I am currently trying to work with Rosetta. I have a peptide sequence and I would like to predict its structure using de novo structure prediction. I have Rosetta installed and I need to do this with Rosetta (so please, do not suggest any webservice such as Robetta). I tried following the Rosetta documentation: the de novo structure prediction tutorial states that required input files are the sequence in the fasta format and 9mer & 3mer fragments files. To obtain the fragment files, the turorial states:
There are multiple ways to obtain those fragment files. You can generate them on your local machine. For that to work you need additional software installed. How to do that is explained in a separate tutorial for fragment picking.
However, the fragment picking tutorial says you need three input files to generate fragments: the fasta sequence (which I have) ; the psipred .Ss2 file (which I have) and the structure (which, of course, I don't have). I have tried running the script for fragments picking: it works well when an input structure is given, but it doesn't work if there is no structure.
Therefore, here is my question: how can I do an ab initio structure prediction if I need fragment files whose generation requires a structure ? How do I generate fragments if I don't have a structure ? Or how do I do ab initio structure prediction if I don't have fragments ?
I am fairly new to Rosetta and the concept of fragments, so if I am missing something basic please tell me.