creating PDBs for OpenMM simulations

There does not seem to be a standard way to create structure files (PDBs) for input to OpenMM simulations using Alexandria FF.

Especially, when simply taking any PDB with the correct structure, OpenMM may complain about a) the atom names and b) the bonds. Currently, fixing the atom names may be done manually, and bonds might be guessed correctly by openbabel. (In principle, OpenMM should be able to guess bonds itself, but in my case that only worked for a single adenine in gas phase, whereas OpenMM raised an error when I tried adenine in water.)