VMD-L Mailing List

From: Dan Wright (dtwright_at_uiuc.edu)
Date: Tue Dec 12 2006 - 16:20:58 CST

Kara,

Before going too deeply into this, I would suggest upgrading VMD. The current
version is 1.8.5, and there have been significant changes since the 1.8.3 Beta
phase.

http://www.ks.uiuc.edu/Research/vmd/

Dan

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.
>