Re: AMBER: snapshots of MD trajectory

From: Xin Hu <hux.mail.rockefeller.edu>
Date: Fri, 27 Aug 2004 17:15:27 -0400

Hi Carlos,
Thank you very much for your help. I will look over the Moilview to figure
out how it works.

Have a good weekend,


Xin

---
----- Original Message ----- 
From: "Carlos Simmerling" <carlos.ilion.bio.sunysb.edu>
To: <amber.scripps.edu>
Sent: Friday, August 27, 2004 3:44 PM
Subject: Re: AMBER: snapshots of MD trajectory
> 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.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.csb.sunysb.edu>
> >> To: <amber.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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Received on Thu Sep 02 2004 - 01:15:11 PDT