---------------------------- Original Message ----------------------------
Subject: Re: [AMBER] Problem in analysing radius of gyration value in CPPTRAJ
From: krishna.2015.iitg.ernet.in
Date: Wed, September 27, 2017 9:37 pm
To: "AMBER Mailing List" <amber.ambermd.org>
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thank you for your kind response.I am uploading two pictures.One is
initial structure and the other is at 32 ns. From the two structure it is
clear that alpha helices and 3-10 helices are already started to be
unfolded. And sometimes beta sheet are appearing. I further run for 60ns.
At 60ns I calculated the percentage of helicity. I found percentage of
helicity is too low at 60ns.That means it is unfolding.But Rg value is
still around 13.8A. Now from your suggestion I can assume that though
unfolding is occurring but the local native contacts(distance between the
alpha-carbons)are not being totally disrupted and the protein structure is
not being stretched.As the distance is not increasing so the compactness
will not change. That means, it will be also true for Solvent Accessible
Surface Area(SASA) of that protein.
Thanking You
Krishna
> 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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>>
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Krishna
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Received on Wed Sep 27 2017 - 12:00:04 PDT
