Free cookie consent management tool by TermsFeed SCoV2-MD

Workbench

Simulation report and files

General information

Name: Nucleoprotein

Included proteins: N

Uniprot ID: P0DTC9

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

PDB ID: 6VYO

Submitted by: Exscalate4CoV - CINECA

Submission date: May 05, 2021

System setup

Ligands: None

Membrane composition: None

Solvent type: None

Total number of atoms: 7782

Simulation details

Software and version: GROMACS 2020.2

Forcefield and version: AMBER 99

Time step : 0.2 fs

Delta : 2.0 ns

Replicates: 1

Accumulated simulation time: 45.4880 µs

Visualization and trajectory sharing powered by NGL Viewer and MDsrv.

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

Viewer

Nucleoprotein ( 6VYO)

Selection

Quick selection
Custom selection
Input your selection using the NGL selection language.

Toolkit

General
Interaction network

Hydrogen bonds

  • Interacting pairs
  • Hide neighbours
  • All
  • Simulation
  • Current frame
  • Summary
RMSD
Trajectory:
Frames:
All
From to
Stride:
Reference: frame from trajectory
Selection:
Protein alpha carbons
Protein CA, CB, C, N, O
Non-hydrogen protein atoms
All protein atoms
RMSF
Trajectory:
Frames:
All
From to
Stride:
Selection:
Protein alpha carbons
Protein CA, CB, C, N, O
Non-hydrogen protein atoms
All protein atoms
Variant impact
No variants found in the sequence of this structure.