AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Sep 08 2008 - 15:46:45 CDT

I would suggest downloading AmberTools 1.2 from the amber web page,
the ptraj version in that will do clustering.

On Mon, Sep 8, 2008 at 4:34 PM, Sasha Buzko <obuzko_at_ucla.edu> wrote:
> Carlos,
> 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 trajectory.
>
> 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 (surprise...).
>
> 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
>
> Sasha
>
>
> Carlos Simmerling wrote:
>
> ptraj
>
> On Wed, Aug 27, 2008 at 8:45 PM, Sasha Buzko <obuzko_at_ucla.edu> 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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> 

-- 
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Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
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Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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