I have xyz positions of my atoms in a
.txt file, how can I extract information about bonding using VMD?
I want to create a LAMMPS input file that contains not only the positions, but also information about the bonding of the structure.
This seems to be what the TopoTools plugin is used for. This has commands for manipulating bonds/angles/dihedrals in VMD and then writing the corresponding information to a LAMMPS input file.