Hi again!
I'm trying to setup a somd2 RBFE run from the API. I'm following the BioSimSpace tutorials on how to setup somd2 runs:
elif engine_query == "SOMD2":
os.makedirs(
f"{main_dir}/outputs/{engine_query}/{lig_0}~{lig_1}/bound", exist_ok=True
)
BSS.Stream.save(
system_bound,
f"{main_dir}/outputs/{engine_query}/{lig_0}~{lig_1}/bound/{lig_0}~{lig_1}",
)
with open(f"{main_dir}/outputs/{engine_query}/{lig_0}~{lig_1}/bound/config.yaml", 'w') as yaml_file:
_yaml.dump(somd2_config, yaml_file)I've done a similar thing where I create the config file directly by constructing a config object, saving it as a yaml file (as above) and then saving my merged BioSimSpace system as a sire object:
merged_ligand_system = self.create_hybrid_molecule()
somd2_config_file = os.path.join(self.working_directory, "config.yaml")
somd2_config = config.Config(
runtime=str(self.recipe.sampling_time),
num_lambda=self.recipe.n_lambdas,
log_file=f"{self.transformation}_somd2_log.txt",
timestep=str(self.recipe.dt),
temperature=str(self.recipe.temperature),
pressure=str(self.recipe.pressure),
integrator="langevin",
cutoff_type="pme",
cutoff=str(self.recipe.nb_cutoff),
platform=compute_platform,
hmr=False,
restraints=None, #how to do this???
constraint="h_bonds",
perturbable_constraint="h_bonds_not_heavy_perturbed",
minimise=True,
minimisation_constraints=False,
minimisation_errors=False,
equilibration_time=str(self.recipe.lambda_equilibration_time),
equilibration_timestep=str(self.recipe.lambda_equilibration_dt),
equilibration_constraints=True,
opencl_platform_index=0,
restart=False,
use_backup=False,
write_config=True,
overwrite=False,
somd1_compatibility=False,
pert_file=None,
output_directory=self.working_directory
)
config_dictionary = somd2_config.as_dict()
with open(somd2_config_file, "w") as ofile:
yaml.dump(config_dictionary, ofile)
sire_system = sire.system.System(merged_ligand_system._sire_object)
sire.stream.save(
obj=sire_system,
filename=f"{self.working_directory}/merged_system.bss"
)I then tried running somd2 with:
somd2 merged_system.bss --config config.yaml
but I get this error:
2026-06-26 13:30:34.088 | INFO | somd2.runner._base:__init__:105 - somd2 version: 2025.2.0.dev+268.gfdad810
2026-06-26 13:30:34.088 | INFO | somd2.runner._base:__init__:106 - sire version: 2025.4.0+8c20f50
2026-06-26 13:30:34.088 | INFO | somd2.runner._base:__init__:107 - biosimspace version: 2025.4.0
2026-06-26 13:30:34.089 | INFO | somd2.runner._base:__init__:109 - ghostly version: 2025.2.0
2026-06-26 13:30:34.338 | INFO | somd2.runner._base:__init__:325 - Applying modifications to ghost atom bonded terms
2026-06-26 13:30:34.383 | WARNING | ghostly._ghostly:_check_rotamer_anchors:2378 - Potential rotamer anchor at λ = 0: bond 12-0 is a rotatable sp3 bond. Surviving anchor dihedrals may allow rotameric transitions of ghost atoms.
2026-06-26 13:30:34.489 | ERROR | somd2.runner._base:_prepare_output:1343 - The following files already exist, use --overwrite to overwrite them: ['/Users/af25016/projects/meze/data/outputs/model_0/vim2/ligand_11~ligand_12/bound/config.yaml']
I don't want to overwrite the file as I have setup the config in a specific way. I also don't see how somd2 would know my config settings if I overwrite/delete the saved config file?
I'm sure I'm not using the scripts/package the right way, so any help with this would be really appreciated, thanks!
Hi again!
I'm trying to setup a somd2 RBFE run from the API. I'm following the BioSimSpace tutorials on how to setup somd2 runs:
I've done a similar thing where I create the config file directly by constructing a config object, saving it as a yaml file (as above) and then saving my merged BioSimSpace system as a sire object:
I then tried running somd2 with:
but I get this error:
I don't want to overwrite the file as I have setup the config in a specific way. I also don't see how somd2 would know my config settings if I overwrite/delete the saved config file?
I'm sure I'm not using the scripts/package the right way, so any help with this would be really appreciated, thanks!