SIRAH-CoV2 initiative: NSP15 Endonuclease (PDB id:6W01) (Q6704821)

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Endoribonuclease NSP15 in its APO form (PDB id: 6W01, Bioassembly 1).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. The file6W01_SIRAHcg_rawdata.tarcontains all 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 using SirahTools can be found at www.sirahff.com. Additionally, thefile6W01_SIRAHcg_10us_prot.tarcontains only the protein coordinates, while6W01_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untarthe file6W01_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6W01_SIRAHcg_prot.prmtop 6W01_cg_prot.ncrst 6W01_SIRAHcg_prot_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 Exequiel Barrera (ebarrera@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).