Re: [AMBER] cpptraj cluster -representative structure

From: Thomas Pochapsky <>
Date: Wed, 14 Dec 2016 14:29:32 -0500


The particular structures were selected as having the best fit to two
sets of RDC restraints and their associated alignment tensors. So in a
sense, they were already pre-selected from the dynamics tracks, and I
wanted to see which of them was "best". It turns out, after I aligned
the backbones, there is little difference between any of the selected
structures, no worse than you see with any NMR ensemble, so the point is
probably moot.

Thanks, Tom P.

On 12/14/16 1:38 PM, Thomas Cheatham wrote:
>> Hi, I have ten best-fit structures of my enzyme extracted from long
>> dynamics tracks; the structures are solvated and have ions for charge
>> neutralization. I want to identify the most representative structure in
>> the group of ten; what is the best way to do this with cpptraj?
> This is a difficult question to directly answer since it depends on your
> definition of "representative" and it also depends on how your 10
> structures were chosen/determined.
> I would approach this problem not by picking only ten structures, but by
> clustering all the trajectory snapshots, creating both average and
> representative structures from the individual clusters. One might then
> argue that the largest cluster contains the best representative
> structures, however this assumes complete sampling. In the real world
> this is tricky, so in fact a minor populated cluster (which took a long
> time to find and perhaps was only found at the end of the MD runs) could
> be, in fact, most representative. Therefore, You likely want to apply an
> arsenal of analyses to get at what is hidden in the trajectory data,
> likely using CPPTRAJ.
> - RMSD
> - 2D RMSD (to get a handle on how many states might be accessible) and
> whether particular conformations are being revisited)
> - clustering
> - MM-PBSA or other energetic analysis of sub-states/clusters
> - PCA (to look at major modes of motion, perhaps in each cluster)
> - if multiple trajectories, combined clustering/PCA across all
> trajectories
> - visualization of dynamics/movies to "see" what was happening
> - grid analysis (on clusters) of ion/water major sites
> In recent papers from my lab over the past couple of years, we try to put
> CPPTRAJ scripts into the supporting information which may be helpful, in
> addition to the CPPTRAJ tutorials/examples in AmberTools.
> The specification of "representative" is subjective and subject to your
> interpretation (what atoms to cluster on, what algorithm, sieving,
> cluster count, ...) which you must defend as the data is presented. So
> try to explore your data as much as possible-- the analyses are likely the
> most people-time consuming part of any MD project.
> --tec3
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Received on Wed Dec 14 2016 - 11:30:02 PST
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