diff --git a/docs/content/docs/developer-guide/architecture.mdx b/docs/content/docs/developer-guide/architecture.mdx
index 61d92c5..1a7d653 100644
--- a/docs/content/docs/developer-guide/architecture.mdx
+++ b/docs/content/docs/developer-guide/architecture.mdx
@@ -180,8 +180,8 @@ graph TD
- **`config.py`**: Pydantic models for local and SLURM execution. `ExecutorConfig` handles local runs; `SlurmExecutorConfig` adds SLURM-specific fields (account, partition, walltime, gres, per-stage overrides). Both serialize to/from YAML via `from_yaml()` and `model_dump()`.
- **`session.py`**: `parsl_session()` context manager that owns the Parsl DataFlowKernel lifecycle. On exit it calls `parsl.clear()` and explicitly `scancel`s any lingering SLURM job IDs.
-- **`apps.py`**: Defines `get_build_app()` (python\_app for system building), `get_grompp_app()` and `get_mdrun_app()` (bash\_apps for GROMACS). Nearly all conditional logic (GPU, MPI, thread counts, restart flags) is resolved in Python before generating the bash script — the only permitted runtime branch is a small `if/elif/else/fi` block for binary detection when `gmx_binary` is set to `auto`.
-- **`stages.py`**: `STAGE_REGISTRY` declares the canonical pipeline (EM → NVT → NPT → Production) as `StageSpec` dataclasses. `run_stage()` is the single generic dispatch function for all stages.
+- **`apps.py`**: Defines `get_build_app()` (python\_app for system building), `get_grompp_app()` and `get_mdrun_app()` (bash\_apps for GROMACS). Nearly all conditional logic (GPU, MPI, thread counts, restart flags) is resolved in Python before generating the bash script — the only permitted runtime branches are a small `if/elif/else/fi` block for binary detection when `gmx_binary` is set to `auto`, and, in the grompp script only, a GROMACS version check that is emitted when the topology's force field needs a minimum GROMACS version (e.g. `amber14sb.ff` needs 2026).
+- **`stages.py`**: `STAGE_REGISTRY` declares the canonical pipeline (EM → NVT → NPT → Production) as `StageSpec` dataclasses. `run_stage()` is the single generic dispatch function for all stages; it derives the minimum GROMACS version from the simulation directory's `topology.top` and passes it to grompp.
- **`build.py`** / **`simulate.py`**: Top-level entry points. `build_systems()` submits parallel build tasks; `run_simulations()` chains stages sequentially per simulation with checkpoint detection and trajectory validation.
- **`tui.py`**: Interactive SLURM configuration wizard using `questionary`. Auto-discovers cluster hardware via `sinfo`/`sacctmgr` and persists the result as a reusable YAML file.
diff --git a/docs/content/docs/installation.mdx b/docs/content/docs/installation.mdx
index 907f9c6..089b3c0 100644
--- a/docs/content/docs/installation.mdx
+++ b/docs/content/docs/installation.mdx
@@ -93,6 +93,14 @@ MDFactory currently supports GROMACS workflows with OpenMM-assisted build steps.
conda install -c conda-forge gromacs
```
+
+The open-source `parametrization: amber` route for `proteinbox` and `protein_mixedbox` uses the
+`amber14sb.ff` force field that ships with **GROMACS 2026 or later**. Builds and simulations fail
+early with a clear error when an older `gmx` is found. The pixi workspace provides ready-made
+environments: `pixi run -e gmx ...` (CPU build, all platforms) and `pixi run -e gmx-cuda ...`
+(CUDA build, linux-64).
+
+
### OpenMM
```bash
diff --git a/docs/content/docs/user-guide/parametrization.mdx b/docs/content/docs/user-guide/parametrization.mdx
index e3505fc..6505d25 100644
--- a/docs/content/docs/user-guide/parametrization.mdx
+++ b/docs/content/docs/user-guide/parametrization.mdx
@@ -3,7 +3,7 @@ title: Parametrization
description: Force field parametrization methods in MDFactory
---
-MDFactory supports two force field parametrization methods for generating molecular mechanics parameters from SMILES strings. Both generate GROMACS-compatible ITP files.
+MDFactory supports two force field parametrization methods for generating molecular mechanics parameters from SMILES strings, SMIRNOFF and CGenFF. Both generate GROMACS-compatible ITP files. Protein systems additionally support an open-source Amber ff14SB + OpenFF Sage route.
## Available parametrization methods
@@ -106,6 +106,55 @@ parametrization: cgenff
CGenFF does not require additional configuration options as it uses the global installation settings.
+### Amber ff14SB + OpenFF Sage (protein systems)
+
+The **amber** parametrization is a fully open-source route for the `proteinbox` and
+`protein_mixedbox` system types. It needs no CGenFF or SILCSBIO license:
+
+- **Protein:** Amber ff14SB, using the `amber14sb.ff` force field that ships with GROMACS, through `gmx pdb2gmx`.
+- **Small-molecule solutes** (`protein_mixedbox`): OpenFF Sage through SMIRNOFF.
+- **Water and ions:** TIP3P and Joung–Cheatham Na⁺/Cl⁻ from `amber14sb.ff`.
+
+
+`amber14sb.ff` is only shipped with, and only correct for, GROMACS ≥ 2026 (older versions silently
+ignore its LEaP dihedral reordering). MDFactory checks the `gmx` version before `pdb2gmx` at build
+time and again before the first `grompp` of `mdfactory simulate`, on the node that runs the job.
+Use the pixi `gmx` environment (`pixi run -e gmx ...`, or `gmx-cuda` for the CUDA build) or point
+`[gromacs] GMX_PATH` at a GROMACS 2026 binary.
+
+
+**Configuration:**
+
+```yaml
+engine: gromacs
+parametrization: amber
+parametrization_config:
+ type: amber
+ forcefield: amber14sb # only amber14sb is supported
+ water_model: tip3p # only tip3p is supported
+ ignore_hydrogens: true
+ merge_all: false
+ sage_forcefield: openff-2.2.0.offxml
+ charge_method: openff-gnn-am1bcc-0.1.0-rc.3.pt
+```
+
+| Option | Default | Description |
+|--------|---------|-------------|
+| `forcefield` | `amber14sb` | Protein force field passed to `pdb2gmx`. Only `amber14sb` is supported. |
+| `water_model` | `tip3p` | Water model passed to `pdb2gmx`. Only `tip3p` is supported. |
+| `ignore_hydrogens` | `true` | Drop input hydrogens and let `pdb2gmx` rebuild them. |
+| `merge_all` | `false` | Merge all chains into one moleculetype. |
+| `sage_forcefield` | `openff-2.2.0.offxml` | OpenFF force field for small-molecule solutes. Ignored for `proteinbox`. |
+| `charge_method` | `openff-gnn-am1bcc-0.1.0-rc.3.pt` | Partial charge method for solutes (see [Charge methods](#charge-methods)). Ignored for `proteinbox`. |
+
+Amber builds install their own run schedule with Sage-style nonbonded settings
+(`rcoulomb = rvdw = 0.9`, PME, `vdw-modifier = Potential-switch`, `rvdw-switch = 0.8`,
+`DispCorr = EnerPres`). Protonation states use Amber residue names directly (e.g. `HIE`, `HID`, `HIP`).
+
+Sage solute parameters share the regular SMIRNOFF parameter cache (see below). The cache is keyed
+by the OpenFF force field only, so a solute parametrized earlier with a different `charge_method`
+is reused as-is.
+
## Choosing a parametrization method
| Use Case | Recommended Method |
@@ -115,6 +164,7 @@ CGenFF does not require additional configuration options as it uses the global i
| Lipid bilayer simulations | CGenFF (CHARMM36 compatible) |
| Quick prototyping | SMIRNOFF (faster, no license) |
| Compatibility with existing CHARMM systems | CGenFF |
+| Protein systems without a CGenFF license | Amber (ff14SB + Sage, GROMACS ≥ 2026) |
## Parameter caching
diff --git a/examples/protein_mixedbox/lysozyme_amber_fixed_box.yaml b/examples/protein_mixedbox/lysozyme_amber_fixed_box.yaml
new file mode 100644
index 0000000..daad2f0
--- /dev/null
+++ b/examples/protein_mixedbox/lysozyme_amber_fixed_box.yaml
@@ -0,0 +1,48 @@
+# Open-source route: Amber ff14SB (amber14sb.ff, GROMACS >= 2026) for the protein,
+# OpenFF Sage for the ethanol solute, and native TIP3P water and ions.
+# No CGenFF/SILCSBIO installation is needed.
+simulation_type: protein_mixedbox
+engine: gromacs
+parametrization: amber
+parametrization_config:
+ type: amber
+ forcefield: amber14sb
+ water_model: tip3p
+ ignore_hydrogens: true
+ sage_forcefield: openff-2.2.0.offxml
+
+system:
+ protein:
+ resname: LYZ
+ count: 1
+ pdb_path: ../proteinbox/1aki.pdb
+ chains: [A]
+ disulfide_bonds:
+ - [CYS6, CYS127]
+ - [CYS30, CYS115]
+ - [CYS64, CYS80]
+ - [CYS76, CYS94]
+ protonation_states:
+ HIS15: HIE
+ species:
+ # ~53 M water leaves room for the 1 M ethanol (about 1.0 g/mL solvent). The
+ # 55 M + 1 M of the CHARMM example over-fills the box for TIP3P + Sage.
+ - smiles: O
+ resname: SOL
+ concentration: 53.0
+ - smiles: CCO
+ resname: ETH
+ concentration: 1.0
+ sizing:
+ type: fixed_box
+ box_size: 72.0
+ padding: 12.0
+ concentration_volume_basis: protein_excluded
+ partial_specific_volume: 0.73
+ relax_steps: 10000
+ ionization:
+ # Salt is added on top of neutralization (and any packed ion species),
+ # resolved against concentration_volume_basis. Set concentration: 0 to add
+ # no salt and set ionic strength via packed ion species instead.
+ neutralize: true
+ concentration: 0.15
diff --git a/examples/protein_mixedbox/lysozyme_amber_water_fixed_box.yaml b/examples/protein_mixedbox/lysozyme_amber_water_fixed_box.yaml
new file mode 100644
index 0000000..831b046
--- /dev/null
+++ b/examples/protein_mixedbox/lysozyme_amber_water_fixed_box.yaml
@@ -0,0 +1,42 @@
+# Open-source route: Amber ff14SB (amber14sb.ff, GROMACS >= 2026) with native
+# TIP3P water and ions only (no small-molecule solutes).
+simulation_type: protein_mixedbox
+engine: gromacs
+parametrization: amber
+parametrization_config:
+ type: amber
+ forcefield: amber14sb
+ water_model: tip3p
+ ignore_hydrogens: true
+ sage_forcefield: openff-2.2.0.offxml
+
+system:
+ protein:
+ resname: LYZ
+ count: 1
+ pdb_path: ../proteinbox/1aki.pdb
+ chains: [A]
+ disulfide_bonds:
+ - [CYS6, CYS127]
+ - [CYS30, CYS115]
+ - [CYS64, CYS80]
+ - [CYS76, CYS94]
+ protonation_states:
+ HIS15: HIE
+ species:
+ - smiles: O
+ resname: SOL
+ concentration: 55.0
+ sizing:
+ type: fixed_box
+ box_size: 72.0
+ padding: 12.0
+ concentration_volume_basis: protein_excluded
+ partial_specific_volume: 0.73
+ relax_steps: 10000
+ ionization:
+ # Salt is added on top of neutralization (and any packed ion species),
+ # resolved against concentration_volume_basis. Set concentration: 0 to add
+ # no salt and set ionic strength via packed ion species instead.
+ neutralize: true
+ concentration: 0.15
diff --git a/examples/protein_mixedbox/protein_mixedbox_amber.csv b/examples/protein_mixedbox/protein_mixedbox_amber.csv
new file mode 100644
index 0000000..95fb29e
--- /dev/null
+++ b/examples/protein_mixedbox/protein_mixedbox_amber.csv
@@ -0,0 +1,2 @@
+simulation_type,engine,parametrization,parametrization_config.type,parametrization_config.forcefield,parametrization_config.water_model,parametrization_config.ignore_hydrogens,system.protein.resname,system.protein.pdb_path,system.protein.chains,system.protein.disulfide_bonds,system.protein.protonation_states.HIS15,system.species.SOL.smiles,system.species.SOL.concentration,system.species.ETH.smiles,system.species.ETH.concentration,system.sizing.type,system.sizing.box_size,system.padding,system.concentration_volume_basis,system.partial_specific_volume,system.relax_steps,system.ionization.neutralize,system.ionization.concentration
+protein_mixedbox,gromacs,amber,amber,amber14sb,tip3p,True,LYZ,../proteinbox/1aki.pdb,A,CYS6-CYS127;CYS30-CYS115;CYS64-CYS80;CYS76-CYS94,HIE,O,53.0,CCO,1.0,fixed_box,72.0,12.0,protein_excluded,0.73,10000,True,0.15
diff --git a/examples/proteinbox/lysozyme_amber14sb.yaml b/examples/proteinbox/lysozyme_amber14sb.yaml
new file mode 100644
index 0000000..cff2b8f
--- /dev/null
+++ b/examples/proteinbox/lysozyme_amber14sb.yaml
@@ -0,0 +1,28 @@
+# Open-source route: Amber ff14SB (amber14sb.ff, GROMACS >= 2026) + TIP3P and
+# Joung-Cheatham ions. No CGenFF/SILCSBIO installation is needed.
