[AMBER] analysizing the trajectory for water interaction

From: Thakur, Abhishek <axt651.miami.edu>
Date: Mon, 25 Sep 2017 22:31:00 +0000

Hi,

I want to check that my ligand in the system is forming a water bridge or not.

By the term water bridge I mean an interaction between ligand - Water - protein is happening or not.


Is there any way of analysis that can help me. if it forms then how long it is forming in my trajectory file.


I have tried by observing the lowest energy structure but I am unable to find any such interactions.


I have also tried clustering by using cpptraj, but here the problem is the structure of protein, ligand, and waters looks distorted.



Any suggestion will be highly appreciated.

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Received on Mon Sep 25 2017 - 16:00:02 PDT
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