Hi,
On Tue, Sep 26, 2017 at 12:07 PM, <krishna.2015.iitg.ernet.in> wrote:
> not happen at all. When a protein unfolds totally then its Rg
> value should go beyond 17-18A which is reported in many
Just because you have a high RMSD and changes in secondary structure
this does not mean you have complete unfolding. High RMSD just means
you are far away from whatever your reference structure is. The
protein could just be adopting a different conformation (or set of
conformations). Your best bet is to actually visualize what is
happening to your system with your favorite visualization program. I
often find that observing trajectory data can reveal details that are
easily lost in comparatively simple plots.
-Dan
> literatures. If you kindly check my inputs whether I am doing
> right or wrong as I am doing these by CPPTRAJ program then it will be
> great pleasure to me.
> I have attached the input file as well as the graphs in attachment.
>
> I will be highly obliged if you kindly help me to figure out the problem.
>
> Thanking you.
>
> Krishna
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Sep 27 2017 - 06:30:02 PDT