+simulation_type: proteinbox
+engine: gromacs
+parametrization: amber
+parametrization_config:
+ type: amber
+ forcefield: amber14sb
+ water_model: tip3p
+ ignore_hydrogens: true
+
+system:
+ protein:
+ resname: LYZ
+ count: 1
+ pdb_path: ./1aki.pdb
+ chains: [A]
+ disulfide_bonds:
+ - [CYS6, CYS127]
+ - [CYS30, CYS115]
+ - [CYS64, CYS80]
+ - [CYS76, CYS94]
+ protonation_states:
+ HIS15: HIE
+ padding: 12.0
+ ionization:
+ neutralize: true
+ concentration: 0.15
diff --git a/examples/proteinbox/proteins_amber.csv b/examples/proteinbox/proteins_amber.csv
new file mode 100644
index 0000000..84ae8e9
--- /dev/null
+++ b/examples/proteinbox/proteins_amber.csv
@@ -0,0 +1,2 @@
+simulation_type,engine,parametrization,parametrization_config.type,parametrization_config.forcefield,parametrization_config.water_model,parametrization_config.ignore_hydrogens,system.protein.resname,system.protein.pdb_path,system.protein.chains,system.protein.disulfide_bonds,system.protein.protonation_states.HIS15,system.padding,system.ionization.neutralize,system.ionization.concentration,system.relax_steps
+proteinbox,gromacs,amber,amber,amber14sb,tip3p,True,LYZ,1aki.pdb,A,CYS6-CYS127;CYS30-CYS115;CYS64-CYS80;CYS76-CYS94,HIE,12.0,True,0.15,100
diff --git a/mdfactory/build.py b/mdfactory/build.py
index 819e000..6ec7769 100644
--- a/mdfactory/build.py
+++ b/mdfactory/build.py
@@ -769,14 +769,23 @@ def _center_in_cubic_box(u: mda.Universe, padding: float) -> float:
def _prepare_protein(protein, config):
"""Check GROMACS, clean the protein PDB, and run pdb2gmx in the current directory.
- ``config`` may be a ``Pdb2gmxConfig`` or ``CharmmConfig``; ``run_pdb2gmx`` only
- reads the fields they share.
+ ``config`` may be a ``Pdb2gmxConfig``, ``CharmmConfig`` or ``AmberConfig``;
+ ``run_pdb2gmx`` only reads the fields they share. A force field that needs a
+ minimum GROMACS version (amber14sb) is checked against the binary first, so
+ an old GROMACS fails before any protein preparation.
"""
from loguru import logger
- from .setup.protein import check_gmx_available, clean_pdb, run_pdb2gmx
+ from .setup.protein import (
+ check_gmx_available,
+ clean_pdb,
+ require_gmx_version,
+ run_pdb2gmx,
+ )
- logger.info(f"Using GROMACS: {check_gmx_available()}")
+ gmx_bin = check_gmx_available()
+ logger.info(f"Using GROMACS: {gmx_bin}")
+ require_gmx_version(gmx_bin, config.forcefield)
cleaned_pdb = Path("cleaned.pdb")
clean_pdb(protein.pdb_path.resolve(), cleaned_pdb)
params = run_pdb2gmx(
@@ -823,15 +832,21 @@ def _relax_protein_system(u, topology, itps, ff_dir_name, protein_indices, **rel
def _finalize_protein_build(inp, system_type, topology, extra_intermediates=()):
"""Install the run schedule, validate with grompp, and drop build intermediates.
- Cleanup only runs on success so a failed build keeps its intermediates.
- ``solvated.pdb`` and ``relaxation/`` are left in place, as in the bilayer build.
+ The run schedule is selected by parametrization, so Amber builds get the
+ Sage-style nonbonded mdps. Cleanup only runs on success so a failed build
+ keeps its intermediates. ``solvated.pdb`` and ``relaxation/`` are left in
+ place, as in the bilayer build.
"""
from loguru import logger
from .setup.protein import validate_with_grompp
RunScheduleManager().copy_run_files_with_check(
- engine=inp.engine, system_type=system_type, target_folder=os.getcwd(), force_copy=True
+ engine=inp.engine,
+ system_type=system_type,
+ target_folder=os.getcwd(),
+ force_copy=True,
+ parametrization=inp.parametrization,
)
logger.info("Run schedule files copied.")
@@ -856,14 +871,16 @@ def build_proteinbox(inp: BuildInput):
from loguru import logger
from .models.composition import ProteinBoxComposition
- from .models.parametrization import Pdb2gmxConfig
+ from .models.parametrization import AmberConfig, Pdb2gmxConfig
from .setup.protein import bundle_forcefield_into_topology, update_topology_molecules
if not isinstance(inp.system, ProteinBoxComposition):
raise TypeError("System must specify a ProteinBoxComposition.")
- if not isinstance(inp.parametrization_config, Pdb2gmxConfig):
- raise TypeError("Parametrization config must be Pdb2gmxConfig for proteinbox.")
+ if not isinstance(inp.parametrization_config, (Pdb2gmxConfig, AmberConfig)):
+ raise TypeError(
+ "Parametrization config must be Pdb2gmxConfig or AmberConfig for proteinbox."
+ )
params = _prepare_protein(inp.system.protein, inp.parametrization_config)
@@ -1040,9 +1057,53 @@ def _stage_protein_topology(params, protein_ff_dir, dest_dir, species, parameter
return topology
+def _protein_solution_parametrizer(config, protein_ff_dir: Path):
+ """Return the parameter-store scheme and parametrizer for protein_mixedbox solutes.
+
+ Native water and ions short-circuit to the bundled protein force field
+ ``protein_ff_dir`` in both cases; the parametrizer only differs for SMILES
+ solutes.
+
+ Parameters
+ ----------
+ config : CharmmConfig or AmberConfig
+ protein_mixedbox parametrization config.
+ protein_ff_dir : Path
+ Bundled force-field directory selected by pdb2gmx.
+
+ Returns
+ -------
+ tuple
+ ``(parametrization, function)``: ``"cgenff"`` with
+ ``parametrize_cgenff_gromacs`` for CHARMM, or ``"smirnoff"`` with
+ ``parametrize_smirnoff_gromacs`` (OpenFF Sage) for Amber.
+
+ """
+ from .models.parametrization import AmberConfig, CharmmConfig
+ from .parametrize import parametrize_cgenff_gromacs, parametrize_smirnoff_gromacs
+
+ if isinstance(config, CharmmConfig):
+ return "cgenff", partial(parametrize_cgenff_gromacs, native_forcefield_dir=protein_ff_dir)
+ if isinstance(config, AmberConfig):
+ return "smirnoff", partial(
+ parametrize_smirnoff_gromacs,
+ smirnoff_config=config.smirnoff_config(),
+ native_forcefield_dir=protein_ff_dir,
+ native_water_model=config.water_model,
+ )
+ raise TypeError(
+ "Parametrization config must be CharmmConfig or AmberConfig for protein_mixedbox, "
+ f"got {type(config).__name__}."
+ )
+
+
@validate_call
def build_protein_mixedbox(inp: BuildInput):
- """Build a protein packed with water, ions, and SMILES solutes under CHARMM/CGenFF.
+ """Build a protein packed with water, ions, and SMILES solutes.
+
+ Under ``charmm`` the protein uses CHARMM36m and the solutes CGenFF; under
+ ``amber`` the protein uses amber14sb and the solutes OpenFF Sage. Native
+ water and ions come from the bundled protein force field in both cases.
Prepares the protein with pdb2gmx, packs the solution molecules around it in a
dilute cubic box, compresses to the target box or density with the protein's
@@ -1056,8 +1117,7 @@ def build_protein_mixedbox(inp: BuildInput):
FixedBoxSizing,
ProteinMixedBoxComposition,
)
- from .models.parametrization import CharmmConfig
- from .parametrize import parametrize_cgenff_gromacs
+ from .models.parametrization import AmberConfig, CharmmConfig
from .setup.protein import bundle_forcefield_into_topology, extract_mass_from_topology
from .simulation.openmm_utils import compress_box
from .utils.setup_utilities import (
@@ -1071,8 +1131,10 @@ def build_protein_mixedbox(inp: BuildInput):
if not isinstance(inp.system, ProteinMixedBoxComposition):
raise TypeError("System must specify a ProteinMixedBoxComposition.")
- if not isinstance(inp.parametrization_config, CharmmConfig):
- raise TypeError("Parametrization config must be CharmmConfig for protein_mixedbox.")
+ if not isinstance(inp.parametrization_config, (CharmmConfig, AmberConfig)):
+ raise TypeError(
+ "Parametrization config must be CharmmConfig or AmberConfig for protein_mixedbox."
+ )
system = inp.system
fixed_box = isinstance(system.sizing, FixedBoxSizing)
@@ -1080,11 +1142,11 @@ def build_protein_mixedbox(inp: BuildInput):
params = _prepare_protein(system.protein, inp.parametrization_config)
# Bundle the selected force field immediately. Native water/ion parameters
- # and CGenFF compatibility checks must use this exact directory rather than
- # an unrelated force field shipped with the global CGenFF installation.
+ # and small-molecule compatibility checks must use this exact directory
+ # rather than an unrelated force field (e.g. one shipped with CGenFF).
protein_ff_name = bundle_forcefield_into_topology(params.topology_file)
if protein_ff_name is None:
- raise RuntimeError("pdb2gmx topology does not include a CHARMM force field.")
+ raise RuntimeError("pdb2gmx topology does not include a force field.")
protein_ff_dir = params.topology_file.parent / protein_ff_name
# Protein mass and charge from the generated topology
@@ -1124,11 +1186,13 @@ def build_protein_mixedbox(inp: BuildInput):
system.concentration_volume_basis,
)
- # Parametrize the solution species with CGenFF (native water/ions short-circuit).
- decorate = retrieve_or_deposit_parameters(engine="gromacs", parametrization="cgenff")
- parametrize_with_db = decorate(
- partial(parametrize_cgenff_gromacs, native_forcefield_dir=protein_ff_dir)
+ # Parametrize the solution species with CGenFF or Sage (native water/ions
+ # short-circuit to the bundled force field).
+ scheme, parametrize_solute = _protein_solution_parametrizer(
+ inp.parametrization_config, protein_ff_dir
)
+ decorate = retrieve_or_deposit_parameters(engine="gromacs", parametrization=scheme)
+ parametrize_with_db = decorate(parametrize_solute)
parameters = [parametrize_with_db(spec) for spec in system.species]
logger.info("Solution-species parametrization complete.")
@@ -1238,8 +1302,9 @@ def build_protein_mixedbox(inp: BuildInput):
).resolve()
# Restrained relaxation of the solution around the fixed protein. The
- # composite topology includes the per-chain/posre itps, the merged CGenFF
- # parameters, and each small-molecule itp; all sit beside topology.top.
+ # composite topology includes the per-chain/posre itps, the merged
+ # small-molecule parameters, and each small-molecule itp; all sit beside
+ # topology.top.
u_relaxed = _relax_protein_system(
u_ionized,
topology_dest,
diff --git a/mdfactory/models/input.py b/mdfactory/models/input.py
index ea1bd43..7e37864 100644
--- a/mdfactory/models/input.py
+++ b/mdfactory/models/input.py
@@ -16,6 +16,7 @@
ProteinMixedBoxComposition,
)
from .parametrization import (
+ AmberConfig,
CgenffConfig,
CharmmConfig,
ParametrizationConfig,
@@ -35,13 +36,14 @@
# Parametrizations each simulation type accepts. Proteins are parametrized with
# gmx pdb2gmx; small-molecule systems use CGenFF or SMIRNOFF. A protein packed
-# with small molecules uses the combined CHARMM/CGenFF parametrization.
+# with small molecules uses the combined CHARMM/CGenFF parametrization. Both
+# protein types also accept the open-source Amber ff14SB + OpenFF Sage route.
allowed_parametrizations = {
"mixedbox": {"cgenff", "smirnoff"},
"bilayer": {"cgenff", "smirnoff"},
"lnp": {"cgenff", "smirnoff"},
- "proteinbox": {"pdb2gmx"},
- "protein_mixedbox": {"charmm"},
+ "proteinbox": {"pdb2gmx", "amber"},
+ "protein_mixedbox": {"charmm", "amber"},
}
@@ -56,7 +58,7 @@ class BuildInput(BaseModel):
| ProteinBoxComposition
| ProteinMixedBoxComposition
)
- parametrization: Literal["cgenff", "smirnoff", "pdb2gmx", "charmm"] = Field(
+ parametrization: Literal["cgenff", "smirnoff", "pdb2gmx", "charmm", "amber"] = Field(
"cgenff", description="Parametrization to use."
