fixed a serious bug in cleanup_moltemplate.sh

This is a disturbing and potentially serious bug that causes "cleanup_moltemplate.sh" to alter the order of improper atoms for all force fields, (including GAFF, GAFF2, OPLSAA, and COMPASS). It is unlikely but also possible it could have caused improper interactions to be incorrectly identified as redundant and deleted. Thanks to bhargavchava97 (again) for catching this!