> 1) I want to know is there any possibility to cluster the trajectories based
> on dihedral angle.
> I tried with the following code
> "cluster out test representative pdb average pdb means clusters 6 dihedral :
> 50.C : 28.CA : 127.CA : 149.C"
>
> and ptraj returns with the error of
> "PTRAJ: cluster out cluster_out representative pdb average pdb means
> clusters 6 dihedral : 50.C : 28.CA : 127.CA : 149.C
> MASK = dihedral
>
> ERROR in tokenize(): wrong syntax"
Where in the AmberTools manual for the cluster command does it say you can
specify "dihedral"? It doesn't. Also, you cannot have a space after the
residue specifier :, i.e. you want :50.C
There is undocumented code to cluster by attribute (i.e. like a set of
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.
> 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
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Received on Fri Mar 25 2011 - 16:00:02 PDT
