choderalab/gaff2xml — pull request #43 by kyleabeauchamp (2014-08-11 01:14:52+00:00)
Title: [WIP] Multiple ligands in single ffXML file

So it seems like dumping multiple molecules into a single XML file is probably the least painful way to do host-guest and mixtures. IMHO it's also good to avoid having several XML files, as the concatenation behavior in OpenMM can be dangerous--I was previously having issues with bonds getting added twice.