AMBER Archive (2008)

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

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Mon Sep 08 2008 - 17:11:04 CDT

Thanks, Carlos.
I downloaded, installed and tested ptraj from the AmberTools
distribution. This version does indeed perform clustering that I need.
Thanks again

Sasha

Carlos Simmerling wrote:
> 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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>
>
>
>

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