The COOR SET command is intended for a single atom, not a 3-atom molecule, so further changes will be needed. Both the initial COOR SET, which put ions at the origin, and the one in the loop need to be changed, probably to COOR TRANSlate.

For placing multi-atom residues, I would probably read the coordinates for each molecule from a file, and then translate it to the desired location. There are some nuances in that depending on the type of file used, and the initial coordinates of the molecule(s) being read.

Rick Venable
computational chemist