VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Mon Jan 07 2008 - 11:22:03 CST

Hi Francesco and the vmd community,

Thanks for pointing out the broken R link. I just updated the the
webpage. CRAN is the Comprehensive R Archive Network, and I type the
wrong ULR. Well, I am glad it ended up in a humanitarian org, and not in
other place in internet.

The xcluster from standord has nothing to do Xcluster from Shroedinger
(I know expensive, but we are fortunate to have it here).

It is a pitty that NMRcluster cannot be found in internet anymore. You
might want to contant the authors, the paper is still easy to find in
pubmed.

As of using ptraj, as suggested by Carlos Simmerling, it is an option. I
have never used it for clustering and I don't remember it has an option,
but certainly it can help you get the rmsd. You will probably need
additional software for that. I am trying to get the paper he points
out, but something is wrong the the web right now.

My plugin won't help you do the clustering, it is only useful for
visualizing the results: nice coloring of clusters and options to
show/hide whole clusters or individual structures. If you need the
itrajcomp plugin to calculate the rmsd let me know, I have no problem
sharing it.

Best,

Luis Gracia

Francesco Pietra said the following on 01/07/2008 05:35 AM:
> 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
>>>
>>>
>>>
>>>
> ____________________________________________________________________________________
>
>>> Never miss a thing. Make Yahoo your home page.
>>> http://www.yahoo.com/r/hs
>>>
>> --
>> 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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