[MMTK] calculate RMSD of a collection of atoms from trajectory

khinsen at cea.fr khinsen at cea.fr
Tue Mar 15 19:28:40 CET 2005

On Mar 15, 2005, at 19:11, Shirley Siu wrote:

> It look suspicious because I use VMD (by running a tcl script) to
> calculate the RMSD of the same chain over the trajectory (which use the
> similar approach: fitting the structure to the reference structure, and
> then calculate), that give me a very different result: range from 0 to
> 1.55. The shapes of the curves are also different. Any idea?
> By the way, is the RMSD in MMTK using "Ang" as unit?

No, and I guess that that's your problem. The length unit in MMTK is 
nm, meaning that your RMSDs are between 0 and 3 Ang.

This doesn't explain the different shape of course. I don't know what 
exactly VMD does, there are a couple of possible differences in the fit 
procedure. One check would be to verify that the optimal superpositions 
are identical or close, by writing out the MMTK fits to a PDB file and 
load it into VMD.

Konrad Hinsen
Laboratoire Léon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr

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