From: Anthony Ivetac (
Date: Wed Jun 18 2008 - 17:52:09 CDT


I would like to calculate the values of bonds/angles/dihedrals (from a MD
trajectory) using the "label" command. However, instead of calculating these
values for pairs/triplets/quads of atoms in the PDB file, I would like to
calculate them for centers-of-mass.

For example, I calculate the xyz coordinates for two centers-of-mass (com1
and com2) and then want to calculate the 'bond length' between these
coordinates with:

label add Bonds 0/${com1} 0/${com2}

But the label command is expecting com1 and com2 to be atoms, not a list of
xyz coordinates - is there a simple workaround for this, please? e.g. to
convert an xyz into a 'pseudo-atom'?

I would rather use the label command than the mathematical functions I've
seen others use to calculate bonds/angles/dihedrals.