It's better to visualize the protein by yourself in this case. (e.g: using
VMD).
Hai
On Tue, Sep 26, 2017 at 12:07 PM, <krishna.2015.iitg.ernet.in> wrote:
>
> Dear Amber Users,
>
> I am doing a work using AMBER12 with a protein in water at 400K
> temperature. I want to see the thermal denaturation of the protein having
> 130 residue.I have already calculated the RMSD and radius of
> gyration (Rg) of that protein. The RMSD value is matching well with
> the reported value. But the radius of gyration is decreasing
> inspite of breaking of the secondary structure of that
> protein. And the breaking of secondary structure of the protein is
> very clear from RMSD as well as secondary structure calculation
> also. But the anomaly is happening with the Rg value which should
> not happen at all. When a protein unfolds totally then its Rg
> value should go beyond 17-18A which is reported in many
> 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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Received on Wed Sep 27 2017 - 06:30:03 PDT
