Member Site › Forums › Rosetta 3 › Rosetta 3 – General › Is it possible to do Abinitio folding from a linear structure.? › Reply To: Is it possible to do Abinitio folding from a linear structure.?
To your first question: ab initio does not require an input structure. It can take an input for RMSD benchmarking (where the correct answer is known, and you are testing if Rosetta gets it right). It only needs the fasta file.
To your second question: A nonapeptide is unlikely to have a rigid structure in solution, so folding it ab initio doesn’t make sense, and folding it with fragments drawn from _folded_ proteins is inappropriate. Why do you want a free nonapeptide “structure”?