Error when running Remodel with EnzDes constraint file

[Anonymous]

Hi,
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:
CST::BEGIN
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
CST::END

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?

-Amanda

[Anonymous]

The fa_standard residue type for proline is at rosetta/rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/PRO.params

The other L canonical amino acids are in the same folder.

You’ll see this:

#rosetta residue topology file
#version 0.1
NAME PRO
IO_STRING PRO P
TYPE POLYMER #residue type
AA PRO
ATOM N Npro N -0.29
ATOM CA CAbb CP1 0.02
ATOM C CObb C 0.51
ATOM O OCbb O -0.51
ATOM CB CH2 CP2 -0.18
…

In the ATOM lines, the columns are: ATOM, PDB atom name, Rosetta atom name, MM atom name, partial charge. That first N is normally Nbb, but as you can see it’s Npro for proline – it is NOT a hydrogen bond donator like Nbb so it has different properties. I don’t know how to fix the enzdes constraint file, but it’s definitely this Npro/Nbb issue – I guess don’t allow mutation to proline?

[Anonymous]

Thank you, the problem was that Proline doesn’t have an Nbb atom. It works when I change the constraint to:

TEMPLATE:: ATOM_MAP: 1 atom_type: Nbb
TEMPLATE:: ATOM_MAP: 1 is_backbone
TEMPLATE:: ATOM_MAP: 1 residue1: ARNDCQEGHILKMFSTWYV

And also change the corresponding blueprint line to:

247 L E PIKAA ARNDCQEGHILKMFSTWYV

[Author]

Posts