Currently, I have these commands to calculate the closest 5 :SIA out of 45 to a binding site each frame

parm ../2_md/CPLX_Neut_Sol.parm7
trajin ../2_md/10.1.produ.nc
rms :1-1469 first # align receptor
closest 5 :132-134 solventmask :SIA closestout SIA2ChainA_Binding_sites.dat name SIA
run
exit

The output file contains

Frame      Molecule      Distance      FirstAtom#

which to my understanding, the distance is from the :SIA atom closest to the center of mass of the residues :132-134. 
  1. Is there some way to do the distance from center of mass :SIA to center of mass residues instead?
    1. ex: [distance of closest :SIA atom to residues] > [distance of :SIA center of mass to residues]
  2. Is there a way to do RMSD calculation of those selected closest ligands to a pdb reference? I was thinking along the lines of "for FRAME in" maybe?

Thank you,
Alex