SIRAH-CoV2 initiative: S2 Spike core fragment in postfusion state (PDB id:6M1V)
DOI10.5281/zenodo.4019350Zenodo4019350MaRDI QIDQ6704838
Dataset published at Zenodo repository.
Exequiel Barrera, Florencia Klein, Martín Soñora, Sergio Pantano, Matías MacHado, Pablo Garay
Publication date: 8 September 2020
Copyright license: Creative Commons Attribution 4.0 International
This dataset contains the trajectory of a 10microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Spike S2 fragment in its postfusion form(PDB id: 6M1V).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 6M1V_SIRAHcg_rawdata_0-5us.tar, and 6M1V_SIRAHcg_rawdata_5-10us.tar, containall the raw information required to visualize (on VMD 1.9.3), 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, thefile6M1V_SIRAHcg_10us_prot.tarcontains only the protein coordinates, while6LU7_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untarthe file 6M1V_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD 1.9.3 using the command line: vmd 6M1V_SIRAHcg_prot.prmtop 6M1V_SIRAHcg_prot.ncrst 6M1V_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: S2 Spike core fragment in postfusion state (PDB id:6M1V)
