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

vivek sharma viveksharma.iitb at gmail.com
Tue Oct 7 12:25:50 CEST 2008

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).

with thanks,

2008/10/6 Steven Kirk <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, S.R.Kirk at physics.org>
> Dept. of Technology, Mathematics & Computer Science  (P)+46 520 223215
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