VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 07 2008 - 11:51:34 CST

Francesco,
  I'd suggest emailing Luis Gracia (his email is listed at the bottom of
the URL I sent) and query him about obtaining the required packages.

Cheers,
  John Stone
  johns_at_ks.uiuc.edu

On Mon, Jan 07, 2008 at 02:35:30AM -0800, Francesco Pietra wrote:
> Hi
>
> I have installed Luis Gracia's plugin with no problems in Debian Linux. Only
> after that I recognize that other software is needed (actually anticipated by
> John's email). Therefore, I would be very grateful receiving information about
> the software needed from users familiar with this plugin. My problem is the
> common problem of choosing the most representative snapshot, or family of
> snapshots' from a long MD (for a protein complex, thus two molecules involved:
> a problem for definying atoms for rmsd?)
>
> The NMRCLUSTER link does not work (as stated by Luis).
>
> The Xcluster link brings to very expensive commercial software, which does not
> fit my current plans. Otherwise, a web search for "xcluster" brings to
> affordable sources, like http://genetics.stanford.edu/~sherlock/cluster.html.
> Which one is the correct xcluster?
>
> The R link brings to some humanitarian associations for Africa
> (http://www.cran.org/). To applaud, though not fitting my present needs.
>
> Thanks for helping
>
> francesco
>
>
> --- John Stone <johns_at_ks.uiuc.edu> wrote:
>
> > Hi,
> > If you have the other required packages installed, you might try
> > out the "Cluster" VMD plugin by Luis Gracia at Cornell:
> > http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/cluster/
> >
> > So far as I'm aware, his plugin doesn't care what file format the trajectory
> > came from.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Sun, Jan 06, 2008 at 02:27:19AM -0800, Francesco Pietra wrote:
> > > Is it possible to carry out a cluster analysis with VMD from Amber
> > mdcrd/prmtop
> > > files? I have combined the various trajectories into a single mdcrd of ca
> > 90
> > > MB.
> > >
> > > Thanks
> > > francesco pietra
> > >
> > >
> > >
> >
> ____________________________________________________________________________________
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> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078