From: Axel Kohlmeyer (
Date: Sun Feb 19 2012 - 11:37:25 CST

On Sun, Feb 19, 2012 at 11:27 AM, mish <> wrote:
> Hello all,
> Can any suggest me some way to measure the distance between geometric center
> ( or center of mass) if two amino acid residues in any any protein?

very straightforward:

1. create one atom selection for each residue and store
its name in a variable each.
2. call measure center with it (this can be
mass weighted or by other properties) and
store the resulting vector in a variable each
3. compute the distance between the two
vectors via veclength/vecsub.

for details check out the VMD users guide.


> Sincerely
> Mish,

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.