This tool is brilliant, but it has a significant drawback - when exporting files into .pdb format, it puts the first atom of monomer n+1 into monomer n. When the input is set to z-matrix, it's impossible to change the head/tail numbers, so that those atoms are at the edges of monomer blocks in .pdb, and it's easier to parse it using scripts.
Is there any other way to have a .pdb file where atoms of a single monomer are in a single block, without any other atoms in-between?