VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Mar 23 2006 - 17:22:15 CST

Hello,

I replicated this problem as well using 1.8.3. However, if I remember
correctly the algorithm itself requires a minimum of 4 atoms to match.

If you just duplicate one atom each for the two molecules the alignment
works just fine.

Brian

On Thu, 23 Mar 2006, Visvaldas Kairys wrote:

> Hi all,
>
> I am trying to use VMD to compute RMSD between selected residues, and for
> practical purposes I superimpose only the atoms under interest.
> Below is an example of molecules (in pdb format) which cause problem.
>
> molecule 1:
>
> CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
> ATOM 1 CA GLU A 1 -29.843 154.588 35.594 0.00 0.00
> ATOM 2 CA GLU A 2 -27.292 160.642 36.936 0.00 0.00
> ATOM 3 CA GLU A 3 -32.648 156.854 50.794 0.00 0.00
> END
>
> molecule 2:
>
> CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
> ATOM 1 CA GLU A 1 44.084 6.298 12.425 0.00 0.00
> ATOM 2 CA GLU A 2 39.046 2.420 14.373 0.00 0.00
> ATOM 3 CA GLU A 3 46.929 -0.875 26.932 0.00 0.00
> END
>
> If I open RMSD calculator extension, unselect backbone button
> and type "all" for atom selection, then click "Align",
> the molecules do not become aligned (it's pretty obvious), and "RMSD"
> is quite high. If I keep clicking "Align" and subsequent "RMSD",
> the position of atoms and RMSD keep changing.
>
> If I simply duplicate each atom in both of molecules above,
> yielding 6 atoms in each, the alignment and RMSD calculation proceeds
> correctly.
>
> I wonder if there is some formatting problem in my molecules or it is a bug.
>
> I had similar errors with two molecules consisting of 2 atoms. I didn't look
> carefully at other sizes of molecules, but big molecules seem to be OK.
>
> I am running VMD 1.8.4a22 on AMD64 Linux machine.
>
> Your help will be appreciated!
>
> Sincerely,
>
> Visvaldas Kairys
> University of Madeira
> Portugal
>
>

************************************************
   Brian Bennion, Ph.D.
   Biosciences Directorate
   Lawrence Livermore National Laboratory
   P.O. Box 808, L-448 bennion1_at_llnl.gov
   7000 East Avenue phone: (925) 422-5722
   Livermore, CA 94550 fax: (925) 424-5513
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