[gmx-users] g_cluster questions

andrea carotti andcar at chimfarm.unipg.it
Tue Oct 2 09:28:57 CEST 2007

Hi all,
I'm using this tool to cluter 2200 structures in this way:
fitting on the backbone, rmsd calculated on key residues (10) of the
Binding site.
Now I created the correct group in the index file and using the
g_cluster giving the trajectory as input i can only choose one group for
fitting and rmsd calculation..So I've tried also to fit the trajectory
before to use it in g_cluster with the option -fit (to jump the fitting
step and choose directly the group for the rmsd calculation; i've tried
also -fit no) but it seems that the program ignore it (on screen, during
the group selection it asks for the "fitting and Rmsd group" and on -fit
line i can see yes)...SO my next strategy is been to calculate the xpm
matrix with g_rms, fitting on the backbone and calculating the rmsd
values on the Bindingsite group. Then I've used the xpm as input in the
g_cluster, but it asks me however for a group for the LSfitting..could
someone explain me this behaviour?
Is my procedure correct for my purpose? Is normal that g_cluster does
not accept the -fit option?
Andrea Carotti
Dipartimento di Chimica e Tecnologia del Farmaco
Via del Liceo, 1
06123 Perugia, Italy
phone: +39 075 585 5169
fax: +39 075 585 5161
www http://rpg.unipg.it
personal www http://iris.chimfarm.unipg.it/users/andcar

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