ChargePlacer with examples and auxillary MD scripts

This is a command line script to determine a reasonably energy minimised proton sequence for an input PDB file (input) for a given charge state (charge). See Basic Usage. A search algorithm is used to sample proton permutations across chargeable side-chains and termini represented as point charges. The algorithm is inspired by the method described by refs 1–3, it produces a reproducible output proton sequence in far fewer steps than required for sampling all permutations.