SIRAH-CoV2 initiative: RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 (PDB id:7BTF)
DOI10.5281/zenodo.3865479Zenodo3865479MaRDI QIDQ6704834
Dataset published at Zenodo repository.
Exequiel Barrera, Florencia Klein, Martín Soñora, Pablo Garay, Sergio Pantano, Matías MacHado
Publication date: 29 May 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 RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 and Zinc (PDB id: 7BTF).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 7BTF_SIRAHcg_rawdata_0-2us.tar, 7BTF_SIRAHcg_rawdata_2-6us.tar, and7BTF_SIRAHcg_rawdata_6-10us.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, thefile 7BTF_SIRAHcg_10us_prot.tarcontains only the protein coordinates, while7BTF_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untarthe file7BTF_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD 1.9.3 using the command line: vmd 7BTF_SIRAHcg_prot.prmtop 7BTF_SIRAHcg_prot.ncrst 7BTF_SIRAHcg_prot_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 Martin Soora (msonora@pasteur.edu.uy) Sergio Pantano (spantano@pasteur.edu.uy).
This page was built for dataset: SIRAH-CoV2 initiative: RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 (PDB id:7BTF)
