Marcus Kubitzki writes:
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/
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Dear Sir,
Thank you so much for your kind help. But now I have another question. I
think g_cluster will do a removing of translation and rotation displacement
automatically. I am not quite sure whether it will do such part on the group
of atoms I pick in the index file? If so is there any way I can specify
which region to do the removement or if I can simply turn off the
removement? I am asking this becuase what I really want to do is to fit all
the snapshots by their cores and then clusterize the loop comformations.
Even if I can just switch off the fitting, it will be good enough since I
can use other routines to fit first.
Best Wishes,
Li Su
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