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COVID-19 Simulation Process
COVID-19 Simulation Process
Run Modeller to generate a mutated version of your system of interest.
Run CHARMM-GUI to dissolve your model in a virtual waterbox.
Use GROMACS to simulate the system for 100 ns.
Convert your files and perform an initial RMSD analysis using VMD.
Run Tool.py to compute interaction energies between proteins.
There are many examples of this process on the COVID-19 Progress page.
The priority is to run 100ns MD simulations for 6M17 and our decoys (with RBD). You have to install Gromacs 2020.4 first.
Dr. Norimatsu has already benchmarked all the systems at 298.15 degrees kelvin (room temperature). Please replicate the smallest system (free decoy) at 310 degrees kelvin, and make sure you get similar results.
SARS-CoV-2 RBD with sACE2 (Residue 21-615)
PDB code: 6M17
The simulation system was prepared using CHARMM-GUI Solution Builder.
Force Field: CHARMM36m
Ions: 142 mM NaCl
Temperature: room temperature (298.15)
Decoy + SARS-CoV-2 RBD
PDB code: 6M17
The simulation system was prepared using CHARMM-GUI Solution Builder.
Force Field: CHARMM36m
Ions: 142 mM NaCl
Temperature: room temperature (298.15)
Free sACE2
PDB code: 1R42
The simulation system was prepared using CHARMM-GUI Solution Builder.
Force Field: CHARMM36m
Ions: 142 mM NaCl
Temperature: room temperature (298.15)
Free Decoy
PDB code: 1R42
The simulation system was prepared using CHARMM-GUI Solution Builder.
Force Field: CHARMM36m
Ions: 142 mM NaCl
Temperature: room temperature (298.15)
Free RBD
PDB code: 6M17
The simulation system was prepared using CHARMM-GUI Solution Builder.
Force Field: CHARMM36m
Ions: 142 mM NaCl
Temperature: room temperature (298.15)
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