[gmx-users] get the center of a cluster using gromacs

[Houcemeddine Othman]

Hi,
I used this command
g_cluster -f  input.pdb -s input.pdb -cl output.pdb -nofit -av

I got a file containing all the structures of the cluster. I am not sure if
the first one is the cluster center?

Houcemeddine

On Mon, Jan 28, 2013 at 9:49 AM, francesco oteri
<francesco.oteri at gmail.com>wrote:

> Hi,
> you can try using g_cluster, taking care to use the option -cl
>
> Francesco
>
>
> 2013/1/28 Houcemeddine Othman <houcemoo at gmail.com>
>
> > Hi,
> > How can I get the center of a cluster from a multiple conformers pdb
> > file (a file containing a cluster of a docking poses). I tried to use
> > g_covar to get an average structure but I get a distorted structure
> > when averaging over the whole atoms of the protein.
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>
> --
> Cordiali saluti, Dr.Oteri Francesco
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