VMD-L Mailing List

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Tue Dec 12 2006 - 13:16:32 CST

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.