Hi,
cpptraj has the ability to do this, create inout for gnuplot, etc.
look at keywords like “dihedral” and histogram
adrian
Sent from my iPad
> On Feb 16, 2018, at 14:36, Yuliana Bosken <ydavi002.ucr.edu> wrote:
>
> 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 - 12:00:03 PST
