[gmx-users] Finding centroid for a bunch of residues

[Justin A. Lemkul]

vivek sharma wrote:
> Hi there,
> 
> This is the question out of gromacs..but I need it urgently.. and I hope 
> this is the only place where I can get such expert to solve my query...
> while trying to restrict my MDRUN for a particular site of the protein 
> molecule I want to visualize the site and find out the centroid for the 
> particular site......
> 
> Is there any visualization tool that can do the same ..
> I mean Is there any molecular visualization tool that can help in 
> finding out the ...centroid between a group of resuidues ?
> 

You will likely have to write a script that will do this for you.  It can be 
accomplished, for example, with VMD, although my own personal experience with 
such scripting is somewhat limited.  See for example:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5963.html

That may give you some ideas.

-Justin

> 
> With Thanks,
> Vivek
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================