SIRAH-CoV2 initiative: co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ)

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ).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. The files 6WIQ_SIRAHcg_rawdata_0-5us.tar, and 6WIQ_SIRAHcg_rawdata_5-10us.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, thefile6WIQ_SIRAHcg_10us_prot.tarcontains only the protein coordinates, while6WIQ_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untarthe file6WIQ_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6WIQ_SIRAHcg_prot.prmtop 6WIQ_SIRAHcg_prot.ncrst 6WIQ_SIRAHcg_10us_prot_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 Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).

This page was built for dataset: SIRAH-CoV2 initiative: co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ)