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getting the center of mass of each part of a molecule

On Thursday, May 18, 2017 at 3:55:01 AM UTC-7, qasi... at gmail.com wrote:
> @jladasky and @Gregory:

> 3) Divide the ligand molecule into two parts (except for ligand heavy atom closest to the COM of the whole ligand) based on the COM previously calculated.

OK, now I agree with Gregory Ewing.  This part of your problem is incompletely defined.  Divide the molecule into two parts... how?  You need to choose a plane in 3-dimensional space which cuts your molecule in two.  Describe the criteria that this cut needs to satisfy.