[AMBER] Working with pytraj

From: MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
Date: Tue, 17 May 2016 00:35:00 +0530

Dear AmberTools developers

In my MD simulations I have five member ring and now I want to calculate
(1) No of residue within given cut-off distance (Geometrical center)
between two residues.
(2) Angle between two normal vectors (Geometrical center) of the five
member ring

For that, I used pytraj and able to print geometrical center of residue and
the normal vector to the plane.
But I am unable to generate over residue. I have total 512 no of residue in
my system, so the output should be
ndarray (total frame , total residue).

import pytraj as pt
traj = pt.iterload(trajectory,Topology)
ring_atoms=traj.top['.C1, @N6, @C2, @C4, @N7']
c_o_G=pt.center_of_geometry(traj,top=ring_atoms)
ring_plane_all=pt.vector.corrplane(traj, top=ring_atoms)

Please guide us how to proceed furthers
Thank you in advance for your help
Regards
Rahman
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Received on Mon May 16 2016 - 12:30:03 PDT
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