Re: [AMBER] Help: Clustering trajectories based on dihedral angle?

From: Rajeswari A. <rajeswari.biotech.gmail.com>
Date: Mon, 28 Mar 2011 18:10:37 +0530

Thank you so much for ur help and both dihedral clustering and decoy
clustering informations are very useful.

Thank you so much once again!

Rajeswari A

On Sat, Mar 26, 2011 at 7:13 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> On Fri, Mar 25, 2011 at 6:35 PM, Thomas Cheatham III <tec3.utah.edu>
> wrote:
> > dihedral angles) however better would be to look in the AmberTools manual
> > for the command called "dihedralcluster". This has a different syntax
> and
> > clusters dihedrals.
>
> I actually made a mistake in the manual, the actual command is
> "clusterdihedral" (to avoid parser confusion with the 'dihedral'
> command). However, I'm not sure it made it into the AmberTools 1.4
> manual, so here is the full description of the command:
>
> clusterdihedral out <filename> cut <clustersize_cutoff> framefile
> <filename>
> clusterinfo <filename>
> [dihedralfile <filename>] | [phibins <bins>
> psibins <bins> <mask>]
>
> Cluster frames in a trajectory using dihedral angles. To define which
> dihedral angles will be used for clustering either an atom mask or an
> input file specified by the dihedralfile keyword should be used. If
> dihedralfile is used, each line in the file should contain a dihedral
> to be binned with format:
>
> ATOM#1 ATOM#2 ATOM#3 ATOM#4 #BINS
>
> where the ATOM arguments are the atom numbers defining the dihedral
> and #BINS is the number of bins to be used (so if #BINS=10 the width
> of each bin will be 36. If an atom mask is specified, only protein
> backbone dihedrals (Phi and Psi defined using atom names C-N-CA-C and
> N-CA-C-N) within the mask will be used, with the bin sizes specified
> by the phibins and psibins keywords (default for each is 10 bins).
>
> Output will either be written to the terminal or the file specified by
> the out keyword. First information about which dihedrals were
> clustered will be printed. Then the number of clusters will be
> printed, followed by detailed information of each cluster. The
> clusters are sorted from most populated to least populated. Each
> cluster line has format
>
> Cluster CLUSTERNUM CLUSTERPOP [ dihedral1bin, dihedral2bin ... dihedralNbin
> ]
>
> followed by a list of frame numbers that belong to that cluster.
>
> If specified by the framefile keyword a file containing cluster
> information for each frame will be written with format
>
> Frame CLUSTERNUM CLUSTERSIZE DIHEDRALBINID
>
> where DIHEDRALBINID is a number that identifies the unique combination
> of dihedral bins this cluster belongs to (specifically it is a
> 3*number-of-dihedral-characters long number composed of the individual
> dihedral bins).
>
> If specified by the clusterinfo keyword a file containing information
> on each dihedral and each cluster will be printed. This file can be
> read by SANDER for use with REMD with a structure reservoir
> (-rremd=3). The file, which is essentially a simplified version of the
> main output file, has the following format:
>
> #DIHEDRALS
>
> dihedral1_atom1 dihedral1_atom2 dihedral1_atom3 dihedral1_atom4
>
> ...
>
> #CLUSTERS
>
> CLUSTERNUM1 CLUSTERSIZE1 DIHEDRALBINID1
>
> ...
>
> If a cutoff is specified by CUT only clusters with population greater
> than CUT will be printed.
>
> Hope this helps.
>
> -Dan
>
>
> >
> >> 2) If clustering is based on the rms deviation can we use reference
> >> structure for clustering. For example, i want to make 3 clusters and i
> have
> >> 3 reference structures. Based on this reference structures' rmsd can we
> >> cluster the trajectory?
> >
> > The final section of the "cluster" command in the manual mentions the
> > "decoy" option with the means clustering algorithm.
> >
> > cluster out decoy-test representative pdb average pdb means clusters 3 \
> > rms decoy decoys.trj .CA
> >
> > To do this, create a AMBER trajectory file from the three reference
> > structures (decoys)
> >
> > trajin decoy1.pdb
> > trajin decoy2.pdb
> > trajin decoy3.pdb
> > trajout decoys.trj nobox
> >
> >
> > --tec3
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Mon Mar 28 2011 - 06:00:06 PDT
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