I don't know if this is the appropriate place to ask this type of question but I have been reading this paper which describes the FastFloppyTail and Abinitio programs:
I am currently trying to generate 500 structures for an IDP called non-phosphorylated 4E-BP2 using the FastFloppyTail method. I used PsiPred DISOPRED3 to generate the secondary structure and disordered prediction files. I then used the Diso_SS2_Reweight_Opt_FFT.py script to reweight the secondary structure prediction based off of the disordered prediction file. I then submit my reweighted secondary structure prediction file and protein sequence into the Robetta web server to generate the 3mer fragments. I then utilize FastFloppyTail to generate the protein structures using the 3mer fragments (I am not using the -diso option, but maybe I should?).
My questions are: Do I have to use AbInitio before I use FastFloppyTail as indicated by Figure 1 in the above paper that I linked or is that only for mostly ordered proteins that have IDRs rather than an IDP? Could I supply the -t _frag option with 9mer fragments instead of 3mer fragments?