VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jul 06 2007 - 01:50:49 CDT

Hi,
yes, it can -- you just need to define which atoms are equivalent in
each case (for example, all atoms in some highly conserved region of the
protein). Making an atom selection for equivalent atoms in each protein
will allow you to calculate an RMSD. The whole concept is rather
ill-defined if you don't have a 1:1 correlation between some subset of
residues in each protein... if you have some other sort of measure in
mind, you should be able to write a tcl script to calculate it.
Peter

hori koshii wrote:
> Hi everybody.
>
> Just wonder if VMD allows calculation of RMSD for several molecules
> with different numbers of amino acids. Very appreciated.
>
>
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