Interaction Energy

Molecular dynamics (MD) simulation systems were built with 6M17 using CHARMM-GUI (see the work flow). One hundred nanosecond imulations were run with Gromacs 2019.4 and 2020.4 (see an output example). NAMD input files (pdb, psf, dcd) were created using VMD, and interaction energies were calculated using Tool.py (see an example) using a parameter file (e.g. par_all36m_prot.prm).

Tool.py gives two options. The first option calculates the non-bonded interaction energy between soluble hACE2 and the viral receptor binding domain (RBD). During the MD simulation, the trajectory (atomic coordinates) was recorded at each nanosecond resulting in 100 snapshots. Therefore, 100 interaction energies were calculated by Tool.py. The second option calculates the pairwise interaction energy between each residue of hACE2 (residue 21-615) and the RBD. At each snapshot, interaction energies were calculated for 595 residues of soluble hACE2. The NAMD configuration file generated by Tool.py is identical for the option #1 and #2 (see explanations of some parameters).

A plot of heavy-atom RMSD across the 100 ns MD simulation was generated with VMD. A plot of mean interaction energies and associated standard deviation (SD) vs residue numbers was created using plot.py. A pdb file (temp.pdb) with the mean interaction energy and SD in column 10 (occupancy) and 11 (b-factor) was created using script.py. In PyMOL, these energy and SD values can be expressed on the protein structure with color gradient using "spectrum q, blue_white_red" and "spectrum b" commands.