yes now it make sense... There is obvious decrease in the angle value
Thank you dan
Regards,
Maryam
On Fri, May 11, 2018 at 3:10 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 - 07:00:03 PDT
