Why not just use the 'angle' command?
angle a1 :196.C,CA,N :199.C,CA,N :203.C,CA,N out angle.dat
-Dan
On Fri, May 11, 2018 at 2:45 AM, maryam azimzadehirani
<maryamai1988.gmail.com> wrote:
> 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 - 06:30:03 PDT