)
parametrization_config: ParametrizationConfig | None = Field(
@@ -223,6 +225,7 @@ def set_default_parametrization_config(self) -> "BuildInput":
"cgenff": CgenffConfig,
"pdb2gmx": Pdb2gmxConfig,
"charmm": CharmmConfig,
+ "amber": AmberConfig,
}[self.parametrization]
object.__setattr__(self, "parametrization_config", config_class())
return self
diff --git a/mdfactory/models/parametrization.py b/mdfactory/models/parametrization.py
index 7302748..f54b3d5 100644
--- a/mdfactory/models/parametrization.py
+++ b/mdfactory/models/parametrization.py
@@ -1,5 +1,5 @@
# ABOUTME: Pydantic models for force field parametrization configuration and results
-# ABOUTME: Defines CGenFF/SMIRNOFF configs and GROMACS parameter set storage
+# ABOUTME: Defines CGenFF/SMIRNOFF/CHARMM/Amber configs and GROMACS parameter set storage
"""Pydantic models for force field parametrization configuration and results."""
import json
@@ -17,7 +17,7 @@
model_validator,
)
-# The proteinbox pipeline solvates with 3-site spc216 coordinates and uses
+# The CHARMM protein pipelines solvate with 3-site spc216 coordinates and use
# CHARMM Force-switch LJ in every mdp, so only these combinations are supported.
SUPPORTED_WATER_MODELS = frozenset({"tip3p", "spc", "spce"})
@@ -139,11 +139,69 @@ def _check_protein_mixedbox_bundle(self) -> "CharmmConfig":
return self
+class AmberConfig(BaseModel):
+ """Configuration for the open-source Amber ff14SB + OpenFF Sage parametrization.
+
+ The protein is built with gmx pdb2gmx and the ``amber14sb.ff`` force field that
+ ships with GROMACS 2026 or later. Native TIP3P water and Joung-Cheatham ions
+ come from the same force-field directory. SMILES solutes are parametrized with
+ OpenFF Sage through SMIRNOFF, so no CGenFF/SILCSBIO installation is needed.
+
+ Used by both ``proteinbox`` and ``protein_mixedbox``. A ``proteinbox`` has no
+ small molecules, so it accepts the Sage fields and ignores them.
+ """
+
+ model_config = ConfigDict(extra="forbid", frozen=True)
+
+ type: Literal["amber"] = Field("amber", description="Config type discriminator.")
+ forcefield: str = Field(
+ "amber14sb",
+ description="Protein force field as recognized by gmx pdb2gmx (only amber14sb).",
+ )
+ water_model: str = Field(
+ "tip3p", description="Water model as recognized by gmx pdb2gmx (only tip3p)."
+ )
+ ignore_hydrogens: bool = Field(
+ True, description="Ignore hydrogens in input PDB (regenerate with pdb2gmx)."
+ )
+ merge_all: bool = Field(False, description="Merge all chains into a single moleculetype.")
+ sage_forcefield: str = Field(
+ SmirnoffConfig.model_fields["forcefield"].default,
+ description="OpenFF force field file for small-molecule solutes.",
+ )
+ charge_method: str = Field(
+ SmirnoffConfig.model_fields["charge_method"].default,
+ description="Partial charge assignment method for small-molecule solutes.",
+ )
+
+ @model_validator(mode="after")
+ def _check_amber_forcefield_and_water(self) -> "AmberConfig":
+ """Reject protein force fields and water models other than amber14sb + tip3p."""
+ if self.forcefield != "amber14sb":
+ raise ValueError(
+ f"Force field '{self.forcefield}' is not supported for the amber "
+ "parametrization. Only 'amber14sb' (bundled with GROMACS >= 2026) is "
+ "supported; its run schedule uses Sage-style nonbonded settings."
+ )
+ if self.water_model != "tip3p":
+ raise ValueError(
+ f"Water model '{self.water_model}' is not supported for the amber "
+ "parametrization. Only 'tip3p' is supported: solvation uses 3-site "
+ "spc216 coordinates and ff14SB is paired with TIP3P."
+ )
+ return self
+
+ def smirnoff_config(self) -> SmirnoffConfig:
+ """Return the SMIRNOFF configuration used for the small-molecule solutes."""
+ return SmirnoffConfig(forcefield=self.sage_forcefield, charge_method=self.charge_method)
+
+
ParametrizationConfig = Annotated[
Annotated[SmirnoffConfig, Tag("smirnoff")]
| Annotated[CgenffConfig, Tag("cgenff")]
| Annotated[Pdb2gmxConfig, Tag("pdb2gmx")]
- | Annotated[CharmmConfig, Tag("charmm")],
+ | Annotated[CharmmConfig, Tag("charmm")]
+ | Annotated[AmberConfig, Tag("amber")],
Discriminator("type"),
]
diff --git a/mdfactory/models/species.py b/mdfactory/models/species.py
index 7c722dd..0c3b93d 100644
--- a/mdfactory/models/species.py
+++ b/mdfactory/models/species.py
@@ -184,7 +184,7 @@ def check_fraction_or_count(self) -> "SolutionSpecies":
expected_resname = native_resnames.get(self.smiles)
if expected_resname is not None and self.resname.upper() != expected_resname:
raise ValueError(
- f"Native CHARMM species {self.smiles!r} must use resname "
+ f"Native water/ion species {self.smiles!r} must use resname "
f"'{expected_resname}', not '{self.resname}'."
)
return self
diff --git a/mdfactory/orchestration/apps.py b/mdfactory/orchestration/apps.py
index 25b6be6..4936cfc 100644
--- a/mdfactory/orchestration/apps.py
+++ b/mdfactory/orchestration/apps.py
@@ -389,6 +389,51 @@ def _get_gromacs_detect_script() -> str:
)
+def _build_gmx_version_check(min_gmx_version: str) -> str:
+ """Return a bash snippet that exits unless ``$GMX_BIN`` is new enough.
+
+ The check runs on the compute node against the exact binary the job will
+ use, right after binary detection and before grompp or any mdrun.
+
+ Parameters
+ ----------
+ min_gmx_version : str
+ Minimum GROMACS version, e.g. ``"2026"`` or ``"2026.1"``.
+
+ Returns
+ -------
+ str
+ Bash block with a leading blank line and trailing newline.
+
+ Raises
+ ------
+ ValueError
+ If *min_gmx_version* is not of the form ``[.]``.
+
+ """
+ major, _, minor = min_gmx_version.partition(".")
+ if not major.isdigit() or (minor and not minor.isdigit()):
+ raise ValueError(f"Invalid minimum GROMACS version: {min_gmx_version!r}")
+ threshold = int(major) * 1000 + int(minor or 0)
+ return f"""
+# Require GROMACS >= {min_gmx_version} for the force field in the topology
+GMX_VERSION=$("$GMX_BIN" --version 2>/dev/null \\
+ | awk '/^GROMACS version:/ && !n {{sub(/^GROMACS version:[ \\t]*/, ""); print; n=1}}' \\
+ || true)
+if [[ "$GMX_VERSION" =~ ^([0-9]+)(\\.([0-9]+))? ]]; then
+ GMX_VERSION_NUM=$(( 10#${{BASH_REMATCH[1]}} * 1000 + 10#${{BASH_REMATCH[3]:-0}} ))
+else
+ GMX_VERSION_NUM=-1
+fi
+if (( GMX_VERSION_NUM < {threshold} )); then
+ echo "ERROR: the topology's force field requires GROMACS >= {min_gmx_version}," >&2
+ echo "but $GMX_BIN ($(command -v "$GMX_BIN")) is GROMACS ${{GMX_VERSION:-unknown}}." >&2
+ echo "Put a newer gmx on PATH, e.g. via the pixi 'gmx' environment." >&2
+ exit 1
+fi
+"""
+
+
def _require_bash_app():
"""Import and return Parsl's ``bash_app`` decorator.
@@ -490,6 +535,7 @@ def _build_grompp_script(
ref_file: str = "",
cpt_file: str = "",
maxwarn: int = 1,
+ min_gmx_version: str = "",
) -> str:
"""Build the bash script for ``gmx grompp``.
@@ -514,6 +560,11 @@ def _build_grompp_script(
Checkpoint file for velocities (-t flag).
maxwarn : int
Maximum number of warnings to allow.
+ min_gmx_version : str, optional
+ Minimum GROMACS version the topology's force field needs, e.g.
+ ``"2026"``. When given, the script exits with an error before grompp
+ if the detected binary is older. Empty (default) means no check, and
+ the script is unchanged.
Returns
-------
@@ -523,13 +574,14 @@ def _build_grompp_script(
"""
ref_flag = f"-r {ref_file}" if ref_file else ""
cpt_flag = f"-t {cpt_file}" if cpt_file else ""
+ version_check = _build_gmx_version_check(min_gmx_version) if min_gmx_version else ""
return f"""
set -euo pipefail # Exit on error, undefined vars, pipe failures
cd {work_dir}
- {_get_gromacs_detect_script()}
+ {_get_gromacs_detect_script()}{version_check}
echo "GROMACS grompp: {mdp_file} -> {tpr_file} (using $GMX_BIN)" >&2
@@ -671,6 +723,7 @@ def run_grompp(
ref_file: str = "",
cpt_file: str = "",
maxwarn: int = 1,
+ min_gmx_version: str = "",
stdout=None,
stderr=None,
inputs=None,
@@ -695,6 +748,8 @@ def run_grompp(
Checkpoint file for velocities (-t flag).
maxwarn : int
Maximum number of warnings to allow.
+ min_gmx_version : str, optional
+ Minimum GROMACS version required by the topology; empty for none.
stdout : str, optional
File path for stdout.
stderr : str, optional
@@ -709,7 +764,15 @@ def run_grompp(
"""
return _build_grompp_script(
- mdp_file, gro_file, top_file, tpr_file, work_dir, ref_file, cpt_file, maxwarn
+ mdp_file,
+ gro_file,
+ top_file,
+ tpr_file,
+ work_dir,
+ ref_file,
+ cpt_file,
+ maxwarn,
+ min_gmx_version,
)
return run_grompp
diff --git a/mdfactory/orchestration/simulate.py b/mdfactory/orchestration/simulate.py
index 48a9967..def5bbf 100644
--- a/mdfactory/orchestration/simulate.py
+++ b/mdfactory/orchestration/simulate.py
@@ -345,7 +345,7 @@ def clean_simulation_outputs(
def _log_dry_run_plan(work_plan: list[dict], config: "ExecutorConfig") -> list[dict]:
"""Log the dry-run work plan with resolved gmx commands per stage."""
from .apps import _build_grompp_script, _build_mdrun_script
- from .stages import _extract_resource_hints
+ from .stages import _extract_resource_hints, min_gmx_version_for_sim_dir
logger.info("=" * 60)
logger.info("DRY RUN - No jobs will be submitted")
@@ -366,6 +366,9 @@ def _log_dry_run_plan(work_plan: list[dict], config: "ExecutorConfig") -> list[d
work_dir = str(Path(item["sim_dir"]).resolve())
stage_config = get_stage_config_or_none(config, item["stages"][0])
hints = _extract_resource_hints(stage_config)
+ min_gmx_version = min_gmx_version_for_sim_dir(item["sim_dir"])
+ if min_gmx_version:
+ logger.info(f" Requires GROMACS >= {min_gmx_version} (checked before grompp)")
for stage_name in item["stages"]:
spec = STAGE_BY_NAME[stage_name]
@@ -386,6 +389,7 @@ def _log_dry_run_plan(work_plan: list[dict], config: "ExecutorConfig") -> list[d
ref_file=spec.ref_file or "",
cpt_file=spec.prereq_cpt or "",
maxwarn=spec.maxwarn,
+ min_gmx_version=min_gmx_version,
)
_log_resolved_script(grompp_script, label="grompp")
diff --git a/mdfactory/orchestration/stages.py b/mdfactory/orchestration/stages.py
index 10f40d1..4b44789 100644
--- a/mdfactory/orchestration/stages.py
+++ b/mdfactory/orchestration/stages.py
@@ -188,6 +188,19 @@ def _extract_resource_hints(stage_config: Any) -> ResourceHints:
return ResourceHints(ntasks=ntasks, disable_gpu=disable_gpu, gmx_binary=gmx_binary)
+def min_gmx_version_for_sim_dir(sim_dir: Path) -> str:
+ """Return the minimum GROMACS version a simulation directory's topology needs.
+
+ Derived from the force field ``topology.top`` includes (e.g.
+ ``amber14sb.ff/forcefield.itp`` needs 2026). Returns ``""`` when there is no
+ requirement (CHARMM and small-molecule builds) or no topology.
+ """
+ from ..setup.protein import format_gmx_version, min_gmx_version_for_topology
+
+ required = min_gmx_version_for_topology(Path(sim_dir) / "topology.top")
+ return format_gmx_version(required) if required is not None else ""
+
+
def run_stage(
spec: StageSpec,
sim_dir: Path,
@@ -272,6 +285,11 @@ def run_stage(
grompp_kwargs["ref_file"] = spec.ref_file
if spec.prereq_cpt:
grompp_kwargs["cpt_file"] = spec.prereq_cpt
+ # Force fields that need a newer GROMACS (amber14sb) make grompp check the
+ # node's binary first; other topologies keep the unchanged script.
