Hi Lizelle,
I am not sure if that would apply to your case, but if you have the
dihedral data for your residues in interest from your trajectory you can
use excel (or any ther statistical software) to create a histogram and you
would be able to see distinct conformations and the number of frames for
each conformation. I used "Minitab" (available for free trial) since the
histogram looks nicer and it gives you the option to plot percent on the y
axis instead of number of frames.
Best,
Yuliana
On Thu, Feb 15, 2018 at 11:56 PM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
wrote:
>
> Dear Amber users,
>
> I have performed MD simulations on a glycoprotein and calculated the
> dihedral angles involved in glycosidic linkages. These were plotted over
> simulation time to identify points of variation. They were also plotted as
> Ramachandran plots of phi vs psi or omega vs phi for each linkage and there
> are distinct populations for each. Could someone please advise me on how
> to calculate the frequency of these angles? In other words, I want to
> produce a table showing the percentage of time occupied by each population
> (eg. omega = 60+/-10 degrees for 80% and 300+/-20 degrees for 20% of
> simulation).
> The angles are all saved as .dat files vs time.
>
> Kind regards
>
> Lizelle Lubbe
>
> PhD (Medical biochemistry) candidate
> Department of Integrative Biomedical Sciences
> University of Cape Town
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--
Yuliana Bosken
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Received on Fri Feb 16 2018 - 12:00:02 PST
