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Simulation report and files

General information

Name: Spike protein in the Open state

Included proteins: Spike

Uniprot ID: P0DTC2

Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)

PDB ID: 6VSB

Submitted by: Amaro Lab

Submission date: October 28, 2020

System setup

Ligands: None

Membrane composition: None

Solvent type: TIP3P (water was filtered out of the simulation output)

Total number of atoms: 72759

Simulation details

Software and version: NAMD 2.14

Forcefield and version: CHARMM36 N/D

Time step : 2.0 fs

Delta : 0.3 ns

Replicates: 1

Accumulated simulation time: 1.0005 µs



References

Casalino, L.; Gaieb, Z.; Goldsmith, J.A.; Hjorth, C.K.; Dommer, A.C.; Harbison, A.M.; Fogarty, C.A.; Barros, E.P.; Taylor, B.C.; McLellan, J.S.; et al. Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein. bioRxiv 2020, 2020.06.11.146522. DOI: 10.1101/2020.06.11.146522


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The interaction network has been generated using Flare Plots, powered by R. Fonseca and A. J. Venkatakrishnan.

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Spike protein in the Open state ( 6VSB)

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