From: Anthony Ivetac (
Date: Wed Jun 18 2008 - 21:32:03 CDT

Thanks Axel, that works great!



On Wed, Jun 18, 2008 at 3:52 PM, Anthony Ivetac <>

> Hi,
> 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.
> Thanks!