Re: [AMBER] water cluster analysis

From: Karl N. Kirschner <>
Date: Tue, 24 Sep 2013 10:23:33 +0200 (CEST)

Hello Subrata,

   I think I understand what you want to do, but let me paraphrase it for clarity. You are looking at pure water cluster with the goal of understanding what type of 3D hydrogen bonded motifs are formed (e.g. prisms, books, cubes of pentamers, octamers, dodecahedrons). I have also used MD simulations to do this, but have not come up with a methodology to do automatic clustering to identify unique motifs. I believe the problem is that the adopted structure of the system is dependent upon the nonbonded forces - meaning that the each waters drastically changes its hydrogen bond partners (and loacation) during the trajectory course. This makes doing an RMSD for such a system, using AmberTools, tough since it is dependent upon the residue names. For biological molecules this is not a problem since they are covalently bonded structures and neighboring residues do not change their partners and their secondary structure is relatively stable (compared to water clusters structures). Our solution has been to extract X n
umber of trajectory snapshots and perform some QM calculations on them; subsequently their structures were manually evaluated to remove redundant motifs. Here are a couple of articles that illustrate this process:

Best regards,

----- Original Message -----
From: "Subrata Paul" <>
To: "AMBER Mailing List" <>
Sent: Tuesday, September 24, 2013 6:30:44 AM
Subject: Re: [AMBER] water cluster analysis

Dear Jason

Actually, I want to calculate hydrogen bonded water cluster.

and how many such kind of water cluster are there.
  Is it possible ? any software ?

*With Best Regards
PhD Student
Dept of Chemistry.
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Received on Tue Sep 24 2013 - 01:30:04 PDT
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