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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Received on Fri Feb 16 2018 - 00:00:02 PST
