“i have run abintio structure prediction and produced nearly 20.000 structure. please help me how to cluster these structures and how to create funnel plot to select native like structure from silent file.”
There’s a clustering application. I don’t know anything about it beyond what is in its documentation (I’ve never used it). http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/app_cluster.html
“Do u think 20,000 structures is good enough to predict native struture of 146 residues.”
If your lowest-energy structures converge to a single solution, yes. If not, no.