[Chimera-users] Measuring angles and distances between planes defined by two aromatic rings

George Tzotzos gtzotzos at me.com
Fri May 27 01:30:17 PDT 2016


Having generated a 100ns trajectory, I’m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I’m dealing with pi-pi stacking interactions.

I’ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven’t managed to find a solution for measuring the angles between the two planes defined by the ring atoms.

I’d appreciate any suggestions on possible solutions to the problem described above. I’m attaching a snapshot of measuring distances between two atoms (not really a good solution).

Thanks in advance

George

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