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

[David van der Spoel]

On 2013-02-01 16:14, Houcemeddine Othman wrote:
> 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?
It says in the cluster.log file.

>
> 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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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se