6 molecular dynamics simulations of coronavirus 2019-nCoV protease model in complex with different conformations of lopinavir.

Molecular dynamics simulations of comparative model of novel coronavirus 2019-nCoV protease Mpro in complex with 6 different conformations based on the Catalophore point-cloud alignment and (re)- docking of lopinavir into the 2019ncov virus protease model. The docking experiment produced 8 clusters of possible conformations, we chose 6 out of 8 conformers and ran an all-atom 300 ps MD at 310 K (=36.85°C).
-The two images in the main folder refers to the docked structures before MD simulation.-The file all_centroids.pse contains the frames representing the centroid of the subsequent MD simulation for each docking cluster.-Each archive contains the centroid in PDB format, the starting frame of the simulation in GRO format and the compressed trajectory in XTC format. In the directory "other_files" there are other data generated during the simulation, i.e. heatmap representing the contact frequency between the ligand atoms and the ones belonging to the homology model.