From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Jan 07 2008 - 04:35:30 CST

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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