+ min_gmx_version = min_gmx_version_for_sim_dir(sim_dir)
+ if min_gmx_version:
+ grompp_kwargs["min_gmx_version"] = min_gmx_version
grompp_fut = grompp_app(**grompp_kwargs)
diff --git a/mdfactory/parametrize.py b/mdfactory/parametrize.py
index 2cd94bb..0275330 100644
--- a/mdfactory/parametrize.py
+++ b/mdfactory/parametrize.py
@@ -11,12 +11,17 @@
from .models.species import SingleMoleculeSpecies
from .settings import settings
from .utils.topology_utilities import (
+ check_atomtype_collisions,
+ check_defaults_compatible,
collect_forcefield_atomtype_definitions,
count_contiguous_strings,
extract_reusable_parts_from_cgenff_gmx_top,
merge_extra_parameter_itps,
+ read_itp_atoms,
run_cgenff_to_gmx,
+ unique_atom_names,
validate_cgenff_atomtype_compatibility,
+ write_itp_with_atom_names,
write_mol2_from_rdkit,
)
from .utils.utilities import lock_local_folder, working_directory
@@ -226,9 +231,38 @@ def parametrize_cgenff_gromacs(
return prm
+NATIVE_ION_MOLECULETYPES = {"[Na+]": "NA", "[Cl-]": "CL"}
+
+
+def _native_smirnoff_parameter_set(
+ species: SingleMoleculeSpecies,
+ smirnoff_config: SmirnoffConfig,
+ forcefield_dir: Path,
+ water_model: str,
+) -> GromacsSingleMoleculeParameterSet:
+ """Return water or ion parameters taken from a GROMACS-native force-field directory."""
+ if species.is_water:
+ moleculetype = "SOL"
+ itp = forcefield_dir / f"{water_model}.itp"
+ else:
+ moleculetype = NATIVE_ION_MOLECULETYPES[species.smiles]
+ itp = forcefield_dir / f"ions_{water_model}.itp"
+ return GromacsSingleMoleculeParameterSet(
+ moleculetype=moleculetype,
+ smiles=species.smiles,
+ parametrization="smirnoff",
+ parametrization_config=smirnoff_config,
+ itp=itp,
+ parameter_itp=None,
+ forcefield_itp=forcefield_dir / "forcefield.itp",
+ )
+
+
def parametrize_smirnoff_gromacs(
species: SingleMoleculeSpecies,
smirnoff_config: Optional[SmirnoffConfig] = None,
+ native_forcefield_dir: Path | None = None,
+ native_water_model: str = "tip3p",
) -> GromacsSingleMoleculeParameterSet:
"""Parametrize a molecule using OpenFF SMIRNOFF force field.
@@ -240,6 +274,15 @@ def parametrize_smirnoff_gromacs(
The molecule species to parametrize.
smirnoff_config : SmirnoffConfig, optional
Configuration for SMIRNOFF parametrization. If None, uses defaults.
+ native_forcefield_dir : Path or None, optional
+ GROMACS force-field directory (e.g. a bundled ``amber14sb.ff``) that
+ provides native water and ion topologies. When given, water returns
+ ``.itp`` and Na+/Cl- return ``ions_.itp`` from
+ it, without any OpenFF work or SMIRNOFF cache access. Other molecules
+ are parametrized with SMIRNOFF as usual. Default None.
+ native_water_model : str, optional
+ Water model selecting the native water and ion files. Only used with
+ ``native_forcefield_dir``. Default ``"tip3p"``.
Returns
-------
@@ -247,16 +290,21 @@ def parametrize_smirnoff_gromacs(
The parameter set containing paths to generated ITP files.
"""
+ # Use provided config or defaults
+ if smirnoff_config is None:
+ smirnoff_config = SmirnoffConfig()
+
+ if native_forcefield_dir is not None and (species.is_water or species.is_ion):
+ return _native_smirnoff_parameter_set(
+ species, smirnoff_config, Path(native_forcefield_dir), native_water_model
+ )
+
# Lazy imports to avoid loading OpenFF when not needed
import numpy as np # noqa: PLC0415
from openff.interchange import Interchange # noqa: PLC0415
from openff.toolkit import ForceField, Topology # noqa: PLC0415
from openff.units import unit # noqa: PLC0415
- # Use provided config or defaults
- if smirnoff_config is None:
- smirnoff_config = SmirnoffConfig()
-
ff_name = smirnoff_config.forcefield
water_model = smirnoff_config.water_model
charge_method = smirnoff_config.charge_method
@@ -551,19 +599,28 @@ def generate_gromacs_topology_with_protein(
"""Write one GROMACS topology for a pdb2gmx protein packed with solution molecules.
Builds a single composite topology in strict include order: the bundled
- CHARMM force field, the merged CGenFF small-molecule parameters (with
- ``[ atomtypes ]`` de-duplicated against the force field and ``[ defaults ]``
- dropped, because the force field already bundles CGenFF), the protein
- moleculetypes and position restraints from pdb2gmx, the CGenFF
- small-molecule moleculetypes, and finally the water and ion topologies the
- pdb2gmx topology already includes. The ``[ molecules ]`` section keeps the
- protein chain entries and appends the solution molecules in the order given,
- so it matches a coordinate file ordered protein → small molecules → water →
- ions.
+ protein force field, the merged small-molecule parameters, the protein
+ moleculetypes and position restraints from pdb2gmx, the small-molecule
+ moleculetypes, and finally the water and ion topologies the pdb2gmx
+ topology already includes. The ``[ molecules ]`` section keeps the protein
+ chain entries and appends the solution molecules in the order given, so it
+ matches a coordinate file ordered protein → small molecules → water → ions.
+
+ The small-molecule parameters are merged according to their scheme:
+
+ - **CGenFF** (CHARMM force field): ``[ atomtypes ]`` already defined by the
+ force field are de-duplicated after a compatibility check, and
+ ``[ defaults ]`` is dropped because the force field bundles CGenFF.
+ - **SMIRNOFF** (e.g. Sage with ``amber14sb.ff``): each file's
+ ``[ defaults ]`` must match the force field's ``forcefield.itp``
+ numerically before it is dropped, and any atom-type name collision with
+ the force field (or a conflicting duplicate between solutes) raises.
+
+ Mixing CGenFF and SMIRNOFF solutes raises ``ValueError``.
Native species (water and supported ions) carry no ``parameter_itp`` and use
the moleculetypes the pdb2gmx force-field includes already provide; only
- CGenFF small molecules contribute an ``.itp`` include and merged parameters.
+ small molecules contribute an ``.itp`` include and merged parameters.
Parameters
----------
@@ -571,7 +628,8 @@ def generate_gromacs_topology_with_protein(
Local pdb2gmx topology whose force-field ``#include`` lines resolve from
its own directory (force field already bundled alongside it).
ff_dir : Path
- The bundled force-field directory, scanned for atom types to de-duplicate.
+ The bundled force-field directory, scanned for atom types (and, for
+ SMIRNOFF solutes, its ``forcefield.itp`` ``[ defaults ]``).
species : list
Non-protein solution species, in the coordinate/packing order.
parameters : list[GromacsSingleMoleculeParameterSet]
@@ -600,27 +658,51 @@ def generate_gromacs_topology_with_protein(
"cannot build composite topology."
)
- # CGenFF small molecules carry a parameter_itp; native water/ions do not and
- # reuse the moleculetypes the pdb2gmx force-field includes already provide.
- cgenff_parameters = [par for par in parameters if par.parameter_itp is not None]
+ # Small molecules carry a parameter_itp; native water/ions do not and reuse
+ # the moleculetypes the pdb2gmx force-field includes already provide.
+ solute_parameters = [par for par in parameters if par.parameter_itp is not None]
+ # Parameter sets without a parametrization tag are treated as CGenFF, the
+ # original (CHARMM-only) behavior.
+ solute_schemes = {getattr(par, "parametrization", "cgenff") for par in solute_parameters}
+ if len(solute_schemes) > 1:
+ raise ValueError(
+ "Cannot mix small-molecule parametrizations in one protein topology: "
+ f"{sorted(solute_schemes)}."
+ )
+ scheme_label = "SMIRNOFF" if solute_schemes == {"smirnoff"} else "CGenFF"
extra_params_include = ""
- if cgenff_parameters:
+ if solute_parameters:
forcefield_types = collect_forcefield_atomtype_definitions(ff_dir)
- prm_files = sorted({str(par.parameter_itp) for par in cgenff_parameters})
- validate_cgenff_atomtype_compatibility(prm_files, ff_dir, forcefield_types)
- merged = merge_extra_parameter_itps(
- prm_files, exclude_atomtypes=forcefield_types, drop_defaults=True
- )
+ prm_files = sorted({str(par.parameter_itp) for par in solute_parameters})
+ if scheme_label == "SMIRNOFF":
+ # SMIRNOFF files carry their own [ defaults ] and private atom types:
+ # the force field's [ defaults ] must be equivalent before it is dropped,
+ # and no atom type may shadow a force-field or another solute's type.
+ for prm in prm_files:
+ check_defaults_compatible(ff_dir / "forcefield.itp", prm)
+ check_atomtype_collisions(prm_files, forcefield_types)
+ merged = merge_extra_parameter_itps(prm_files, drop_defaults=True)
+ else:
+ validate_cgenff_atomtype_compatibility(prm_files, ff_dir, forcefield_types)
+ merged = merge_extra_parameter_itps(
+ prm_files, exclude_atomtypes=forcefield_types, drop_defaults=True
+ )
(out_dir / "extra_params.itp").write_text(f"; merged from {prm_files}\n{merged}")
extra_params_include = '#include "extra_params.itp"\n'
# Copy each unique small-molecule ITP next to the topology and include it once.
+ # SMIRNOFF ITPs name atoms by element only; the copies get the unique names
+ # that topology_atom_names() also gives the coordinates.
itps: dict[str, Path] = {}
- for par in cgenff_parameters:
+ for par in solute_parameters:
itps.setdefault(par.itp.name, par.itp)
for itp_name, itp_path in itps.items():
- shutil.copy(itp_path, out_dir / itp_name)
+ if scheme_label == "SMIRNOFF":
+ names = [name for name, _ in read_itp_atoms(itp_path)]
+ write_itp_with_atom_names(itp_path, out_dir / itp_name, unique_atom_names(names))
+ else:
+ shutil.copy(itp_path, out_dir / itp_name)
smallmol_include_block = "".join(f'#include "{name}"\n' for name in itps)
# Copy up to [ molecules ], inserting merged parameters after the force field,
@@ -630,7 +712,7 @@ def generate_gromacs_topology_with_protein(
for i in range(molecules_idx):
line = lines[i]
if i == water_include_idx and smallmol_include_block:
- new_lines.append("; Include CGenFF small-molecule topologies\n")
+ new_lines.append(f"; Include {scheme_label} small-molecule topologies\n")
new_lines.append(smallmol_include_block)
stripped = line.strip()
if (
@@ -645,12 +727,12 @@ def generate_gromacs_topology_with_protein(
continue
new_lines.append(line)
if i == ff_include_idx and extra_params_include:
- new_lines.append("; Include merged CGenFF parameters\n")
+ new_lines.append(f"; Include merged {scheme_label} parameters\n")
new_lines.append(extra_params_include)
# No water include: append the small-molecule moleculetypes here instead.
if smallmol_include_block and water_include_idx is None:
- new_lines.append("; Include CGenFF small-molecule topologies\n")
+ new_lines.append(f"; Include {scheme_label} small-molecule topologies\n")
new_lines.append(smallmol_include_block)
protein_mol_lines = []
diff --git a/mdfactory/run_schedules/__init__.py b/mdfactory/run_schedules/__init__.py
index 617c0aa..b66b4ed 100644
--- a/mdfactory/run_schedules/__init__.py
+++ b/mdfactory/run_schedules/__init__.py
@@ -46,17 +46,35 @@ def _load_schedules(self):
except yaml.YAMLError as e:
raise ValueError(f"Error parsing YAML file: {e}")
- def _get_config(self, engine: str, system_type: str, version: Optional[str] = None) -> Dict:
- """Get the configuration for a specific engine/system_type combination."""
- matching_configs = [
+ def _get_config(
+ self,
+ engine: str,
+ system_type: str,
+ version: Optional[str] = None,
+ parametrization: Optional[str] = None,
+ ) -> Dict:
+ """Get the configuration for a specific engine/system_type combination.
+
+ Entries may carry an optional ``parametrization`` key. An entry whose key
+ matches *parametrization* wins; otherwise the entries without the key
+ are used, so callers that pass no parametrization (or one without a
+ dedicated schedule) get the generic schedule.
+ """
+ type_configs = [
config
for config in self._schedules
if config.get("engine") == engine and config.get("system_type") == system_type
]
+ matching_configs = [
+ config
+ for config in type_configs
+ if parametrization is not None and config.get("parametrization") == parametrization
+ ] or [config for config in type_configs if "parametrization" not in config]
if not matching_configs:
raise ValueError(
f"No configuration found for engine='{engine}', system_type='{system_type}'"
+ + (f", parametrization='{parametrization}'" if parametrization else "")
)
if version is None:
@@ -70,16 +88,26 @@ def _get_config(self, engine: str, system_type: str, version: Optional[str] = No
)
return version_configs[0]
- def get_settings(self, engine: str, system_type: str, version: Optional[str] = None) -> Dict:
+ def get_settings(
+ self,
+ engine: str,
+ system_type: str,
+ version: Optional[str] = None,
+ parametrization: Optional[str] = None,
+ ) -> Dict:
"""Get the computational settings for a specific configuration."""
