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    Unrecognized atom warnings are common and usually unimportant. It means there are atoms in the PDB file that do not match the expected atoms defined in the residue parameters files. You can compare the atom names in the PDB file to the atom names in the minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types/l_caa/*.params to see where there is an atom name mismatch (spaces count). I would guess it’s either the backbone alpha hydrogen or a virtual atom. You will also get these errors when reading fullatom PDBs into a centroid mode pose and vice versa.

    I don’t know the exact numbers (I never relax things) but I think relax mode is not suggested for proteins larger than 100 residues. I know its runtime scales poorly with protein length, so 200+ is going to be very slow. This is the sort of thing someone really ought to put into the relax documentation…