If you have the average structure and the reference, you can use g_confrms to fit them and obtain the rms value. In addition you might want to try the fitting routine (align) in PyMol ( pymol.sourceforge.net), which can omit outliers.
Cheers,
Tsjerk
On 3/20/06, raja <[EMAIL PROTECTED]
> wrote:
Dear GMXIONs,
How to find out RMSD value between two RNA structures in
GROMACS ? I want to compare the crystal structure of the RNA
of my interst with the average structure of RNA after
simulation. Swisspdb viewer not helpful for this case.
With thanks !
B.Nataraj
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raja
[EMAIL PROTECTED]
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
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