From: Axel Kohlmeyer (
Date: Tue Aug 23 2011 - 09:48:38 CDT

On Tue, Aug 23, 2011 at 9:59 AM, George Tzotzos <> wrote:
> Using the RMSD calculator extension for the alignment of two identical proteins (the first one is the crystallographic model and the second a structure derived from an AMBER trajectory) gives the attached error message.
> I fail to understand why, as I performed similar jobs in the past successfully. I have double checked and the number of residues of both models is identical.

the number of residues doesn't matter. it is the number of _atoms_ that
matters and for some reason it appears that you have a different number
of atoms when applying the fit selection to the two molecules. i would
suggest to test this manually on the vmd script console. perhaps some
atoms are named differently in the two molecules and thus not caught
by the selection.


> Your help in troubleshooting this problem will be much appreciated
> George

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.