AMBER Archive (2008)

Subject: Re: AMBER: Is there a way to cluster frames of a trajectory?

From: Sasha Buzko (
Date: Mon Sep 08 2008 - 15:34:22 CDT

I've worked through the relevant sections of the amber manual, but
apparently ptraj doesn't do it.

It does things like averaging, PCA and NMA analysis, but It doesn't seem
to go far enough to produce a set of structure clusters based on their
mutual rmsd or generate representative pdb-formatted structures from a
run. If it does, and I missed something, I would very much appreciate if
someone could provide a reference to the relevant line in the manual
(I'm using Amber 9.0). None of the examples in the manual or in
tutorials show how to get actual representative pdb structures from a

As a side note, Ross Walker mentioned in his Tutorial 8, section 6.2,
that in order to run cluster analysis, one requires MMTSB toolset. I did
find the distribution, but have been unable to compile it just yet

So, if ptraj actually can produce a set of representative pdb structures
from a trajectory via clustering, any pointers would be very much
appreciated. Having an example would be simply terrific.

Thanks in advance


Carlos Simmerling wrote:
> ptraj
> On Wed, Aug 27, 2008 at 8:45 PM, Sasha Buzko <> wrote:
>> Hi all,
>> could you possibly suggest an existing piece of software to run clustering
>> of frames in a trajectory (by mutual RMSD). We are trying to get an estimate
>> of which conformations of a protein are prevalent and how much time the
>> protein spends in each conformational group (within some rmsd tolerance).
>> Thanks for any hints
>> Sasha
>> Urszula Uciechowska wrote:
>> Dear Amber users,
>> I am trying to use ptraj (amber 9) to analysis LES trajectoreis but I am
>> getting only one traj file (I
>> made 5 copies) I appreciate very much if somebody could tell me how to do
>> this properly with ptraj or
>> maybe there are other possibilities?
>> thanks in advance
>> Urszula
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