From: Anuradha Mittal (
Date: Tue Apr 11 2006 - 13:47:06 CDT

I am trying to find the RMSD of protein between each frame of a dcd file and
a reference pdb file. The PDB and DCD files have different number of water
While running the script pasted below, it is giving an error of "incorrect
number of atoms".

proc myrmsd { frame } {
  global ref sel all
  $all move [measure fit $sel $ref]
  puts "$frame: [measure rmsd $sel $ref]"

mol load psf prot.psf # for prot.dcd
set all [atomselect top all]
set ref [atomselect top "name CA" frame 0]
set sel [atomselect top "name CA"]
animate read pdb protein.pdb
bigdcd myrmsd prot.dcd

Is there any way of calulating rmsd from files with different number of