I'm trying to import a pdb file using pose_from_pdb() function. But, I'm getting the following error:
File: /home/benchmark/rosetta/source/src/core/energy_methods/RamaPreProEnergy.cc:149 [ ERROR ] UtilityExitException ERROR: Error in core::scoring::methods::RamaPreProEnergy::residue_pair_energy(): The RamaPrePro term is incompatible with cyclic dipeptides (as is most of the rest of Rosetta).
Is there something wrong with the pdb file? How can I fix it?
Thank you very much
The energy function says it dislikes your protein by claiming there is a diketopiperazine —does it have anything odd? Say GFP chromophore, MIO cofactor encoded oddly.
Does it load after stripping in pymol everything bar peptides? Rosetta is fine with crosslinks (LINK records in PDBs) and CONECT records are ignored mostly but this would clean up bad formatting.
What scorefunction are you using?