0 ns and 75 ns configurations of glycosylated ACE2-FC and its interaction with SARS-CoV-2 binding domains

These are initial and final (75ns) configurations in PDB format of  glycosylated ACE2-FC fusion proteins which are promising targets for a COVID-19 therapeutic. Some of them are in interaction witha fragment of the receptor-binding domain (RBD) of the Spike Protein S of the SARS-CoV-2 virus. We used two  glycosylation variants for ACE2-FC, variant 1 is fully glycosylated with Man8 glycans, variant 2 is fully glycosylated with GnGnXF3. The Spike RBD is glycosylated with ANaF^6.

Methods
Molecular Dynamics Simulations using Gromacs

Details:

Fuse ACE2 with Fc to ACE2-Fc using Modeller 
Model Zn2+ and coordinating residues with MCPB.py 
Attach glycans using glycam.org 
Merge structures from 2. and 3. using github.com/austenb28/MCPB_Glycam_merge 
Generate topology files using AmberTools 
Convert topology files to Gromacs format using Acpype 
Perform rigid energy minimization (EM) of glycans using github.com/austenb28/GlyRot
Perform EM (emtol = 1000 kJ/mol/nm)
Solvate and add ions
Perform 10 ps constant volume (NVT) (dt = 0.2 fs, T = 310 K)
Perform EM (emtol = 1000 kJ/mol/nm)
Perform 100 ps NVT (dt = 2 fs, T = 310 K)
Perform 100 ps constant pressure (NPT) (dt = 2 fs, T = 310 K, P = 1 atm)
Perform 75 ns production NPT (dt = 2 fs, T = 310 K, P = 1 atm)