo Garay (pgaray@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).