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getting the center of mass of each part of a molecule

The center of mass of the whole ligand that I calculated is the center of geometry (the average/mean atomic positions) from the sample input file provided. I don't take other things into account, such as knowledge of the mass of each atom and so on. The difference between the center of mass and the center of geometry/atom positions is probably small, and my aim is only to select the atom closest to the center of geometry.

Dear Gregory Ewing, lets consider I get the center of geometry (the average positions of atoms - X, Y, Z) of the whole molecule. Then I can compare those average positions X, Y and Z and find the greatest one, and list separately the ligand atoms according to the greatest average position out of X, Y and Z (The greatest one is the "longest" axis of the molecule in some sense). This way, the ligand atoms will have been divided in two parts, right? After that, I can calculate the center of geometry of each part. Does this procedure make sense? If no, what do you suggest me to divide the ligand/molecule in two parts?