VMD-L Mailing List

From: Visvaldas Kairys (kairys_at_uma.pt)
Date: Thu Mar 23 2006 - 13:38:09 CST

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