Not an expert here (a beginner in fact) but I was thinking about that exact
same problem. My idea was just to get the coordinates of 2 equivalent
backbone atoms near the ends of the helix and calculate a vector by hand,
and then compare it to another vector of interest e.g. another alpha helix
orientation. Of course you would need to redo the calculation for both
vectors every frame. Maybe a simple script that reads the trajectory file
could do this for every frame.
-Joel
On Sat, Feb 27, 2016 at 10:50 AM, Emilio Angelina <
emilioluisangelina.hotmail.com> wrote:
> Dear Amber users,
>
> I wonder I there is a way of drawing a vector along the axis of an alpha
> helix with ptraj or cpptraj so that I can then follow the angle formed
> between this vector along the trajectory, with some other vector in a
> reference structure.
>
> Thanks in advance
> Emilio
>
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Received on Sat Feb 27 2016 - 13:00:03 PST
