VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 26 2013 - 11:11:15 CST
Do your structures have the same sequence? If so, then you can
use the other RMS aligment and RMSD measurement tools in the
Extensions menu to do this. Multiseq is better in cases where the
structures are not exactly the same, but it does assume that the
input files use PDB atom and residue naming conventions, etc.
On Tue, Nov 26, 2013 at 03:07:48PM +0100, Dawid das wrote:
> I have couple of .xyz files and I wanted to align these structures and
> calculate RMSD for them. When I do so using MultiSeq module I got
> following error:
> It's a P!!!
> error: begin of sequence not found in PDB file
> Error in domain 0 object 1
> while executing
> "error $out"
> How can I calculate RMSD for my structures without converting them int pdb
> Thanks in advance,
> Dawid Grabarek
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/