Add option of periodic chain topology to pdb2gmx
Currently pdb2gmx cannot generate a periodically connected chain topology, useful e.g. for a polymer or DNA/RNA systems. In addition to not being supported, pdb2gmx can make the "manual" topology generation difficult because it will refuse to generate topologies with missing bonds. It would at least help to have a flag allowing the user trying to manually modify the topology to generate such broken topologies (note: to my understanding this is what the -missing flag should do, but in practice this flag does not always avoid the fatal error of "dangling bonds").