SIRAH-CoV2 initiative: Main Protease (PDB id:6LU7)

DOI10.5281/zenodo.3748665Zenodo3748665MaRDI QIDQ6704823

Dataset published at Zenodo repository.

Author name not available (Why is that?)

Publication date: 11 April 2020

Copyright license: No records found.

Description

This dataset contains the trajectory of a 15 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Main protease in its APO form (PDB id: 6LU7, Bioassembly 1).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 6LU7_SIRAHcg_rawdata1.tar, 6LU7_SIRAHcg_rawdata2.tar, and 6LU7_SIRAHcg_rawdata3.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, thefile6LU7_SIRAHcg_15us_prot.tarcontains only the protein coordinates, while6LU7_SIRAHcg_15us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untarthe file6LU7_SIRAHcg_15us_prot_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6LU7_SIRAHcg_prot.prmtop 6LU7_SIRAHcg_prot.ncrst 6LU7_SIRAHcg_prot_15us_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 contactSergio Pantano (spantano@pasteur.edu.uy).

This page was built for dataset: SIRAH-CoV2 initiative: Main Protease (PDB id:6LU7)