[gmx-users] g_cluster analysis for structure refirement

[James Starlight]

Hi Tsjerk,


thanks for suggestions! Some additional questions regarding g_cluster
method.

1- how most correctly select cutoff value for clustering of the
surface-exposed loops assuming big number of clusters? In literature I've
found cutoff ~ 1.3 A for enzymes active-site loops applicable for analysis
of the md trajectory. In my case I suppose cutoff might be higher due to
the Modeller loop prediction based on the SA (which gives bigger RMSD
variance of the DATA) as well as that fact that loops in my case are
surface expoced.

2- What flag in g_cluster could be used to save from each cluster of its
most representative (not averaged!) structure as the individual pdb?

Thanks a lot,

James


2014-07-25 12:56 GMT+04:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:

> Hi James,
>
> The first part is just conformational clustering, for which you can use
> g_cluster. The easiest is then to collect the structures belonging to the
> different clusters in different files (which g_cluster can do), which you
> process separately to extract those properties you're interested in. Then
> you can easily plot the selected properties per cluster.
>
> Hope it helps,
>
> Tsjerk
>
>
> On Fri, Jul 25, 2014 at 9:53 AM, James Starlight <jmsstarlight at gmail.com>
> wrote:
>
> > Dear Gromacs users!
> >
> > I'd like to use g_cluster utility to cluster a big set of models produced
> > by Modeller as the result of the refirement of some parts of my protein.
> In
> > this case all structures differs only in the conformation of 1 longest
> loop
> > (~ 30 amino acids including 2 disulphide bridges) so I need to cluster
> all
> > models based on the RMSD in this region.   As the result I'd like to
> obtain
> > projection of all set of conformers onto the plane of some coordinates
> >  correspond to some selected structural criteriums (for instance percent
> of
> > the occurence of secondary structure elements  in the refined (loop)
> > region; and/or some geometrical criteriums like distance between pair of
> > residues, occurence of the salt-bridges in this region etc. As the result
> > I'd like to visualize data and chose most representative structures from
> > each cluster for further MD simulation. Could such processing be
> performed
> > by g_cluster taking into account that I have gromacs-like trr consisted
> of
> > my conformers ? On what cluster algoritms and parameters  should I pay a
> > lot of attention?
> >
> > Many thanks for suggestion,
> >
> > James
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
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