- config = self._get_config(engine, system_type, version)
+ config = self._get_config(engine, system_type, version, parametrization)
return config.get("settings", {})
def get_all_run_file_paths(
- self, engine: str, system_type: str, version: Optional[str] = None
+ self,
+ engine: str,
+ system_type: str,
+ version: Optional[str] = None,
+ parametrization: Optional[str] = None,
) -> Dict[str, Path]:
"""Get paths to all run files for a specific configuration."""
- config = self._get_config(engine, system_type, version)
+ config = self._get_config(engine, system_type, version, parametrization)
run_files = config.get("run_files", [])
# ``template_dir`` lets a system type reuse another type's run files.
template_dir = self.config_dir / engine / config.get("template_dir", system_type)
@@ -100,12 +128,13 @@ def check_target_folder(
system_type: str,
target_folder: Union[str, Path],
version: Optional[str] = None,
+ parametrization: Optional[str] = None,
) -> Tuple[bool, Dict[str, bool], List[str]]:
"""Check if run files already exist in the target folder."""
target_folder = Path(target_folder)
# Get the expected run files for this configuration
- config = self._get_config(engine, system_type, version)
+ config = self._get_config(engine, system_type, version, parametrization)
expected_files = config.get("run_files", [])
file_status = {}
@@ -129,6 +158,7 @@ def copy_run_files_with_check(
target_folder: Union[str, Path],
version: Optional[str] = None,
force_copy: bool = False,
+ parametrization: Optional[str] = None,
) -> Dict[str, bool]:
"""Copy run files to the target folder after checking for conflicts.
@@ -144,6 +174,9 @@ def copy_run_files_with_check(
Configuration version string. Uses the latest when *None*.
force_copy : bool, optional
Overwrite existing files if True. Default is False.
+ parametrization : str, optional
+ Parametrization of the build. Selects an entry with a matching
+ ``parametrization`` key when one exists; otherwise the generic entry.
Returns
-------
@@ -154,7 +187,7 @@ def copy_run_files_with_check(
"""
# First check if files already exist
has_existing, file_status, existing_files = self.check_target_folder(
- engine, system_type, target_folder, version
+ engine, system_type, target_folder, version, parametrization
)
if has_existing and not force_copy:
@@ -172,7 +205,12 @@ def copy_run_files_with_check(
logger.debug("No existing files found. Proceeding with copy.")
return self.copy_run_files(
- engine, system_type, target_folder, version, overwrite=force_copy
+ engine,
+ system_type,
+ target_folder,
+ version,
+ overwrite=force_copy,
+ parametrization=parametrization,
)
def copy_run_files(
@@ -182,6 +220,7 @@ def copy_run_files(
target_folder: Union[str, Path],
version: Optional[str] = None,
overwrite: bool = False,
+ parametrization: Optional[str] = None,
) -> Dict[str, bool]:
"""Copy run files to a target folder.
@@ -197,6 +236,8 @@ def copy_run_files(
Configuration version string. Uses the latest when *None*.
overwrite : bool, optional
Overwrite existing files if True. Default is False.
+ parametrization : str, optional
+ Parametrization of the build; see :meth:`copy_run_files_with_check`.
Returns
-------
@@ -207,7 +248,7 @@ def copy_run_files(
target_folder = Path(target_folder)
target_folder.mkdir(parents=True, exist_ok=True)
- file_paths = self.get_all_run_file_paths(engine, system_type, version)
+ file_paths = self.get_all_run_file_paths(engine, system_type, version, parametrization)
copy_results = {}
for filename, source_path in file_paths.items():
@@ -240,13 +281,14 @@ def list_available_configs(self) -> List[Dict[str, str]]:
"""List all available engine/system_type/version combinations."""
configs = []
for config in self._schedules:
- configs.append(
- {
- "engine": config.get("engine"),
- "system_type": config.get("system_type"),
- "version": str(config.get("version")),
- }
- )
+ entry = {
+ "engine": config.get("engine"),
+ "system_type": config.get("system_type"),
+ "version": str(config.get("version")),
+ }
+ if "parametrization" in config:
+ entry["parametrization"] = str(config["parametrization"])
+ configs.append(entry)
return configs
def list_engines(self) -> List[str]:
diff --git a/mdfactory/run_schedules/gromacs/proteinbox_amber/em.mdp b/mdfactory/run_schedules/gromacs/proteinbox_amber/em.mdp
new file mode 100644
index 0000000..9c301ff
--- /dev/null
+++ b/mdfactory/run_schedules/gromacs/proteinbox_amber/em.mdp
@@ -0,0 +1,20 @@
+; Energy minimization parameters for protein systems (Amber ff14SB + OpenFF Sage)
+integrator = steep
+emtol = 1000.0
+emstep = 0.01
+nsteps = 50000
+
+; Neighbor searching
+nstlist = 1
+cutoff-scheme = Verlet
+ns_type = grid
+pbc = xyz
+
+; Electrostatics and VdW (Sage-style nonbonded settings)
+coulombtype = PME
+rcoulomb = 0.9
+rvdw = 0.9
+vdwtype = cutoff
+vdw-modifier = Potential-switch
+rvdw-switch = 0.8
+DispCorr = EnerPres
diff --git a/mdfactory/run_schedules/gromacs/proteinbox_amber/md.mdp b/mdfactory/run_schedules/gromacs/proteinbox_amber/md.mdp
new file mode 100644
index 0000000..0361a96
--- /dev/null
+++ b/mdfactory/run_schedules/gromacs/proteinbox_amber/md.mdp
@@ -0,0 +1,57 @@
+; MD production run for protein systems (Amber ff14SB + OpenFF Sage)
+title = MD production run
+
+; Run parameters
+integrator = md
+nsteps = 50000000
+dt = 0.002
+
+; Output control
+nstxout = 0
+nstvout = 0
+nstfout = 0
+nstenergy = 5000
+nstlog = 5000
+nstxout-compressed = 5000
+compressed-x-grps = System
+
+; Bond parameters
+continuation = yes
+constraint_algorithm = lincs
+constraints = h-bonds
+lincs_iter = 1
+lincs_order = 4
+
+; Neighbor searching
+cutoff-scheme = Verlet
+ns_type = grid
+nstlist = 10
+pbc = xyz
+
+; Electrostatics and VdW (Sage-style nonbonded settings)
+coulombtype = PME
+pme_order = 4
+fourierspacing = 0.16
+rcoulomb = 0.9
+rvdw = 0.9
+vdwtype = cutoff
+vdw-modifier = Potential-switch
+rvdw-switch = 0.8
+DispCorr = EnerPres
+
+; Temperature coupling
+tcoupl = V-rescale
+tc-grps = Protein Non-Protein
+tau_t = 0.1 0.1
+ref_t = 300 300
+
+; Pressure coupling (Parrinello-Rahman for production)
+pcoupl = Parrinello-Rahman
+pcoupltype = isotropic
+tau_p = 5.0
+ref_p = 1.0
+compressibility = 4.5e-5
+refcoord_scaling = com
+
+; Velocity generation
+gen_vel = no
diff --git a/mdfactory/run_schedules/gromacs/proteinbox_amber/npt.mdp b/mdfactory/run_schedules/gromacs/proteinbox_amber/npt.mdp
new file mode 100644
index 0000000..c77ded5
--- /dev/null
+++ b/mdfactory/run_schedules/gromacs/proteinbox_amber/npt.mdp
@@ -0,0 +1,54 @@
+; NPT equilibration for protein systems (Amber ff14SB + OpenFF Sage)
+title = NPT equilibration
+define = -DPOSRES
+
+; Run parameters
+integrator = md
+nsteps = 50000
+dt = 0.002
+
+; Output control
+nstxout = 500
+nstvout = 500
+nstenergy = 500
+nstlog = 500
+
+; Bond parameters
+continuation = yes
+constraint_algorithm = lincs
+constraints = h-bonds
+lincs_iter = 1
+lincs_order = 4
+
+; Neighbor searching
+cutoff-scheme = Verlet
+ns_type = grid
+nstlist = 10
+pbc = xyz
+
+; Electrostatics and VdW (Sage-style nonbonded settings)
+coulombtype = PME
+pme_order = 4
+fourierspacing = 0.16
+rcoulomb = 0.9
+rvdw = 0.9
+vdwtype = cutoff
+vdw-modifier = Potential-switch
+rvdw-switch = 0.8
+DispCorr = EnerPres
+
+; Temperature coupling
+tcoupl = V-rescale
+tc-grps = Protein Non-Protein
+tau_t = 0.1 0.1
+ref_t = 300 300
+
+; Pressure coupling
+pcoupl = Berendsen
+pcoupltype = isotropic
+tau_p = 2.0
+ref_p = 1.0
+compressibility = 4.5e-5
+
+; Velocity generation
+gen_vel = no
diff --git a/mdfactory/run_schedules/gromacs/proteinbox_amber/nvt.mdp b/mdfactory/run_schedules/gromacs/proteinbox_amber/nvt.mdp
new file mode 100644
index 0000000..bcbf37f
--- /dev/null
+++ b/mdfactory/run_schedules/gromacs/proteinbox_amber/nvt.mdp
@@ -0,0 +1,52 @@
+; NVT equilibration for protein systems (Amber ff14SB + OpenFF Sage)
+title = NVT equilibration
+define = -DPOSRES
+
+; Run parameters
+integrator = md
+nsteps = 50000
+dt = 0.002
+
+; Output control
+nstxout = 500
+nstvout = 500
+nstenergy = 500
+nstlog = 500
+
+; Bond parameters
+continuation = no
+constraint_algorithm = lincs
+constraints = h-bonds
+lincs_iter = 1
+lincs_order = 4
+
+; Neighbor searching
+cutoff-scheme = Verlet
+ns_type = grid
+nstlist = 10
+pbc = xyz
+
+; Electrostatics and VdW (Sage-style nonbonded settings)
+coulombtype = PME
+pme_order = 4
+fourierspacing = 0.16
+rcoulomb = 0.9
+rvdw = 0.9
+vdwtype = cutoff
+vdw-modifier = Potential-switch
+rvdw-switch = 0.8
+DispCorr = EnerPres
+
+; Temperature coupling
+tcoupl = V-rescale
+tc-grps = Protein Non-Protein
+tau_t = 0.1 0.1
+ref_t = 300 300
+
+; Pressure coupling off for NVT
+pcoupl = no
+
+; Velocity generation
+gen_vel = yes
+gen_temp = 300
+gen_seed = -1
diff --git a/mdfactory/run_schedules/run_schedules.yaml b/mdfactory/run_schedules/run_schedules.yaml
index bc18a9f..82ca002 100644
--- a/mdfactory/run_schedules/run_schedules.yaml
+++ b/mdfactory/run_schedules/run_schedules.yaml
@@ -63,3 +63,35 @@
num_gpus: 1
num_cores: 8
walltime: 24:00:00
+
+# Amber ff14SB + OpenFF Sage builds use Sage-style nonbonded settings. Entries with
+# a `parametrization` key are preferred for builds with that parametrization.
+- engine: gromacs
+ system_type: proteinbox
+ parametrization: amber
+ version: 1.0
+ template_dir: proteinbox_amber
+ run_files:
+ - em.mdp
+ - nvt.mdp
+ - npt.mdp
+ - md.mdp
+ settings:
+ num_gpus: 1
+ num_cores: 8
+ walltime: 24:00:00
+
+- engine: gromacs
+ system_type: protein_mixedbox
+ parametrization: amber
+ version: 1.0
+ template_dir: proteinbox_amber
+ run_files:
+ - em.mdp
+ - nvt.mdp
+ - npt.mdp
+ - md.mdp
+ settings:
+ num_gpus: 1
+ num_cores: 8
+ walltime: 24:00:00
diff --git a/mdfactory/setup/protein.py b/mdfactory/setup/protein.py
index 4002875..7b8d246 100644
--- a/mdfactory/setup/protein.py
+++ b/mdfactory/setup/protein.py
@@ -1,5 +1,5 @@
# ABOUTME: Protein preparation utilities for the proteinbox simulation type
-# ABOUTME: Wraps PDBFixer for cleaning and gmx pdb2gmx for topology generation
+# ABOUTME: Wraps PDBFixer cleaning, gmx pdb2gmx topology generation, and GROMACS version gates
"""Protein preparation utilities for the proteinbox simulation type."""
import hashlib
@@ -16,7 +16,12 @@
from loguru import logger
-from ..models.parametrization import GromacsProteinParameterSet, Pdb2gmxConfig
+from ..models.parametrization import (
+ AmberConfig,
+ CharmmConfig,
+ GromacsProteinParameterSet,
+ Pdb2gmxConfig,
+)
from ..settings import settings
_DISULFIDE_CUTOFF_ANGSTROM = 2.2
@@ -345,6 +350,171 @@ def check_gmx_available() -> Path:
return Path(gmx_path)
+# Force fields that need a minimum GROMACS version, keyed by the ``.ff`` directory
+# stem, as (year, minor). amber14sb.ff ships with GROMACS 2026 and relies on the
+# LEaP dihedral atom reordering that grompp gained in 2026; older versions ignore
+# ``_FF_AMBER_LEAP_ATOM_REORDERING`` silently. Single source of truth for the
+# build-time gate and the simulate-time grompp script check.
