[AMBER] Vector math: a couple of questions

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 03 Oct 2017 20:42:09 +0200

I’m interested in calculating the time evolution of the angle between two helices.

Looking in the manual, I think that the vectormath analysis comment of cpptraj may be appropriate

 vectormath vec1 v1 vec2 v2 dotangle out dotproduct.dat name acos(|V1|*|V2|)

Where v1 and v2 are masks of the type :res_start-res_end

I’d like to use the corresponding vectors of an X-ray structure as a reference doing something. I’ve tried various permutations using something like

parm solv.prmtop
parm X-ray.pdb
trajin traj.nc
reference X-ray.pdb parm X-ray.pdb [A]

and then vectormath to no avail.

I’d be grateful for any suggestions


AMBER mailing list
Received on Tue Oct 03 2017 - 12:00:02 PDT
Custom Search