Re: [AMBER] Calculation of binding energy associated with a single water molecule

From: Pratul Agarwal <>
Date: Mon, 28 Jan 2019 16:47:24 +0000


As per my understanding, there is not an easy or direct way to do this type of analysis. Others can also provide their input.

My group performs such an analysis for ligands/proteins interacting with other proteins, and it can be easily extended to water. See protein-substrate interactions section of this paper:
If something like this will work for you, let me know and I will walk you through the steps.


Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 1/28/2019 1:04 AM, Leena Aggarwal wrote:

Dear Amber Users

In case of protein-water system, I want to calculate the binding energy or
interaction energy of a single water molecule with all the protein atoms
and all other water molecules in a system. It's like evaluating the pair
interaction between two selected group of atoms.
Is there any inbuilt function in AMBER or any way to calculate the pair
interaction between two selected group of atoms.

Leena Aggarwal
University of Delhi
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Received on Mon Jan 28 2019 - 09:00:02 PST
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