The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab
I have been trying to dock heparan sulfate with my protein. I set it as an ordinary ligand and have created two .tbl restraints file, one for distance and one for dihedral restraints generated from NMR experiments. I have not been successful with the docking as it always have an error. Previously due to error in sanitizing the ligand. Now I have the ligan.param and ligand.top incorporated in my .toml file. However, as I was trying to start the run now, it says that there is something wrong with the config file. Full error is below:
“[2025-09-24 13:12:39,036 libutil ERROR] Something is wrong with the config file.
Traceback (most recent call last):
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/toml/decoder.py”, line 511, in loads
ret = decoder.load_line(line, currentlevel, multikey,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/toml/decoder.py”, line 778, in load_line
value, vtype = self.load_value(pair[1], strictly_valid)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/toml/decoder.py”, line 880, in load_value
return (self.load_array(v), “array”)
^^^^^^^^^^^^^^^^^^
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/toml/decoder.py”, line 1026, in load_array
nval, ntype = self.load_value(a[i])
^^^^^^^^^^^^^^^^^^^^^
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/toml/decoder.py”, line 866, in load_value
raise ValueError(“Reserved escape sequence used”)
ValueError: Reserved escape sequence used
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/haddock/gear/config.py”, line 220, in loads
cfg_dict = toml.loads(cfg) # Try to load it with the toml library
^^^^^^^^^^^^^^^
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/toml/decoder.py”, line 514, in loads
raise TomlDecodeError(str(err), original, pos)
toml.decoder.TomlDecodeError: Reserved escape sequence used (line 19 column 1 char 521)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/haddock/gear/config.py”, line 138, in load
return loads(Path(fpath).read_text())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/haddock/gear/config.py”, line 222, in loads
raise ConfigurationError(
haddock.core.exceptions.ConfigurationError: Some thing is wrong with the config file: Reserved escape sequence used (line 19 column 1 char 521)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/haddock/libs/libutil.py”, line 378, in log_error_and_exit
yield
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/haddock/clis/cli.py”, line 151, in main
params, other_params = setup_run(
^^^^^^^^^^
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/haddock/gear/prepare_run.py”, line 277, in setup_run
config_files = read_config(workflow_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/root/haddock3-work/hd3-venv/lib/python3.12/site-packages/haddock/gear/config.py”, line 140, in load
raise ConfigurationError(
haddock.core.exceptions.ConfigurationError: Something is wrong with the config file.
[2025-09-24 13:12:39,052 libutil ERROR] Something is wrong with the config file.”
Please help. I don’t know what to do anymore as I have been tryng for days now 
. Thank you! I will also attach here my run parameters taken from this website as well:
run_dir = “run1-full”
mode = “batch”
debug = true
concat = 5
queue_limit = 100
molecules = [
“data/neuraminidase-2BAT.pdb”,
“data/oseltamivir_zwitterion.pdb”
]
[topoaa]
autohis = true
ligand_param_fname = “data/ligand-prodrg.param”
ligand_top_fname = “data/ligand-prodrg.top”
delenph = false
[rigidbody]
tolerance = 5
ambig_fname = “data/ambig-active-rigidbody.tbl”
ligand_param_fname = “data/ligand-prodrg.param”
ligand_top_fname = “data/ligand-prodrg.top”
sampling = 1000
w_vdw = 1.0
[caprieval]
[seletop]
select = 200
[caprieval]
[flexref]
tolerance = 5
ambig_fname = “data/ambig-passive.tbl”
ligand_param_fname = “data/ligand-prodrg.param”
ligand_top_fname = “data/ligand-prodrg.top”
mdsteps_rigid = 0
mdsteps_cool1 = 0
[caprieval]
[rmsdmatrix]
resdic_A = [ 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199 ]
[clustrmsd]
criterion = ‘maxclust’
n_clusters = 4 # the number of clusters to be formed
[seletopclusts]
top_models = 4
[caprieval]
