Error: ResidueType CYS does not have an atom of type SG

[hsshhj020-creator]

I am trying to run invrotzyme.py with a motif PDB and CST file, but I keep getting an error about CYS not having an SG atom, even though my PDB seems correct.

Here are the details:

My motif PDB:

CRYST1 97.917 97.917 65.186 90.00 90.00 120.00 P 32 2 1 1
ATOM 1 N GLY A 163 23.538 53.433 59.186 1.00 14.78 N
ATOM 2 CA GLY A 163 22.351 53.801 58.418 1.00 13.50 C
ATOM 3 C GLY A 163 22.664 54.845 57.361 1.00 13.52 C
ATOM 4 O GLY A 163 23.819 55.259 57.162 1.00 13.10 O
ATOM 5 N CYS A 164 21.659 55.258 56.578 1.00 11.00 N
ATOM 6 CA CYS A 164 21.852 55.985 55.347 1.00 14.18 C
ATOM 7 C CYS A 164 22.404 57.387 55.434 1.00 14.90 C
ATOM 8 O CYS A 164 22.919 57.858 54.406 1.00 17.44 O
ATOM 9 CB CYS A 164 20.539 56.162 54.573 1.00 16.91 C
ATOM 10 SG CYS A 164 19.872 54.593 54.009 1.00 20.42 S
ATOM 11 N PHE A 165 22.327 58.014 56.606 1.00 12.50 N
ATOM 12 CA PHE A 165 22.853 59.349 56.715 1.00 12.18 C
ATOM 13 C PHE A 165 24.347 59.321 56.906 1.00 12.39 C
ATOM 14 O PHE A 165 24.950 60.393 56.818 1.00 11.12 O
ATOM 15 CB PHE A 165 22.204 60.087 57.910 1.00 12.34 C
ATOM 16 CG PHE A 165 22.392 59.429 59.255 1.00 12.46 C
ATOM 17 CD1 PHE A 165 23.570 59.604 59.973 1.00 13.14 C
ATOM 18 CD2 PHE A 165 21.369 58.679 59.822 1.00 11.86 C
ATOM 19 CE1 PHE A 165 23.743 59.065 61.253 1.00 14.95 C
ATOM 20 CE2 PHE A 165 21.577 58.059 61.061 1.00 13.26 C
ATOM 21 CZ PHE A 165 22.726 58.281 61.783 1.00 12.82 C
TER
END

My CST file:

#######################################################################

CST 1 | NAR <-> Cys164

#######################################################################
CST::BEGIN

TEMPLATE:: ATOM_MAP: 1 atom_name: C2 O4 C1
TEMPLATE:: ATOM_MAP: 1 residue3: NAR

TEMPLATE:: ATOM_MAP: 2 atom_type: SG
TEMPLATE:: ATOM_MAP: 2 residue3: CYS

CONSTRAINT:: distanceAB: 3.81 0.2 100. 1 0
CONSTRAINT:: angle_A: 70.84 10.0 50.0 360. 0
CONSTRAINT:: angle_B: 166.10 20.0 50.0 360. 0
CONSTRAINT:: torsion_A: -10.62 20.0 50.0 360. 0
CONSTRAINT:: torsion_AB: 0.0 20.0 50.0 360. 0
CONSTRAINT:: torsion_B: 0.0 40.0 50.0 360. 0

ALGORITHM_INFO:: match
IGNORE_UPSTREAM_PROTON_CHI
ALGORITHM_INFO::END

CST::END

#######################################################################

CST 2 | Cys164 <-> His303

#######################################################################
CST::BEGIN

TEMPLATE:: ATOM_MAP: 1 atom_type: SG
TEMPLATE:: ATOM_MAP: 1 residue3: CYS

TEMPLATE:: ATOM_MAP: 2 atom_name: NE2 CE1 CD2
TEMPLATE:: ATOM_MAP: 2 residue3: HIS

CONSTRAINT:: distanceAB: 3.60 0.2 100 0 0
CONSTRAINT:: angle_A: 166.10 20.0 50 360. 0
CONSTRAINT:: angle_B: 0.0 40.0 50 360. 0
CONSTRAINT:: torsion_A: 0.0 40.0 25 360. 0
CONSTRAINT:: torsion_AB: 38.22 25.0 0 180. 2
CONSTRAINT:: torsion_B: 0.0 20.0 25 180. 0

ALGORITHM_INFO:: match
SECONDARY_MATCH: UPSTREAM_CST 1
IGNORE_UPSTREAM_PROTON_CHI
MAX_DUNBRACK_ENERGY 5.0
ALGORITHM_INFO::END

CST::END

Command:

python invrotzyme.py
--cstfile NAR_cys164_his303.cst
--params NAR.params
--N_len 2
--C_len 2
--secstruct_per_cst H H
--dunbrack_prob 0.6
--motif_for_cst 1:2:cys164.pdb
--keep_his_tautomer 2:HIS_D
--max_random_rotamers 5

Error:

PyRosetta-4 2024 [Rosetta PyRosetta4.conda.linux.cxx11thread.serialization.CentOS.python310.Release 2024.39+release.59628fbc5bc09f1221e1642f1f8d157ce49b1410 2024-09-23T07:49:48] retrieved from: http://www.pyrosetta.org
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: PyRosetta4.conda.linux.cxx11thread.serialization.CentOS.python310.Release r387 2024.39+release.59628fb 59628fb http://www.pyrosetta.org 2024-09-23T07:49:48
core.init: Rosetta extras: [cxx11thread, serialization]
core.init: command: PyRosetta -extra_res_fa NAR.params -run:preserve_header -database /data/zcxu/miniconda3/envs/diffusion/lib/python3.10/site-packages/pyrosetta/database
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1074404074 seed_offset=0 real_seed=-1074404074 thread_index=0
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1074404074 RG_type=mt19937
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 986 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.841207 seconds.
Error: ResidueType CYS does not have an atom of type SG

ERROR:: Exit from: /home/benchmark/rosetta/source/src/protocols/toolbox/match_enzdes_util/EnzCstTemplateRes.cc line: 548
Traceback (most recent call last):
File "/data/zcxu/serine-hydrolase-design/scripts/invrotzyme/invrotzyme.py", line 451, in
main(args)
File "/data/zcxu/serine-hydrolase-design/scripts/invrotzyme/invrotzyme.py", line 273, in main
cst_io.read_enzyme_cstfile(args.cstfile)
RuntimeError:

File: /home/benchmark/rosetta/source/src/protocols/toolbox/match_enzdes_util/EnzCstTemplateRes.cc:548
[ ERROR ] UtilityExitException
ERROR:

Could you please advise what could be wrong? Is it related to --motif_for_cst 1:2:cys164.pdb and the resno_in_motif specification?

Thank you for your help!

[roccomoretti]

You're using atom_type: SG in your constraint file. The type of the sulfur atom in a CYS residue is SH1 (in ref2015 and later -- it's S for talaris and before).

Change that line to (e.g.) TEMPLATE:: ATOM_MAP: 1 atom_name: SG CB CA.

(You need to provide all three atoms with atom_name -- the atom_type is intended primarily for things like ASP/GLU, where you have the same functional group but with a different naming scheme. For cases like CYS where you know what the atom names are, it's preferred to specify all three explicitly.)