The XML structure format was designed to remediate some of the shortcomings of the flat-file format. By use of XML, issues related to extra fields in the file or columns merging together can easily be remedied. Additionally, APBS will only parse the necessary information from the XML file and will ignore all other information, so users wishing to store extra data related to a residue or atom can do so inline without affecting APBS.
This data format has the following form:
# Comments <roottag> <residue> <atom> <x>x</x> <y>y</y> <z>z</z> <charge>charge</charge> <radius>radius</radius> </atom> ... </residue> ... </roottag>