[gmx-users] g_cluster questions

Erik Marklund erikm at xray.bmc.uu.se
Tue Oct 2 10:20:06 CEST 2007


Hi,

Try -nofit

2 okt 2007 kl. 09.28 skrev andrea carotti:

> 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?
> Thanks
> Andrea
> -- 
> ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
> 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
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys





More information about the gromacs.org_gmx-users mailing list