From: Dmitry Lupyan (
Date: Fri Jan 11 2008 - 15:26:38 CST

You need to use MultiSeq plugin, not "RMSD Calc" plugin to align two
proteins that are not identical.

On Jan 10, 2008 6:33 AM, aneesh cna <> wrote:
> hello vmd users,
> I would like to superimpose two proteins ( one from
> yeast and other from human) with ~70% amino acid sequence similarity. Both
> proteins are structurally similar but amino acid sequence somewhat
> different. When I am trying to align these two structure in VMD its not
> aligning properly.Is there anyway to superimpose these type of proteins?
> regards
> Aneesh