SIRAH-CoV2 initiative: UPDATED TRAJECTORY of SARS-Cov2 Spike´s RBD / ACE2-B0AT1 complex (PDB id:6M17)
DOI10.5281/zenodo.3942566Zenodo3942566MaRDI QIDQ6704837
Dataset published at Zenodo repository.
Author name not available (Why is that?)
Publication date: 14 July 2020
Copyright license: No records found.
This dataset contains an updated trajectory of a four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spikes RBD, ACE2, and B0AT1 (PDB id: 6M17). It substitutes the previous one on the same system, which was performed in the absence of disulfide bridges. 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.Zinc ions were parameterized as reported inKlein et al. 2020. The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar,6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tarcontainall 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, thefile6M17_SIRAHcg_4us_prot.tarcontains only the protein coordinates, while6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untarthe file6M17_SIRAHcg_4us_prot_skip10ns.tar 2- Open the trajectory on VMD 1.9.3 using the command line: vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot.ncrst 6M17_SIRAHcg_4usprot_skip.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: UPDATED TRAJECTORY of SARS-Cov2 Spike´s RBD / ACE2-B0AT1 complex (PDB id:6M17)
