Re: [gmx-users] g_cluster analysis

[Tsjerk Wassenaar]

Hi Sapna,

How should we know how many clusters you should have?

A cutoff of 0.2 is quite tight, and will give many clusters. Whether that's
what you want/need or whether that's meaningful/helpful for your goals is
something you should consider. We don't know what you're trying or doing.

Cheers,

Tsjerk

On Mon, May 23, 2016 at 9:03 AM, SAPNA BORAH  wrote:

> Dear all,
>
> I am trying to use g_cluster protocol to get representative snapshots of
> the simulations. I have concatenated 9 set of simulations and run g_cluster
> for the same. The result shows a total of 198 clusters.
>
> Is this correct?
>
> Following is the command I have used:
>
> g_cluster -s models.gro -f concatenated.xtc -dm rmsd-matrix.xpm -o
> clusters.xpm -sz cluster_size.xvg -clid cluster-id-over-time.xvg -cl
> all_clusters.pdb -cutoff 0.2 -method gromos
>
> Thanks in advance.
>
> Regards,
> Sapna.
>
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
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> Gromacs Users mailing list
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> posting!
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>



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[gmx-users] g_cluster analysis

[SAPNA BORAH]

Dear all,

I am trying to use g_cluster protocol to get representative snapshots of
the simulations. I have concatenated 9 set of simulations and run g_cluster
for the same. The result shows a total of 198 clusters.

Is this correct?

Following is the command I have used:

g_cluster -s models.gro -f concatenated.xtc -dm rmsd-matrix.xpm -o
clusters.xpm -sz cluster_size.xvg -clid cluster-id-over-time.xvg -cl
all_clusters.pdb -cutoff 0.2 -method gromos

Thanks in advance.

Regards,
Sapna.

Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India
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Re: [gmx-users] g_cluster analysis for structure refirement

[James Starlight]

Thanks!


That was very usefull. BTW have someone tried some software for
visualization of such clusters and compution of the percents of the SS
elements in each cluster (for instance by comparison of the most
representative structures from each cluster etc). Might this VMD plugin
http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/clustering/
be usefull for such task?


James


2014-07-26 11:40 GMT+04:00 Thomas Evangelidis teva...@gmail.com:

 On 26 July 2014 10:15, James Starlight jmsstarli...@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 tsje...@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 
 jmsstarli...@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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Gromacs Users mailing list
   
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   --
   Tsjerk A. Wassenaar, Ph.D.
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   * Please search the archive at
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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: tev...@pharm.uoa.gr

   teva...@gmail.com


 website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [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 tsje...@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 jmsstarli...@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
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
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 --
 Tsjerk A. Wassenaar, Ph.D.
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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[gmx-users] g_cluster analysis for structure refirement

[James Starlight]

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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Gromacs Users mailing list

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Re: [gmx-users] g_cluster analysis for structure refirement

[Tsjerk Wassenaar]

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 jmsstarli...@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
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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-- 
Tsjerk A. Wassenaar, Ph.D.
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Gromacs Users mailing list

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