[gmx-users] g_cluster for ligand clustering

Mark Abraham mark.j.abraham at gmail.com
Mon Jun 16 18:09:52 CEST 2014

On Sat, Jun 14, 2014 at 5:18 PM, <mbalint at caesar.elte.hu> wrote:

> Dear all,
> I have a trajectory file of a protein+ligand binding simulation.
> What I would like to do is to cluster the ligands positions from the
> simulation trajectory. But although I have tried quite a few possibilities,
> the RMSD calculation using g_cluster will change the reference coordinates
> with respect to the receptor.

Isn't that expected, from what g_cluster -h says about the -fit option? The
coordinates in your -s file determine the result.


I have tried to select the ligand's group for the RMSD calculation, but
> this option gave me only one cluster (which cannot be real), even if I have
> decreased the cutoff.
> Command line used:
> g_cluster -f full_4.xtc -s pr.tpr -method gromos -cutoff 0.1 -cl proba.pdb
> I have also tried to make a clustering from a cumulative pdb file
> (containing all the frames) with -s being the reference pdb file, but the
> result was the same.
> I assume there must be a relatively easy way to do this task, but now I
> just can't see how.
> Could you please let me give me another idea how can I cluster my ligand?
> With the kindest regards,
> Monika Balint
> PhD Student
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