[gmx-users] a qiestion about using g_cluster

[Marcus Kubitzki]

Hi Li,
first, generate an appropriate index file with make_ndx. There you can
select the loops you want to analyze. Second, run g_cluster -s -f -n.

Marcus

Li Su wrote:
> Dear Sir/Madam,
> I am trying to use g_cluster to clusterize my protein trajectories. The 
> proein core is very rigid, only loops will fluctuate. When I clusterize 
> I want to clusterize only on the loops in stead of the whole protein. 
> But when I use g_cluster it only offer choices on whole protein or c 
> alpha or backbone and so on, all of which focus on the whole protein. I 
> am wondering is there any way I can choose a part of the protein to 
> clusterize? Thank you very much for your help!
> 
> 
> Best Wishes,
> Li Su
> 
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-- 
Marcus Kubitzki
Max Planck Institute for Biophysical Chemistry
Computational Biomolecular Dynamics Group
Am Fassberg 11
D-37077 Göttingen
Germany
phone: ++49-551-2012312
fax: ++49-551-2012302
Email: mkubitz[at]gwdg.de
www: http://www.mpibpc.mpg.de/groups/de_groot/