Though it’s sequence clearly folds into this particular structure (as proved by the crystal structure) why can’t abinitio performs a successful simulation and result in a funnel shaped plot?
to be blunt — this is because structure prediction is an unsolved problem! while abinitio is relatively good at solving some structures, it isn’t able to solve them all!
Should I change the abinitio protocol from the tutorial, or run it multiple times, or generate more fragments to be able to computationally model the true shape of this protein and get a funnel plot?
Generally the field has strayed away from using abinitio exclusively, and has added iterative rounds of rosetta hybridize as described here https://www.ncbi.nlm.nih.gov/pubmed/26677056 I’m aware of many scenarios where a seemingly failed abinitio run can be signifigantly improved via 4-10 rounds of iterativehybridize. Also described in that paper is using predicted contacts to drive abinitio folding, which is sometihng you may be interested in using (sergeys gremlin protocol)
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