Re: [AMBER] Query regarding pi-pi stacking interaction

From: David A Case via AMBER <>
Date: Fri, 3 Nov 2023 08:35:24 -0600

On Wed, Nov 01, 2023, Sourav Bhowmik via AMBER wrote:
>I have built up a system of 60 amino acid molecules of the same type. After
>the simulation, I want to determine the pi-pi stacking interaction among
>them. Could you please help me to calculate the same?

I think you have a programming task ahead of you. First, you would need to
define (mathematically) what you mean by "pi-pi stacking": is this an energy
or some geomtric criterion? Do you want interactions for specific pairs of
amino acids? Once you have a specific requirement, you might ask back here
with details, if you can't see how to carry out the calculation.


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Received on Fri Nov 03 2023 - 08:00:03 PDT
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