ACE2 fragment as a decoy for novel SARS-Cov-2 virus

Fabiana Renzi; Dario Ghersi

Simulations were performed using GROMACS (17, 18) with the all-atom OPLS force field. Non-protein atoms were removed from the PDB files. The protein structures were placed in a cubic box with 10Ã… from the box edge and solvated with spc216.gro, an equilibrated 3-point solvent model. Next, we added ions to the system with the genion module and performed 50,000 steps of energy minimization. We then carried out equilibration in two steps: NVT (canonical) ensemble followed by NPT (isothermic-isobaric). For the NVT equilibration phase, we set the target temperature to 300 K and inspected the temperature graph over time (100 ps) to make sure the system was stabilized around the target temperature value. For the NPT equilibration phase, we used the Parrinello-Rahman barostat, and inspected the density values over time (100 ps) to check the stability of the system. After the equilibration steps, we ran a 100 ns production run on a GPU-accelerated machine. All MD simulations were performed with the same protocol and a time step of 2 fs. The trajectories were visually inspected in UCSF Chimera (16) , and the RMSD with respect to the initial energy-minimized conformer was obtained with the rms module in the GRO-MACS suite.