I'm trying to use Remodel with a constraint file and it is exiting with an error regarding atom type. The error does not occur if I remove the enzdes:cstfile flag.
My flags look like this:
'/netapp/home/noah/rosetta/remodel_r51420', '-database /netapp/home/noah/rosetta/database_r51404', '-run:chain B', '-s 1AUT_PAR1_renum_ppk_0001.pdb', '-remodel:blueprint blueprint_1', '-ex1', '-ex2', '-use_input_sc', '-nstruct 1', '-enzdes:cstfile constraint_1'
constraint_1 looks like this:
TEMPLATE:: ATOM_MAP: 1 atom_type: Nbb
TEMPLATE:: ATOM_MAP: 1 is_backbone
TEMPLATE:: ATOM_MAP: 1 residue3: ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR
TEMPLATE:: ATOM_MAP: 2 atom_type: Nbb
TEMPLATE:: ATOM_MAP: 2 is_backbone
TEMPLATE:: ATOM_MAP: 2 residue3: ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR
CONSTRAINT:: distanceAB: 10.00 0.20 50.00 0
blueprint_1 looks like this (excerpt):
210 S .
211 W . CST1B
212 G .
240 D .
241 L L CST1A
242 D L
Remodel exits with the following error:
Error: ResidueType PRO does not have an atom of type Nbb
ERROR:: Exit from: src/protocols/toolbox/match_enzdes_util/EnzCstTemplateRes.cc line: 488
The documentation for Remodel shows an example for the cst file with two atom types "Nbb" and "OCbb" and notes that "the atom_type fields expect Rosetta atom types," but I'm not sure where to learn about the correct syntax for Rosetta atom types as I haven't come across them before and they aren't the same format as PDB atom types. I'd like to know if I'm using the Rosetta atom types correctly.
Also, is possible the error is related to the residue type being proline?