AMBER Archive (2004)

Subject: Re: AMBER: snapshots of MD trajectory

From: Xin Hu (hux_at_mail.rockefeller.edu)
Date: Fri Aug 27 2004 - 11:36:06 CDT

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
> >
> >
> > ---
> >
> >
> >
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu