AMBER Archive (2008)

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

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Wed Aug 27 2008 - 19:57:07 CDT

Thanks, Adrian.
Will work through the manual..

Sasha

Adrian Roitberg wrote:
> ptraj can do this
>
> 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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>>
>

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