[AMBER] Clustering analysis

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Wed, 18 Mar 2020 22:33:59 +0000

Hello Daniel,

I have been trying to follow your advice *clustering is an art form and requires various different trial and error sessions.*

My aims were simple
I am working on a NMR structure (10 conformers in the pdb file) a Med25 ACID protein domain and trying to answer 2 questions

  1. How different are the 10 models from each other?
  2. We did run some plain TIP3P water explicit solvent simulations (10 different runs on 10 different NMR models)
Trying to analyse the conformations and how do the 10 conformers behave during the explicit solvent simulations.

So I focused on k-means and hierarchical clustering methods just to learn the basics of setting up clustering in cpptraj.
So I played with the cluster number and also the epsilon value (distance between cluster points) and got a wide array of results!
Now I am getting drowned in statistics and literally lost.
Can anyone suggest “how to analyse” my outputs and how to make sense of my results?
What I am looking to compare between the different outputs and how to analyse the avg structures I got the representative structures I got ?
Any help will be super grateful.


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Received on Wed Mar 18 2020 - 16:00:02 PDT
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