Does anyone know if the the Rosetta 3.0 release structure prediction Flag file requires one of the three types of secondary structure files (i.e Jones . etc) as input in order to run properly? I do not have a native pdb file to provide as input. However, I was able to run the program without any issues with only the FASTA sequence file, and the fragment libraries as input, to generate an ensemble. I am concerned that the decoys generated without a secondary structure file present will not be useful.
I have attempted to input one of the three secondary structure files into the flag folder but the program fails to recognize it (likely because I am probably not calling it with the correct cmd, etc?) and won't run.
Thank you for reading this.