+GMX_MIN_VERSION_BY_FORCEFIELD: dict[str, tuple[int, int]] = {
+ "amber14sb": (2026, 0),
+}
+
+_GMX_VERSION_LINE = re.compile(r"^\s*GROMACS version:\s*(\S+)", re.MULTILINE)
+_GMX_VERSION_NUMBER = re.compile(r"^(\d+)(?:\.(\d+))?(?!\d)")
+
+
+def parse_gmx_version(text: str) -> tuple[int, int]:
+ """Parse a GROMACS version from ``gmx --version`` output or a version string.
+
+ Parameters
+ ----------
+ text : str
+ Full ``gmx --version`` output (the ``GROMACS version:`` line is used) or
+ a bare version string such as ``2026.3-conda_forge``, ``2024.3``,
+ ``2026.0-dev-20250101-abcdef`` or ``2026-beta1``.
+
+ Returns
+ -------
+ tuple of int
+ ``(year, minor)``; a missing minor version (``2026-beta1``) is 0.
+
+ Raises
+ ------
+ ValueError
+ If no GROMACS version can be read from *text*.
+
+ """
+ line = _GMX_VERSION_LINE.search(text)
+ version = line.group(1) if line else text.strip()
+ match = _GMX_VERSION_NUMBER.match(version)
+ if match is None:
+ raise ValueError(f"Could not parse a GROMACS version from {text.strip()[:200]!r}.")
+ return int(match.group(1)), int(match.group(2) or 0)
+
+
+def format_gmx_version(version: tuple[int, int]) -> str:
+ """Format a ``(year, minor)`` GROMACS version, omitting a zero minor version."""
+ year, minor = version
+ return f"{year}" if minor == 0 else f"{year}.{minor}"
+
+
+def min_gmx_version_for_forcefield(forcefield: str) -> tuple[int, int] | None:
+ """Return the minimum GROMACS version a force field needs, or None if any works.
+
+ Parameters
+ ----------
+ forcefield : str
+ Force-field name or ``.ff`` directory name (e.g. ``amber14sb`` or
+ ``amber14sb.ff``).
+
+ """
+ return GMX_MIN_VERSION_BY_FORCEFIELD.get(forcefield.removesuffix(".ff"))
+
+
+def min_gmx_version_for_topology(top_path: Path) -> tuple[int, int] | None:
+ """Return the minimum GROMACS version the force field included by a topology needs.
+
+ Reads the ``#include ".ff/forcefield.itp"`` lines of *top_path* (not
+ following includes) and returns the highest requirement among them.
+
+ Parameters
+ ----------
+ top_path : Path
+ GROMACS topology, e.g. a simulation directory's ``topology.top``.
+
+ Returns
+ -------
+ tuple of int or None
+ ``(year, minor)``, or None if the file does not exist or its force
+ field has no version requirement.
+
+ """
+ top_path = Path(top_path)
+ if not top_path.is_file():
+ return None
+ requirements = []
+ with open(top_path) as fb:
+ for line in fb:
+ stripped = line.strip()
+ if not stripped.startswith("#include") or '"' not in stripped:
+ continue
+ parts = Path(stripped.split('"')[1]).parts
+ if len(parts) < 2 or parts[-1] != "forcefield.itp" or not parts[-2].endswith(".ff"):
+ continue
+ required = min_gmx_version_for_forcefield(parts[-2])
+ if required is not None:
+ requirements.append(required)
+ return max(requirements) if requirements else None
+
+
+def get_gmx_version(gmx_bin: str | Path) -> tuple[tuple[int, int], str]:
+ """Run ``gmx --version`` and return the parsed and the reported version.
+
+ Returns
+ -------
+ tuple
+ ``((year, minor), reported)`` where *reported* is the raw version string,
+ e.g. ``2026.3-conda_forge``.
+
+ Raises
+ ------
+ RuntimeError
+ If the binary cannot be run or reports no parseable version.
+
+ """
+ try:
+ result = subprocess.run(
+ [str(gmx_bin), "--version"],
+ text=True,
+ capture_output=True,
+ timeout=30,
+ check=False,
+ )
+ except (OSError, subprocess.SubprocessError) as exc:
+ raise RuntimeError(f"Could not run '{gmx_bin} --version': {exc}") from exc
+ output = result.stdout + result.stderr
+ try:
+ version = parse_gmx_version(output)
+ except ValueError as exc:
+ raise RuntimeError(
+ f"Could not read the GROMACS version of '{gmx_bin}' "
+ f"(exit code {result.returncode}): {exc}"
+ ) from exc
+ line = _GMX_VERSION_LINE.search(output)
+ reported = line.group(1) if line else format_gmx_version(version)
+ return version, reported
+
+
+def require_gmx_version(gmx_bin: str | Path, forcefield: str) -> None:
+ """Fail early if *gmx_bin* is too old for *forcefield*.
+
+ Force fields without an entry in :data:`GMX_MIN_VERSION_BY_FORCEFIELD` are
+ accepted without running the binary.
+
+ Raises
+ ------
+ RuntimeError
+ If the binary is older than the force field requires.
+
+ """
+ required = min_gmx_version_for_forcefield(forcefield)
+ if required is None:
+ return
+ version, reported = get_gmx_version(gmx_bin)
+ if version < required:
+ raise RuntimeError(
+ f"Force field '{forcefield}' requires GROMACS >= {format_gmx_version(required)}, "
+ f"but '{gmx_bin}' is GROMACS {reported}. Use a newer GROMACS, e.g. the pixi "
+ "'gmx' environment (`pixi run -e gmx ...`), or point [gromacs] GMX_PATH in "
+ "the mdfactory config at a GROMACS >= "
+ f"{format_gmx_version(required)} binary."
+ )
+ logger.info(
+ f"GROMACS {reported} satisfies the '{forcefield}' requirement "
+ f">= {format_gmx_version(required)}."
+ )
+
+
def download_forcefield(name: str) -> Path:
"""Download a force field from the registry to the local data directory.
@@ -632,7 +802,7 @@ def _run_gmx(
def run_pdb2gmx(
pdb_path: Path,
- config: Pdb2gmxConfig,
+ config: Pdb2gmxConfig | CharmmConfig | AmberConfig,
disulfide_bonds: list[tuple[str, str]],
protonation_states: dict[str, str],
output_dir: Path,
@@ -644,8 +814,10 @@ def run_pdb2gmx(
----------
pdb_path : Path
Cleaned PDB file.
- config : Pdb2gmxConfig
- Force field and water model configuration.
+ config : Pdb2gmxConfig or CharmmConfig or AmberConfig
+ Force field and water model configuration. Only the shared
+ ``forcefield``, ``water_model``, ``ignore_hydrogens`` and ``merge_all``
+ fields are read.
disulfide_bonds : list[tuple[str, str]]
Cysteine residue pairs for disulfide bonds, e.g. [("CYS6", "CYS127")].
protonation_states : dict[str, str]
diff --git a/mdfactory/tests/test_amber_gmx_build.py b/mdfactory/tests/test_amber_gmx_build.py
new file mode 100644
index 0000000..d4bb369
--- /dev/null
+++ b/mdfactory/tests/test_amber_gmx_build.py
@@ -0,0 +1,155 @@
+# ABOUTME: Opt-in real-GROMACS test for the Amber ff14SB + OpenFF Sage protein topology
+# ABOUTME: Runs pdb2gmx amber14sb, a Sage solute composite topology, and grompp -maxwarn 0
+"""Opt-in real-GROMACS test of the Amber ff14SB + OpenFF Sage protein route.
+
+Skipped unless a GROMACS >= 2026 binary is available (configured or on PATH).
+The module name contains ``build``, so ``pytest -k "not build"`` (CI) skips it.
+"""
+
+import shutil
+from pathlib import Path
+
+import MDAnalysis as mda
+import numpy as np
+import pytest
+
+from mdfactory.build import _protein_solution_parametrizer, _stage_protein_topology
+from mdfactory.models.parametrization import AmberConfig
+from mdfactory.models.species import SolutionSpecies
+from mdfactory.run_schedules import RunScheduleManager
+from mdfactory.settings import settings
+from mdfactory.setup import protein
+from mdfactory.utils.setup_utilities import topology_atom_names
+
+# Lys1-Val2-Phe3 heavy atoms from PDB 1AKI (hen egg-white lysozyme).
+PEPTIDE_PDB = """\
+ATOM 1 N LYS A 1 35.365 22.342 -11.980 1.00 22.28 N
+ATOM 2 CA LYS A 1 35.892 21.073 -11.427 1.00 21.12 C
+ATOM 3 C LYS A 1 34.741 20.264 -10.844 1.00 16.85 C
+ATOM 4 O LYS A 1 33.945 20.813 -10.081 1.00 18.94 O
+ATOM 5 CB LYS A 1 36.872 21.435 -10.306 1.00 20.78 C
+ATOM 6 CG LYS A 1 37.453 20.248 -9.565 1.00 18.47 C
+ATOM 7 CD LYS A 1 38.688 20.649 -8.775 1.00 20.32 C
+ATOM 8 CE LYS A 1 39.057 19.508 -7.837 1.00 24.76 C
+ATOM 9 NZ LYS A 1 40.423 19.771 -7.299 1.00 28.27 N
+ATOM 10 N VAL A 2 34.739 18.961 -11.042 1.00 19.96 N
+ATOM 11 CA VAL A 2 33.903 17.998 -10.333 1.00 18.10 C
+ATOM 12 C VAL A 2 34.800 17.312 -9.294 1.00 19.39 C
+ATOM 13 O VAL A 2 35.759 16.605 -9.665 1.00 22.14 O
+ATOM 14 CB VAL A 2 33.140 17.034 -11.232 1.00 16.81 C
+ATOM 15 CG1 VAL A 2 32.251 16.084 -10.434 1.00 21.92 C
+ATOM 16 CG2 VAL A 2 32.294 17.714 -12.290 1.00 19.46 C
+ATOM 17 N PHE A 3 34.491 17.546 -8.038 1.00 19.89 N
+ATOM 18 CA PHE A 3 35.185 16.903 -6.918 1.00 17.43 C
+ATOM 19 C PHE A 3 34.742 15.441 -6.771 1.00 15.70 C
+ATOM 20 O PHE A 3 33.525 15.162 -6.862 1.00 18.52 O
+ATOM 21 CB PHE A 3 34.967 17.632 -5.594 1.00 17.94 C
+ATOM 22 CG PHE A 3 35.944 18.737 -5.375 1.00 16.78 C
+ATOM 23 CD1 PHE A 3 35.666 20.050 -5.798 1.00 15.97 C
+ATOM 24 CD2 PHE A 3 37.000 18.557 -4.473 1.00 19.95 C
+ATOM 25 CE1 PHE A 3 36.577 21.076 -5.568 1.00 17.32 C
+ATOM 26 CE2 PHE A 3 37.869 19.589 -4.157 1.00 17.65 C
+ATOM 27 CZ PHE A 3 37.636 20.873 -4.666 1.00 17.91 C
+END
+"""
+
+BOX_A = 40.0
+
+
+def _new_enough_gmx():
+ try:
+ gmx = protein.check_gmx_available()
+ version, _ = protein.get_gmx_version(gmx)
+ except RuntimeError:
+ return None
+ return gmx if version >= (2026, 0) else None
+
+
+pytestmark = pytest.mark.skipif(_new_enough_gmx() is None, reason="needs GROMACS >= 2026")
+
+
+def _solution_universe(species, names, offsets):
+ """Place each species' RDKit conformer at an offset; use the topology atom names."""
