AMBER Archive (2004)

Subject: Re: AMBER: snapshots of MD trajectory

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Fri Aug 27 2004 - 14:44:36 CDT

For clustering, you need a newer version of ptraj than the one included
with AMBER8,
but Tom Cheatham will need to clarify how to get it.
Carlos

===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Guanglei Cui wrote:

> 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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>>
>>
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