Reply To: some application troubles when using resfile flag

[Anonymous]

after performed as your suggestion, it was improved a lot.

and this time the bug showed

apps.backrub: Processing chaind.pdb…
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue cym 60
core.conformation.Conformation: [ WARNING ] missing heavyatom: CT1 on residue cym 60
core.conformation.Conformation: [ WARNING ] missing heavyatom: CT2 on residue cym 60
core.conformation.Conformation: [ WARNING ] missing heavyatom: NI1 on residue cym 60
core.conformation.Conformation: [ WARNING ] missing heavyatom: CI2 on residue cym 60
core.conformation.Conformation: [ WARNING ] missing heavyatom: CK on residue cym 60
core.conformation.Conformation: [ WARNING ] missing heavyatom: OL on residue cym 60
core.conformation.Conformation: [ WARNING ] missing heavyatom: CT2 on residue cym 60
core.conformation.Conformation: [ WARNING ] missing heavyatom: NI1 on residue cym 60
core.conformation.Conformation: [ WARNING ] missing heavyatom: CK on residue cym 60
core.conformation.Conformation: [ WARNING ] missing heavyatom: OL on residue cym 60
core.conformation.Conformation: [ WARNING ] missing heavyatom: CT2 on residue cym 60
core.pack.task: Packer task: initialize from command line()
core.pack.pack_missing_sidechains: packing residue number 60 because of missing atom number 9 atom name CZ
core.pack.rotamer_set.RotamerSet_: [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 60 cym
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1 rotamers at 1 positions.
core.pack.pack_rotamers: IG: 452 bytes
protocols.moves.BackrubMover: Segment lengths: 3-34 atoms
protocols.moves.BackrubMover: Main chain pivot atoms: CA
protocols.moves.BackrubMover: Adding backrub segments for residues 60-62
protocols.moves.BackrubMover: Total Segments Added: 3
apps.backrub: Score After PDB Load:
core.mm.MMBondAngleLibrary: No parameters for X-X-C

ERROR: t3mapIN7utility4keys9Key2TupleIjjEEjSt4lessIS4_ESaISt4pairIKS4_jEEESaISB_EE
ERROR:: Exit from: src/core/mm/MMBondAngleLibrary.cc line: 188
`

and in the PDB file there was actually e.g C01 C03 C05.. instead of e.g CZ CT1 CT2 in the params file. How could it be like that? I think I`ve copied the adduct in my modified PDB (decorate cys into my adduct) in order to keep the enumeration consistent.

Thanks!