The .prmtop file is a text file as used by the AMBER software for molecular dynamics simulations and contains the topology of the molecular system. Any text editor should be able to read the file, though it is designed towards being used by the program. The .nc file is a binary file format for trajectories created by the AMBER software. .prmtop and .nc files can be read by the program CPPTRAJ (of the AmberTools software suite: https://ambermd.org/) or molecular viewers like VMD (https://www.ks.uiuc.edu/Research/vmd/).