[AMBER] Angle calculation between three amino acids

From: maryam azimzadehirani <maryamai1988.gmail.com>
Date: Fri, 11 May 2018 08:45:27 +0200

Dear Amber users,
Is there any way to calculate the angle between 3 amino acids?
I am aware of the angle between two vectors and I used it as below:

trajin 50ns.nc
vector v1 :196.C,CA,N' :199.C,CA,N'
vector v2 :199.C,CA,N' :203.C,CA,N'
vectormath vec1 v1 vec2 v2 out vector.dat name axisangle dotangle

but I am observing an increase in the value for the angle whereas the loop
including these three amino acids is becoming more compact in the
simulation and thus the angle must be decreasing. This let me to think
maybe I am doing something wrong.
Please advice me
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Received on Fri May 11 2018 - 00:00:02 PDT
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