VMD-L Mailing List

From: Christoph Schneider (csc_at_imb-jena.de)
Date: Wed Aug 19 1998 - 04:05:51 CDT

Hi everybody,

I wonder that the fitting option in vmd is unnatural.
When I compare 2 molecules (dinucleotides, same names/number of atoms),
which should be almost the same in card. coord. (rmsd ~ 0.00x)
it makes a great difference if I compare
***
heavy atoms (rmsd ~ 3.4 A) NOT TRUE!! and bad superposition or
backbone atoms (rmsd ~ 0.004 A) TRUE!! and exact superposition.
all atoms (rmsd ~ 2.38 A) NOT TRUE!!
***
But the result should almost be the same, I think.
I think this is an important tool for checking equilibration runs and
should not be underestimated!!
Any comments?

Greetings Christoph 

-- 
 Christoph Schneider                       csc_at_imb-jena.de       
 Institute for Molecular Biotechnology                         
 Beutenbergstrasse 11, -Biocomputing-      Tel.: +49-3641-65-6205
 P.O. Box 100 813, D-07708 Jena, Germany   Fax:  +49-3641-65-6210
 http://www.imb-jena.de/~csc/