Re: [AMBER] Cation-pi interaction characterization

From: Daniel Roe <>
Date: Wed, 30 Dec 2020 09:49:51 -0500


On Tue, Dec 22, 2020 at 2:44 PM Ramanathan Rajesh
<> wrote:
> How can cation-pi interaction be characterized using cpptraj.I want to know
> how to incorporate the angle between the cation and the aromatic ring along

If your cation is a single atom (like e.g. a sodium) you can't really
define an angle between the cation and the ring. However, if it's a
bonded atom you could potentially do this by calculating the vector
normal to the ring (with 'vector corrplane', the vector between the
two atoms, then use 'vectormath dotangle' to get the angle between the
vectors. You can then use that angle together with the distance
between the center of mass of the ring and the cation and use the
'calcstate' analysis to analyze the interaction. See the manual for
full details on the commands.


> with the distance cut off and get the percentage of the interaction for the
> total simulation like H-bond analysis.
> Thank you in advance
> Ramanathan R
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Received on Wed Dec 30 2020 - 07:00:04 PST
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