AMBER Archive (2004)

Subject: Re: AMBER: snapshots of MD trajectory

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Fri Aug 27 2004 - 14:38:44 CDT

Hi, Xin

I haven't done cluster analysis with ptraj myself. I'd done it with
moilview though. Perhaps someone on the list can help you with that.

Best,

Guanglei

Xin Hu wrote:

> Hi Guanglei,
> Could you please instruct me more details on the cluster analysis using
> ptraj? I checked the manual of Amber8 and only found "average" command in
> ptraj could be useful. Do you mean the "analyze modes" for cluster
> anallysis?
>
> Thanks for your help.
>
>
> Xin
>
> ---
>
>
>
>
> ----- Original Message -----
> From: "Guanglei Cui" <cuigl_at_csb.sunysb.edu>
> To: <amber_at_scripps.edu>
> Sent: Friday, August 27, 2004 11:27 AM
> Subject: Re: AMBER: snapshots of MD trajectory
>
>
>
>>You can use ptraj to extract snapshot and do cluster analysis. It's part
>>of amber suite.
>>
>>Guanglei
>>
>>Xin Hu wrote:
>>
>>
>>>Hello,
>>>I have a question about the analysis of MD trajectory from Amber 8. How
>>>can I extract all the snapshots (such as save as PDB file) from the MD
>>>trajectory, and generally, is there a way to cluster these ensembles of
>>>MD snapshot?
>>>
>>>Thank you very much for your help.
>>>
>>>
>>>Xin
>>>
>>>
>>>---
>>>
>>>
>>>
>>>
>>
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