To bridge this gap, we have developed phbuilder, a Python-based command line tool that automates the constant pH specific preparation steps when setting up MD simulations. phbuilder generates initial structures, topology, and parameter files, and also adds the appropriate number of ions and neutralizing buffer particles to keep the simulation box neutral during the constant pH MD run. To demonstrate the tool, we use it to build constant pH MD simulations starting from protein structures taken from the Protein Data Bank (PDB), as well as starting from structures prepared for regular MD simulations.