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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Received on Fri Apr 08 2016 - 03:00:03 PDT
