SIRAH-CoV2 initiative: Papain-like Protease (PDB id:6W9C)
SIRAH-CoV2 initiative: Papain-like Protease (PDB id:6W9C) (Dataset published at Zenodo repository.)
DOI10.5281/zenodo.3766270Zenodo3766270MaRDI QIDQ6704828
Dataset published at Zenodo repository.
Author name not available (Why is that?)
Publication date: 25 April 2020
Copyright license: No records found.
This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Papain-like protease in its APO form with Zn ions bound (PDB id: 6W9C).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 6W9C_SIRAHcg_rawdata_0-5us.tar, 6W9C_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, thefile6W9C_SIRAHcg_10us_prot.tarcontains only the protein coordinates, while6W9C_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untarthe file6W9C_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6W9C_SIRAHcg_prot.prmtop 6W9C_SIRAHcg_prot.ncrst 6W9C_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 FlorenciaKlein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
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