+ positions, atom_names, resindex, resnames = [], [], [], []
+ for i, (spec, spec_names, offset) in enumerate(zip(species, names, offsets)):
+ xyz = spec.rdkit_molecule.GetConformer().GetPositions()
+ positions.append(xyz - xyz.mean(axis=0) + offset)
+ atom_names += spec_names
+ resindex += [i] * len(spec_names)
+ resnames.append(spec.resname)
+ u = mda.Universe.empty(
+ len(atom_names), n_residues=len(species), atom_resindex=resindex, trajectory=True
+ )
+ u.add_TopologyAttr("names", atom_names)
+ u.add_TopologyAttr("resnames", resnames)
+ u.add_TopologyAttr("resids", np.arange(1, len(species) + 1))
+ u.atoms.positions = np.vstack(positions)
+ return u
+
+
+def test_amber_sage_composite_topology_passes_grompp_build(tmp_path, monkeypatch):
+ monkeypatch.setattr(settings, "parameter_store", tmp_path / "parameters")
+ pdb = tmp_path / "peptide.pdb"
+ pdb.write_text(PEPTIDE_PDB)
+ config = AmberConfig()
+
+ params = protein.run_pdb2gmx(
+ pdb_path=pdb,
+ config=config,
+ disulfide_bonds=[],
+ protonation_states={},
+ output_dir=tmp_path / "pdb2gmx",
+ )
+ ff_name = protein.bundle_forcefield_into_topology(params.topology_file)
+ assert ff_name == "amber14sb.ff"
+ ff_dir = params.topology_file.parent / ff_name
+
+ _, parametrize = _protein_solution_parametrizer(config, ff_dir)
+ species = [
+ SolutionSpecies(smiles="CCO", resname="ETH", count=1),
+ SolutionSpecies(smiles="O", resname="SOL", count=1),
+ ]
+ parameters = [parametrize(spec) for spec in species]
+ assert parameters[0].parameter_itp is not None
+ assert parameters[1].itp == ff_dir / "tip3p.itp"
+
+ build_dir = tmp_path / "system"
+ build_dir.mkdir()
+ topology = _stage_protein_topology(params, ff_dir, build_dir, species, parameters, [1, 1])
+
+ u_protein = mda.Universe(str(params.structure_file))
+ u_protein.atoms.translate(np.full(3, BOX_A / 2) - u_protein.atoms.center_of_geometry())
+ solution = _solution_universe(
+ species,
+ [topology_atom_names(spec, par) for spec, par in zip(species, parameters)],
+ [np.array([5.0, 5.0, 5.0]), np.array([35.0, 35.0, 35.0])],
+ )
+ u = mda.Merge(u_protein.atoms, solution.atoms)
+ u.dimensions = [BOX_A, BOX_A, BOX_A, 90, 90, 90]
+ structure = build_dir / "system.gro"
+ u.atoms.write(str(structure))
+ # OpenMM's PDB reader drops atoms whose name repeats within a residue, so the
+ # Sage solute must carry unique names for the OpenMM compression/relaxation.
+ from openmm import app
+
+ pdb_out = build_dir / "system.pdb"
+ u.atoms.write(str(pdb_out))
+ assert app.PDBFile(str(pdb_out)).topology.getNumAtoms() == u.atoms.n_atoms
+
+ mdp = RunScheduleManager().get_all_run_file_paths(
+ "gromacs", "protein_mixedbox", parametrization="amber"
+ )["em.mdp"]
+ shutil.copy(mdp, build_dir / "em.mdp")
+
+ text = topology.read_text()
+ for include in ("forcefield.itp", "tip3p.itp", "ions_tip3p.itp"):
+ assert f'#include "amber14sb.ff/{include}"' in text
+ assert f'#include "{parameters[0].itp.name}"' in text
+ extra = (build_dir / "extra_params.itp").read_text()
+ assert "[ defaults ]" not in extra and "ETH_0" in extra
+
+ # The peptide carries a net charge (+1); accept only grompp's net-charge warning.
+ protein.validate_with_grompp(
+ topology, structure, build_dir / "em.mdp", build_dir, allow_net_charge=True
+ )
+ assert Path(build_dir / "topology.top").is_file()
diff --git a/mdfactory/tests/test_orchestration_gmx_version.py b/mdfactory/tests/test_orchestration_gmx_version.py
new file mode 100644
index 0000000..5d95c3e
--- /dev/null
+++ b/mdfactory/tests/test_orchestration_gmx_version.py
@@ -0,0 +1,133 @@
+# ABOUTME: Tests for the simulate-time GROMACS version check in generated grompp scripts
+# ABOUTME: Covers requirement detection from topology.top, run_stage wiring, and the bash check
+"""Tests for the simulate-time GROMACS version check in generated grompp scripts."""
+
+import shutil
+import subprocess
+import textwrap
+from unittest.mock import MagicMock
+
+import pytest
+
+from mdfactory.orchestration.apps import _build_grompp_script
+from mdfactory.orchestration.stages import STAGE_BY_NAME, min_gmx_version_for_sim_dir, run_stage
+
+AMBER_TOP = '#include "amber14sb.ff/forcefield.itp"\n#include "amber14sb.ff/tip3p.itp"\n'
+CHARMM_TOP = '#include "charmm36-feb2026_cgenff-5.0.ff/forcefield.itp"\n'
+
+
+def _script(work_dir, min_gmx_version=""):
+ return _build_grompp_script(
+ "em.mdp",
+ "system.pdb",
+ "topology.top",
+ "min.tpr",
+ str(work_dir),
+ min_gmx_version=min_gmx_version,
+ )
+
+
+class TestRequirementDetection:
+ @pytest.mark.parametrize(("top", "expected"), [(AMBER_TOP, "2026"), (CHARMM_TOP, "")])
+ def test_from_topology(self, tmp_path, top, expected):
+ (tmp_path / "topology.top").write_text(top)
+ assert min_gmx_version_for_sim_dir(tmp_path) == expected
+
+ def test_missing_topology_has_no_requirement(self, tmp_path):
+ assert min_gmx_version_for_sim_dir(tmp_path) == ""
+
+ @pytest.mark.parametrize(("top", "expected"), [(AMBER_TOP, "2026"), (CHARMM_TOP, None)])
+ def test_run_stage_passes_requirement_only_when_needed(self, tmp_path, top, expected):
+ (tmp_path / "topology.top").write_text(top)
+ grompp_app = MagicMock(return_value=MagicMock())
+ run_stage(STAGE_BY_NAME["EM"], tmp_path, None, grompp_app, MagicMock())
+ assert grompp_app.call_args.kwargs.get("min_gmx_version") == expected
+
+
+class TestGromppScript:
+ def test_no_check_without_minimum(self, tmp_path):
+ script = _script(tmp_path)
+ assert "GMX_VERSION" not in script
+ assert script == _build_grompp_script(
+ "em.mdp", "system.pdb", "topology.top", "min.tpr", str(tmp_path)
+ )
+
+ def test_check_runs_after_detection_and_before_grompp(self, tmp_path):
+ script = _script(tmp_path, "2026")
+ assert "GROMACS >= 2026" in script
+ detect = script.index("GMX_BIN=gmx")
+ check = script.index("GMX_VERSION=")
+ assert detect < check < script.index("$GMX_BIN grompp")
+
+ @pytest.mark.parametrize("bad", ["abc", "2026.x", "-1"])
+ def test_rejects_invalid_minimum(self, tmp_path, bad):
+ with pytest.raises(ValueError, match="Invalid minimum GROMACS version"):
+ _script(tmp_path, bad)
+
+
+def _fake_gmx(bin_dir, name="gmx"):
+ """Write a fake gmx that reports $FAKE_VERSION and records grompp calls."""
+ bin_dir.mkdir(exist_ok=True)
+ fake = bin_dir / name
+ fake.write_text(
+ textwrap.dedent("""\
+ #!/bin/bash
+ if [ "$1" = "--version" ]; then
+ echo " :-) GROMACS - gmx, $FAKE_VERSION (-:"
+ echo
+ echo "GROMACS version: $FAKE_VERSION"
+ echo "Precision: mixed"
+ exit 0
+ fi
+ echo "$@" >> "$FAKE_LOG"
+ while [ $# -gt 0 ]; do
+ if [ "$1" = "-o" ]; then touch "$2"; fi
+ shift
+ done
+ """)
+ )
+ fake.chmod(0o755)
+ return fake
+
+
+@pytest.mark.skipif(shutil.which("bash") is None, reason="bash is unavailable")
+class TestVersionCheckExecution:
+ @pytest.mark.parametrize(
+ ("version", "passes"),
+ [
+ ("2026.3-conda_forge", True),
+ ("2026.0-dev-20250101-abcdef", True),
+ ("2024.3", False),
+ ("2025.4", False),
+ ("garbage", False),
+ ],
+ )
+ def test_fake_gmx(self, tmp_path, version, passes):
+ sim_dir = tmp_path / "sim"
+ sim_dir.mkdir()
+ bin_dir = tmp_path / "bin"
+ _fake_gmx(bin_dir)
+ log = tmp_path / "grompp.log"
+ result = subprocess.run(
+ ["bash", "-c", _script(sim_dir, "2026")],
+ capture_output=True,
+ text=True,
+ env={
+ "PATH": f"{bin_dir}:/usr/bin:/bin",
+ "FAKE_VERSION": version,
+ "FAKE_LOG": str(log),
+ },
+ timeout=30,
+ check=False,
+ )
+ if passes:
+ assert result.returncode == 0, result.stderr
+ assert (sim_dir / "min.tpr").is_file()
+ assert "grompp" in log.read_text()
+ else:
+ assert result.returncode != 0
+ assert "requires GROMACS >= 2026" in result.stderr
+ assert str(bin_dir / "gmx") in result.stderr
+ # grompp (and therefore any mdrun) never ran.
+ assert not log.exists()
+ assert not (sim_dir / "min.tpr").exists()
diff --git a/mdfactory/tests/test_protein_mixedbox.py b/mdfactory/tests/test_protein_mixedbox.py
index c408504..b688ba5 100644
--- a/mdfactory/tests/test_protein_mixedbox.py
+++ b/mdfactory/tests/test_protein_mixedbox.py
@@ -17,6 +17,7 @@
PROTEIN_MIXEDBOX_RMSD_TOLERANCE_A,
_check_no_protein_clashes,
_check_no_solution_clashes,
+ _protein_solution_parametrizer,
_reimage_protein_centered,
ionize_solvated_system,
)
@@ -27,11 +28,12 @@
ProteinMixedBoxComposition,
)
from mdfactory.models.input import BuildInput
-from mdfactory.models.parametrization import CharmmConfig
+from mdfactory.models.parametrization import AmberConfig, CharmmConfig
from mdfactory.models.species import ProteinSpecies, SolutionSpecies
from mdfactory.parametrize import (
generate_gromacs_topology_with_protein,
parametrize_cgenff_gromacs,
+ parametrize_smirnoff_gromacs,
)
from mdfactory.prepare import df_to_build_input_models
from mdfactory.run_schedules import RunScheduleManager
@@ -45,8 +47,15 @@
charmm_native_atom_names,
create_protein_mixedbox_universe,
cubic_box_edge_for_density,
+ native_atom_names,
protein_displaced_volume_a3,
resolve_solution_counts,
+ topology_atom_names,
+)
+from mdfactory.utils.topology_utilities import (
+ read_itp_atoms,
+ unique_atom_names,
+ write_itp_with_atom_names,
)
from .conftest import protein_input_data
@@ -111,7 +120,7 @@ def test_rejects_invalid_amounts(self, kwargs, match):
[("O", "WAT"), ("[Na+]", "SOD"), ("[Cl-]", "CLA")],
)
def test_native_species_require_charmm_resname(self, smiles, wrong_resname):
- with pytest.raises(ValueError, match="Native CHARMM species"):
+ with pytest.raises(ValueError, match="Native water/ion species"):
SolutionSpecies(smiles=smiles, resname=wrong_resname, count=1)
@@ -763,3 +772,321 @@ def test_protein_mixedbox_run_files_on_disk(self):
assert set(paths) == {"em.mdp", "nvt.mdp", "npt.mdp", "md.mdp"}
for path in paths.values():
assert path.is_file()
+
+
+AMBER_FORCEFIELD_ITP = """\
+#define _FF_AMBER
+
+[ defaults ]
+; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
+1 2 yes 0.5 0.83333333333333333
+
+#include "ffnonbonded.itp"
+"""
+
+SAGE_PARAMS_ITP = """\
+[ defaults ]
+; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
+ 1 2 yes {fudge_lj} {fudge_qq}
+
+[ atomtypes ]
+;type, bondingtype, atomic_number, mass, charge, ptype, sigma, epsilon
+{type_a} 6 12.01078 0.0000000000000000 A 0.33795317 {eps}
+ETH_1 8 15.99943 0.0000000000000000 A 0.30398122 0.87950232
+"""
+
+
+def _amber_ff_dir(tmp_path):
+ """Write a minimal amber14sb.ff whose forcefield.itp and atom types mirror GROMACS 2026."""
+ ff_dir = tmp_path / "amber14sb.ff"
+ ff_dir.mkdir()
+ (ff_dir / "forcefield.itp").write_text(AMBER_FORCEFIELD_ITP)
+ (ff_dir / "ffnonbonded.itp").write_text(
+ "[ atomtypes ]\n"
+ " CT 6 12.01 0.0000 A 0.339966950842 0.457729600000\n"
+ " OW_tip3p 8 16.0 0.0000 A 0.315075240658 0.635968000000\n"
+ )
+ for name in ("tip3p.itp", "ions_tip3p.itp"):
+ (ff_dir / name).write_text(f"; {name}\n")
+ return ff_dir
+
+
+def _sage_parameters(tmp_path, name="ETH0", **fmt):
+ """Write a Sage-style parameter file and moleculetype ITP; return a parameter stand-in."""
+ values = {"fudge_lj": "0.500000", "fudge_qq": "0.833333", "type_a": "ETH_0", "eps": "0.45"}
+ values.update(fmt)
+ src = tmp_path / "params" / name
+ src.mkdir(parents=True)
+ params = src / f"{name}_params.itp"
+ params.write_text(SAGE_PARAMS_ITP.format(**values))
+ itp = src / f"{name}.itp"
+ # Interchange names atoms by element only, so names repeat within the molecule.
