I was running Abinitio protocol and I have noticed that a certain sequence yield sequeced models (S_000001, S_000002, S_000003) in the absence of the secondary structure predicition file. Conversely, in the presence of this file in the protocol some models where not generated (or, at least, not recorded). In fact, I have something like the sequence: S_00002, S_00009, S_00013, etc. From 100,000 models required only around 10,000 were possible to be extract. Is there any resonable reason for this fact?
Addicionaly, I was wondering where is the secondary structure prediction file used in the modelling (and its weight in the score)?