Dear Amber Users,
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"
can some one help me on this?
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?
Thank you. Waiting for ur reply.
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Received on Fri Mar 25 2011 - 02:00:04 PDT
