Workbench
General information
Name: Gromacs 60 ns MD of SARS-CoV-2 spike trimer, All Atom model (60 ns)
Included proteins: Spike
Uniprot ID: P0DTC2
Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
PDB ID: 6VXX
Description: This trajectory is from a 60 ns MD simulation of the SARS-CoV-2 spike protein. The proteinwas solvated in a 20 x 20 x 20 nm water box containing 0.1 M NaCl. The simulation was performedwith Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Charmm27 force field. The interval between frames is 80 ps. The simulation was conducted in the NPT ensemble (1 bar). This trajectory is all atom.
Extracted from: BioExcel (ID: MCV1900064)
Author: Dmitry Morozov
Submission date: October 22, 2020
System setup
Ligands: None
Membrane composition: None
Solvent type: TIP3P (water was filtered out of the simulation output)
Total number of atoms: 52329
Simulation details
Software and version: GROMACS 2018.8
Forcefield and version: charmm27
Time step : 2.0 fs
Delta : 0.08 ns
Replicates: 1
Accumulated simulation time: 0.0578 µs
References
SARS-CoV-2 Spike Protein Model for Computational Screening of Therapeutic COVID-19 Drugs. Dmitry Morozov1, Gerrit Groenhof1, Vladimir Mironov2
1. Department of Chemistry and Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
2. Chemistry Department, Moscow State University, 119991 Moscow, Russia
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
Selection
Site of interest
Region of interest
Coiled-coil region
Domain of interest
Toolkit
Select a variant from the sequence to obtain its impact score as well as mutation effect and time-dependent descriptors:
Select a variant from the sequence above to obtain its impact score as well as mutation effect and time-dependent descriptors.
| Substitution scores | ||
|---|---|---|
| BLOSUM90 score | ||
| Δ charge | ||
| Epstein's coefficient of difference | ||
| Experimental exchangeability | ||
| Grantham's distance | ||
| Miyata's distance | ||
| Sneath's index | ||
| Δ hydrophobicity | ||
| Conservation | ||
|---|---|---|
| Frequency (‰) | ||
| SIFT4G Score | ||
| SIFT4G Median IC | ||
| Structure | ||
|---|---|---|
| Post-translational modification | ||
| Surface accessibility | ||
| FoldX ΔΔG | ||
| Experimental | ||
|---|---|---|
| Mean Experimental Antibody Escape | ||
| Max. Experimental Antibody Escape | ||
| Others | ||
|---|---|---|
| Annotation | ||
| Parameter | Average | Weight average | SD | Weight SD | |
| RMSD |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| RMSF |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| SASA |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| CHI1 |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| All contacts |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| Hydrogen bond contacts |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| Salt bridge contacts |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| Hydrophobic contacts |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| Pi-cation contacts |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| Pi-stacking contacts |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| T-stacking contacts |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| Van der Waals contacts |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| Water bridge contacts |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
| Extended water bridge contacts |
|
|
|||
|
Please select a variant from the sequence above. |
|||||
Upload your own descriptors according to this template.