VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 12 2006 - 13:50:47 CST

Hi,
  It's hard for me to give specific advice on this since you're running
a several year old beta version of VMD (you said 1.8.3 beta 1 below),
given that it's a beta version, you may be running into a bug that's
already been fixed a couple of years ago.

My first recommendation would be to consider upgrading to one of the more
recent released versions (1.8.4, or 1.8.5) and try again, as the RMSD tool
your using has been updated a number of times since then, and there's a
new easy to use RMSD trajectory tool now as well.

If you can't upgrade, then I'll need to know more about the atom selections
you're using, as the atom count error you're getting would be the result of
two atom selections that resulted in a different number of atoms.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Dec 12, 2006 at 11:16:32AM -0800, Kara Di Giorgio wrote:
> I'm trying to align two pdb files and calculate the RMSD using VMD.
> The files are the results of two different MD runs (using Amber) with
> different starting conformations. On two of the sets I'm looking at I
> got the following error when I clicked on the "Align" button in the
> RMSD calculator:
>
> Error: measure fit: selections must have the same numer of atoms
>
> Looking at the main VMD window, it says that they both have 740 atoms.
> Also, the files should be identical in atoms, just different in
> position.
>
> Does anyone have any info about what to do? The other 6 sets I
> compared all worked fine. I'm willing to send anyone the pdb files if
> that would help.
>
> Thanks,
>
> Kara Di Giorgio
>
> p.s. I'm running VMD 1.8.3b1 on a Macintosh G4 computer.
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078