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.?
You should remove the -flexpep_prepack flag, this flag should be used once to create ‘prepacked’ structure and then for the production run you should not use it.
Regarding your question, if you believe the peptide is ‘close to linear’ in its native conformation, FlexPepDock should still serve your needs, however, it wouldn’t fold it into a helix or a beta hair-pin. If this is the level of sampling you’re looking for, the next rosetta release will include the FlexPepDock ab-initio protocol that would have a much larger sampling range.