Improper Dihedrals

  1. Yes the order of the impropers does matter.

  2. If your force field defines 7-1-6-2 as an improper which cannot be identified by bond topology information (most softwares AMBERTOOLS, moletemplate, vmd topo tools identify angles, dihedralsand impropers based on bond information), then you have to manually incorporate those in a data file using sed or awk script.

I am not sure if this helps !