Can VMD load PDB files containing more than 99,999 atoms?
Yes. VMD can load a properly formatted PDB file with an arbitrary number of atoms. VMD is able to do this because it ignores the atom indices stored the PDB file itself and instead it uses its own internal numbering scheme. As long as your PDB file follows the strict column rules from the PDB spec, VMD doesn’t care how many atoms are in the file.
