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

[Justin A. Lemkul]

vivek sharma wrote:
> Hi all experts,
> 
> Can I select all the residue which are lying within a given distance 
> from one residue ?, using any of the tool in pymol, vmd, chimera or gromacs.
> Whether the option of g_hbond which gives the pair within a particular 
> distance can be used for the same purpose ?, FYI, I am having one pdb 
> entry for the same (no .trr and .tpr).

Use g_dist -dist, it will report atoms within a given distance from your chosen 
reference.

-Justin

> 
> with thanks,
> Vivek
> 
> 2008/10/6 Steven Kirk <steven.kirk at hv.se <mailto:steven.kirk at hv.se>>
> 
> 
>         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 ?
> 
> 
>     Pymol has a script that computes the center of mass for a selection,
>     and optionally, moves this center of mass to the origin:
> 
>     http://pymolwiki.org/index.php/COM
> 
>     Haven't used it myself, so I can't vouch for its effectiveness.
> 
>     Steve Kirk
>     -- 
>     Dr. Steven R. Kirk           <steven.kirk at hv.se
>     <mailto:steven.kirk at hv.se>, S.R.Kirk at physics.org
>     <mailto:S.R.Kirk at physics.org>>
>     Dept. of Technology, Mathematics & Computer Science  (P)+46 520 223215
>     University West                                      (F)+46 520 223299
>     Trollhattan 461 86 SWEDEN                     http://beacon.webhop.org
> 
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-- 
========================================

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

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