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
