SIRAH-CoV2 initiative: NSP16 - NSP10 Complex (PDB id:6W4H)
DOI10.5281/zenodo.3779057Zenodo3779057MaRDI QIDQ6704829
Dataset published at Zenodo repository.
Martín Soñora, Pablo Garay, Matías MacHado, Exequiel Barrera, Florencia Klein, Sergio Pantano
Publication date: 30 April 2020
Copyright license: Creative Commons Attribution 4.0 International
This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 NSP16 - NSP10 Complexwith Zn ions bound (PDB id: 6W4H).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 file6W4H_SIRAHcg_rawdata.tarcontainsall 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, thefile6W4H_SIRAHcg_10us_prot_Zn.tarcontains only the protein coordinates, while6W4H_SIRAHcg_10us_prot_Zn_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untarthe file6W4H_SIRAHcg_10us_prot_Zn_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6w4h_SIRAHcg_prot.prmtop 6w4h_SIRAHcg_prot.ncrst 6w4h_SIRAHcg_prot_Zn_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 Martn Soora (msonora@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
This page was built for dataset: SIRAH-CoV2 initiative: NSP16 - NSP10 Complex (PDB id:6W4H)
