[gmx-users] g_cluster analysis for structure refirement

[Thomas Evangelidis]

On 26 July 2014 10:15, James Starlight <jmsstarlight at gmail.com> wrote:

> 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.
>
>
You decide about the cutoff based on the final cluster populations.



> 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?
>
>
"-cl" , but without using the "-av" flag.



> 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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-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/