AMBER Archive (2008)

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

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Wed Aug 27 2008 - 19:45:01 CDT

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
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu