SIRAH-CoV2 initiative: RBD triple glycosylated at Asn331, 343, and 481 from PDB structure 6XEY (Q6704841)

This dataset contains the trajectory of a 10microseconds-long coarse-grained molecular dynamics simulation of aSpikes RBD fromSARS-CoV2glycosylated at Asn331,343, and 481 with Man9 glycosylation trees. The initial coordinates correspond to amino acids 327 to 532taken from the PDB structure 6XEY. Missing loops and glycosylation trees were added with CHARMM-GUI (http://www.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 inMachado et al. JCTC 2019, adding 150 mM NaCl according toMachado Pantano JCTC 2020.Glycan parameters correspond to those reported by Garay et al. The files 6XEY-RBD-3Man9_SIRAHcg_0-4us.tar, 6XEY-RBD-3Man9_SIRAHcg_4-8us.tar, and6XEY-RBD-3Man9_SIRAHcg_8-10us.tar, containall the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzingCG trajectories usingSirahToolscan be found at www.sirahff.com. Additionally, thefile6XEY-RBD-3Man9_SIRAHcg_glycoprot_10us.tarcontains only the protein coordinates, while6XEY-RBD-3Man9_SIRAHcg_glycoprot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untarthe file6XEY-RBD-3Man9_SIRAHcg_glycoprot_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6XEY-RBD-3Man9_SIRAHcg_glycoprot.prmtop 6XEY-RBD-3Man9_SIRAHcg_glycoprot.ncrst 6XEY-RBD-3Man9_SIRAHcg_10us_skip10ns.nc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc.,and coloring byrestype, element, name, etc. This dataset is part of the SIRAH-CoV2initiative. For further details, please contact Pablo Garay (pgaray@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).