I need to calculate backbone RMSD for Protein-RNA complex. the command
given below is the one i used to calculate backbone RMSD, I would like to
know whether it is sufficient to cover all the information about both
protein and RNA backbone. I have 199 residues in my complex. Among them 177
are amino acids and 22 are RNA.
trajin md1.mdcrd
trajin md2.mdcrd
rms first out backbone.rms :1-199
On Fri, Apr 8, 2016 at 3:00 PM, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Dear Sreemol,
>
> > I have done simulation for protein-RNA complex for 10 ns, I want to
> > calculate the backbone RMSD for the complex. How to calculate the
> backbone
> > RMSD for protein-RNA complex.
>
> backbone RMSD calculations are a very basic analysis technique. For such
> analyses, many people have created excellent tutorials available from
> the amber webpage ambermd.org. A first example of the RMSD analysis is
> given in the very first tutorial:
>
> http://ambermd.org/tutorials/basic/tutorial0/
>
> The second tutorial deals with DNA, so you might also want to have a
> look at that.
>
> Additionally, the documentation of the Amber suite contains a detailed
> description of all programs and input parameters (cf
> http://ambermd.org/doc12/).
>
> All the best,
>
> Anselm
>
> Dr.rer.nat.
> Bioinformatik
> Friedrich-Alexander-Universität Erlangen-Nürnberg
> Germany
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With kind regards,
G. Sreemol
M.Tech (Computational Biology)
Anna university
Chennai.
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Received on Fri Apr 08 2016 - 04:30:03 PDT
