Re: [AMBER] clustering

From: Bill Ross <>
Date: Tue, 31 Jan 2017 10:11:20 -0800

Not sure if it has been pointed out, but average structures from
trajectories can be quite unrealistic if the system has interesting
changes going on.


On 1/31/17 9:59 AM, Daniel Roe wrote:
> On Tue, Jan 31, 2017 at 10:03 AM, Sowmya Indrakumar <> wrote:
>> running the above commands gives me 5 representative structures. It is not very clear to me what is it taking as the reference structure. Comparing the five generated representative pdb structure to the average pdb (from the trajectory) does not give show any trend in RMSD.
> The representative structure of each cluster is the frame with the
> lowest cumulative "distance" (in your case RMSD) to every other frame
> in the cluster. A cluster representative is just that; it's supposed
> to be representative of what that cluster looks like (although this
> may not always be the case). I can see how comparing representative
> structures to the average structure of the cluster could be
> informative ('avgout', 'avgfmt'), but it's not clear to me what
> insight you can gain from comparing representatives to the overall
> average structure.
> -Dan

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