Re: [AMBER] to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.

From: Jason Swails <>
Date: Mon, 11 Jul 2016 13:33:02 -0400

On Mon, Jul 11, 2016 at 5:19 AM, 朱 婧涵 <> wrote:

> Dear Amber members:
> I want to calculate the binding energy between the protein and a
> ligand,the protein has two ligands at different binding sites.I would like
> to know how to write or add some commands in file.I have not
> seen any previous examples of this problem.

​I suggest reviewing the theory behind MM/PBSA (there are references in the
Amber manual as well as a descriptive illustration on the tutorial page

MM/PBSA computes a binding energy between any two species (typically called
"receptor" and "ligand") that are non-covalently bound​ given trajectories
of the bound and unbound states (the unbound trajectories can be extracted
from the bound trajectory as a common approximation).

So your question is the same as asking us to define what your "receptor"
and "ligand" should be. Common choices are:

1. "receptor" = protein + 1 ligand, "ligand" = 1 ligand
​2. "receptor" = protein, "ligand" = 2 ligands​
3. "receptor" = protein, "ligand" = 1 ligand

And some combinations thereof. It should hopefully be obvious that each of
these assignments, while potentially modelling an interesting and useful
scenario, are fundamentally different. The "right" choice is defined by
exactly what it is you are trying to learn. And since only you know that,
you will have to decide which of those 3 scenarios (or maybe a completely
different one) is right for your study.


Jason M. Swails
AMBER mailing list
Received on Mon Jul 11 2016 - 11:00:02 PDT
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