[gmx-users] Computing RMSD for RNA structure

[Tsjerk Wassenaar]

Hi Raja,

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 <raja_28 at fastmail.us> 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
> --
>   raja
>   raja_28 at fastmail.us
>
> --
> http://www.fastmail.fm - Send your email first class
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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