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
George
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Received on Tue Oct 03 2017 - 12:00:02 PDT
