Consistent XYZvector length() zero failure in EnzDes

[Anonymous]

So…a bunch of other posts says to just rerun it if Rosetta fails with “cannot normalize xyzVector of length() zero”. But what if you DO get this error consistently across different runs with different seeds? Like, every time? Where should I start looking to even solve this problem? I’m running EnzDes in Rosetta 3.8 (working on updating to 3.10), and it fails here. I am using a NCAA and a water molecule in the active site. 

protocols.enzdes.EnzdesBaseProtocol: Doing a pose minimization... the backbone is allowed to move at positions: 3, 4, 5, 6, 7, 8, 9, 37, 38, 39, 40, 41, 42, 84, 85, 86, 87, 88, 100, 101, 102, 103, 104, 183, 184, 185, 186, 187, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 218, 219, 220, 221, 222, 223, 224, 225, 257, 258, 259, 260, 261, 262, 263, 264, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 287, 288, 289, 290, 292, 293, 294, 295, 296,

protocols.ligand_docking.LigandBaseProtocol: Moved ligand FOLD_TREE  EDGE 1 291 -1  EDGE 291 298 -1  EDGE 291 299 1

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL1

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL2

core.conformation.Residue: Building atom OVL1 based on standard internal coordinates.

core.conformation.Residue: Building atom OVL2 based on standard internal coordinates.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_upper OVU1

core.conformation.Residue: Building atom OVU1 based on standard internal coordinates.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL1

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL2

core.conformation.Residue: Building atom OVL1 based on standard internal coordinates.

core.conformation.Residue: Building atom OVL2 based on standard internal coordinates.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom GLY:protein_cutpoint_upper OVU1

core.conformation.Residue: Building atom OVU1 based on standard internal coordinates.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom THR:protein_cutpoint_lower OVL1

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom THR:protein_cutpoint_lower OVL2

core.conformation.Residue: Building atom OVL1 based on standard internal coordinates.

core.conformation.Residue: Building atom OVL2 based on standard internal coordinates.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom GLY:protein_cutpoint_upper OVU1

core.conformation.Residue: Building atom OVU1 based on standard internal coordinates.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom GLY:protein_cutpoint_lower OVL1

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom GLY:protein_cutpoint_lower OVL2

core.conformation.Residue: Building atom OVL1 based on standard internal coordinates.

core.conformation.Residue: Building atom OVL2 based on standard internal coordinates.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom THR:protein_cutpoint_upper OVU1

core.conformation.Residue: Building atom OVU1 based on standard internal coordinates.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL1

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL2

core.conformation.Residue: Building atom OVL1 based on standard internal coordinates.

core.conformation.Residue: Building atom OVL2 based on standard internal coordinates.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_upper OVU1

core.conformation.Residue: Building atom OVU1 based on standard internal coordinates.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL1

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL2

core.conformation.Residue: Building atom OVL1 based on standard internal coordinates.

core.conformation.Residue: Building atom OVL2 based on standard internal coordinates.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering for matched variants.

core.chemical.PatchOperations.hh: AddAtom::apply: OVU1 VIRT VIRT 0

core.chemical.PatchOperations.hh: AddBond::apply: N OVU1

core.chemical.PatchOperations.hh: SetBackboneHeavyatom::apply: OVU1

core.chemical.PatchOperations.hh: SetICoor::apply: OVU1 N CA CA1

Error: [ ERROR ] Must call shutdown() when finished using job distributor!

caught exception Cannot normalize xyzVector of length() zero

 

[Anonymous]

Updating to 3.10 (or a more recent weekly) is definitely recommended. There’s been some updates with regards ot normalize xyzVector which should make such errors less likely. (Not fixed, but less likely.)

Failing that, if you can bundle up an example of where it happens consistently, you can post it here and I might be able to debug it if I can reproduce it locally.

[Author]

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