+ itp.write_text(
+ f"[ moleculetype ]\n{name} 3\n\n[ atoms ]\n"
+ " 1 ETH_0 1 ETH C 1 -0.09 12.01078\n"
+ " 2 ETH_0 1 ETH C 1 0.13 12.01078\n"
+ " 3 ETH_1 1 ETH O 1 -0.04 15.99943 ; hydroxyl\n"
+ "\n[ bonds ]\n 1 2 1\n"
+ )
+ return SimpleNamespace(
+ moleculetype=name, parameter_itp=params, itp=itp, parametrization="smirnoff"
+ )
+
+
+def _write_amber_protein_topology(path):
+ path.write_text(
+ textwrap.dedent("""\
+ #include "amber14sb.ff/forcefield.itp"
+
+ [ moleculetype ]
+ Protein_chain_A 3
+
+ #include "amber14sb.ff/tip3p.itp"
+ #include "amber14sb.ff/ions_tip3p.itp"
+
+ [ system ]
+ Protein in water
+
+ [ molecules ]
+ ; Compound #mols
+ Protein_chain_A 1
+ """)
+ )
+
+
+def _gen_amber(tmp_path, parameters, counts=None):
+ top = tmp_path / "topol_protein.top"
+ _write_amber_protein_topology(top)
+ out = tmp_path / "topology.top"
+ species = [
+ SolutionSpecies(smiles="CCO", resname=f"ET{i}", count=1) for i in range(len(parameters))
+ ]
+ generate_gromacs_topology_with_protein(
+ top,
+ _amber_ff_dir(tmp_path),
+ species,
+ parameters,
+ counts or [5] * len(parameters),
+ "protein_mixedbox",
+ out_path=out,
+ )
+ return out.read_text()
+
+
+class TestAmberSolutionParametrization:
+ def test_native_water_and_ions_come_from_forcefield_dir(self, tmp_path, monkeypatch):
+ monkeypatch.setattr(settings, "parameter_store", tmp_path / "parameters")
+ ff_dir = _amber_ff_dir(tmp_path)
+ config = AmberConfig().smirnoff_config()
+
+ results = {
+ smiles: parametrize_smirnoff_gromacs(
+ SolutionSpecies(smiles=smiles, resname=resname, count=1),
+ smirnoff_config=config,
+ native_forcefield_dir=ff_dir,
+ )
+ for smiles, resname in (("O", "SOL"), ("[Na+]", "NA"), ("[Cl-]", "CL"))
+ }
+
+ assert results["O"].itp == ff_dir / "tip3p.itp"
+ assert results["[Na+]"].itp == ff_dir / "ions_tip3p.itp"
+ assert results["[Cl-]"].itp == ff_dir / "ions_tip3p.itp"
+ assert [r.moleculetype for r in results.values()] == ["SOL", "NA", "CL"]
+ for result in results.values():
+ assert result.parameter_itp is None
+ assert result.forcefield_itp == ff_dir / "forcefield.itp"
+ assert result.parametrization == "smirnoff"
+ assert result.parametrization_config == config
+ # The native short-circuit never touches the SMIRNOFF cache.
+ assert not (tmp_path / "parameters" / "gromacs" / "smirnoff").exists()
+
+ def test_parametrizer_selection(self, tmp_path):
+ scheme, function = _protein_solution_parametrizer(CharmmConfig(), tmp_path)
+ assert scheme == "cgenff"
+ assert function.func is parametrize_cgenff_gromacs
+ assert function.keywords == {"native_forcefield_dir": tmp_path}
+
+ config = AmberConfig(charge_method="am1bcc")
+ scheme, function = _protein_solution_parametrizer(config, tmp_path)
+ assert scheme == "smirnoff"
+ assert function.func is parametrize_smirnoff_gromacs
+ assert function.keywords["native_forcefield_dir"] == tmp_path
+ assert function.keywords["native_water_model"] == "tip3p"
+ assert function.keywords["smirnoff_config"] == config.smirnoff_config()
+
+ def test_native_atom_names_and_alias(self):
+ assert native_atom_names("O") == ["OW", "HW1", "HW2"]
+ assert native_atom_names("[Na+]") == ["NA"]
+ assert native_atom_names("CCO") is None
+ assert charmm_native_atom_names is native_atom_names
+
+ def test_topology_atom_names_for_sage_solute(self, tmp_path):
+ species = SolutionSpecies(smiles="CO", resname="MEO", count=1)
+ elements = [atom.GetSymbol() for atom in species.rdkit_molecule.GetAtoms()]
+ masses = {"C": 12.011, "O": 15.999, "H": 1.008}
+ # Interchange writes element-only names; coordinates get them numbered.
+ atoms = "".join(
+ f"{i:5d} MEO_{i - 1} 1 MEO {el} 1 0.0 {masses[el]}\n"
+ for i, el in enumerate(elements, 1)
+ )
+ counts = {}
+ names = []
+ for el in elements:
+ counts[el] = counts.get(el, 0) + 1
+ names.append(f"{el}{counts[el]}")
+ itp = tmp_path / "MEO.itp"
+ itp.write_text(f"[ moleculetype ]\nMEO 3\n\n[ atoms ]\n{atoms}\n[ bonds ]\n")
+ params = tmp_path / "MEO_params.itp"
+ params.write_text("[ atomtypes ]\n")
+ parameter_set = SimpleNamespace(itp=itp, parameter_itp=params)
+ assert topology_atom_names(species, parameter_set) == names
+
+
+class TestUniqueAtomNames:
+ @pytest.mark.parametrize(
+ ("names", "expected"),
+ [
+ (["C1", "C2", "O3"], ["C1", "C2", "O3"]),
+ (["C", "C", "O", "H", "H"], ["C1", "C2", "O1", "H1", "H2"]),
+ ],
+ )
+ def test_unique_atom_names(self, names, expected):
+ assert unique_atom_names(names) == expected
+
+ def test_write_itp_with_atom_names_rejects_count_mismatch(self, tmp_path):
+ itp = tmp_path / "a.itp"
+ itp.write_text("[ atoms ]\n1 X 1 RES C 1 0.0 12.0\n")
+ with pytest.raises(ValueError, match="1 atoms but 2 names"):
+ write_itp_with_atom_names(itp, tmp_path / "b.itp", ["C1", "C2"])
+
+
+class TestAmberCompositeTopology:
+ def test_matching_defaults_dropped_and_sage_types_merged(self, tmp_path, monkeypatch):
+ monkeypatch.setattr(
+ "mdfactory.parametrize.validate_cgenff_atomtype_compatibility",
+ lambda *a, **k: pytest.fail("CGenFF validation must not run for SMIRNOFF solutes"),
+ )
+ text = _gen_amber(tmp_path, [_sage_parameters(tmp_path)])
+
+ merged = (tmp_path / "extra_params.itp").read_text()
+ assert "[ defaults ]" not in merged
+ assert "ETH_0" in merged and "ETH_1" in merged
+ # The copied ITP carries unique atom names (the source keeps element names).
+ assert [name for name, _ in read_itp_atoms(tmp_path / "ETH0.itp")] == ["C1", "C2", "O1"]
+ assert "; hydroxyl" in (tmp_path / "ETH0.itp").read_text()
+ source_names = read_itp_atoms(tmp_path / "params" / "ETH0" / "ETH0.itp")
+ assert [name for name, _ in source_names] == ["C", "C", "O"]
+ assert text.count('#include "amber14sb.ff/forcefield.itp"') == 1
+ assert '#include "extra_params.itp"' in text
+ assert text.index('#include "extra_params.itp"') > text.index("forcefield.itp")
+ assert text.index('#include "ETH0.itp"') < text.index("amber14sb.ff/tip3p.itp")
+ assert (tmp_path / "ETH0.itp").is_file()
+ assert "ETH0" in text.split("[ molecules ]", 1)[1]
+
+ @pytest.mark.parametrize(
+ "overrides",
+ [{"fudge_qq": "1.0"}, {"fudge_lj": "1.0"}],
+ )
+ def test_mismatching_defaults_raise(self, tmp_path, overrides):
+ with pytest.raises(ValueError, match="Incompatible \\[ defaults \\]"):
+ _gen_amber(tmp_path, [_sage_parameters(tmp_path, **overrides)])
+
+ def test_mismatching_comb_rule_raises(self, tmp_path):
+ par = _sage_parameters(tmp_path)
+ par.parameter_itp.write_text(
+ par.parameter_itp.read_text().replace("1 2 yes", "1 3 yes")
+ )
+ with pytest.raises(ValueError, match="amber14sb.ff/forcefield.itp"):
+ _gen_amber(tmp_path, [par])
+
+ def test_forcefield_atomtype_collision_raises(self, tmp_path):
+ with pytest.raises(ValueError, match="'CT'.*already defined by the force field"):
+ _gen_amber(tmp_path, [_sage_parameters(tmp_path, type_a="CT")])
+
+ def test_conflicting_duplicate_between_solutes_raises(self, tmp_path):
+ first = _sage_parameters(tmp_path, name="ETH0")
+ second = _sage_parameters(tmp_path, name="ETH1", eps="0.99")
+ with pytest.raises(ValueError, match="'ETH_0' is defined with different parameters"):
+ _gen_amber(tmp_path, [first, second])
+
+ def test_identical_duplicate_between_solutes_accepted(self, tmp_path):
+ _gen_amber(
+ tmp_path, [_sage_parameters(tmp_path, "ETH0"), _sage_parameters(tmp_path, "ETH1")]
+ )
+ merged = (tmp_path / "extra_params.itp").read_text()
+ assert merged.count("ETH_0 ") == 1
+
+ def test_mixed_cgenff_and_smirnoff_raises(self, tmp_path):
+ cgenff = _sage_parameters(tmp_path, name="CG0")
+ cgenff.parametrization = "cgenff"
+ with pytest.raises(ValueError, match="Cannot mix small-molecule parametrizations"):
+ _gen_amber(tmp_path, [_sage_parameters(tmp_path), cgenff])
+
+
+class TestAmberExamplesAndSchedule:
+ @pytest.mark.parametrize(
+ ("filename", "resnames"),
+ [
+ ("lysozyme_amber_fixed_box.yaml", {"SOL", "ETH"}),
+ ("lysozyme_amber_water_fixed_box.yaml", {"SOL"}),
+ ],
+ )
+ def test_yaml_loads(self, filename, resnames):
+ inp = BuildInput(**yaml.safe_load((EXAMPLES_DIR / filename).read_text()))
+ assert inp.parametrization == "amber"
+ assert isinstance(inp.parametrization_config, AmberConfig)
+ assert {s.resname for s in inp.system.species} == resnames
+
+ def test_csv_loads(self):
+ models, errors = df_to_build_input_models(
+ pd.read_csv(EXAMPLES_DIR / "protein_mixedbox_amber.csv")
+ )
+ assert errors == {}
+ assert [m.parametrization for m in models] == ["amber"]
+ assert isinstance(models[0].parametrization_config, AmberConfig)
+
+ @pytest.mark.parametrize("system_type", ["proteinbox", "protein_mixedbox"])
+ def test_amber_schedule_has_sage_nonbonded_settings(self, system_type):
+ from mdfactory.orchestration.mdp import get_mdp_value, parse_mdp
+
+ manager = RunScheduleManager()
+ amber = manager.get_all_run_file_paths(
+ engine="gromacs", system_type=system_type, parametrization="amber"
+ )
+ charmm = manager.get_all_run_file_paths(engine="gromacs", system_type=system_type)
+ assert set(amber) == set(charmm) == {"em.mdp", "nvt.mdp", "npt.mdp", "md.mdp"}
+ expected = {
+ "coulombtype": "pme",
+ "rcoulomb": "0.9",
+ "rvdw": "0.9",
+ "vdwtype": "cutoff",
+ "vdw_modifier": "potential-switch",
+ "rvdw_switch": "0.8",
+ "dispcorr": "enerpres",
+ }
+ for name, path in amber.items():
+ assert path.parent.name == "proteinbox_amber"
+ parsed = parse_mdp(path)
+ settings_found = {key: (get_mdp_value(parsed, key) or "").lower() for key in expected}
+ assert settings_found == expected, name
+ for path in charmm.values():
+ assert path.parent.name == "proteinbox"
+ assert get_mdp_value(parse_mdp(path), "vdw_modifier").lower() == "force-switch"
+
+ def test_unknown_parametrization_falls_back_to_generic(self):
+ manager = RunScheduleManager()
+ charmm = manager.get_all_run_file_paths("gromacs", "proteinbox", parametrization="pdb2gmx")
+ assert {p.parent.name for p in charmm.values()} == {"proteinbox"}
+
+ def test_finalize_installs_amber_schedule(self, tmp_path, monkeypatch):
+ from mdfactory import build
+
+ monkeypatch.chdir(tmp_path)
+ monkeypatch.setattr("mdfactory.setup.protein.validate_with_grompp", lambda *a, **k: None)
+ inp = SimpleNamespace(
+ engine="gromacs",
+ parametrization="amber",
+ system=SimpleNamespace(ionization=IonizationConfig()),
+ )
+ build._finalize_protein_build(inp, "protein_mixedbox", tmp_path / "topology.top")
+ assert "Potential-switch" in (tmp_path / "md.mdp").read_text()
diff --git a/mdfactory/tests/test_proteinbox.py b/mdfactory/tests/test_proteinbox.py
index 6d326c8..85bbf51 100644
--- a/mdfactory/tests/test_proteinbox.py
+++ b/mdfactory/tests/test_proteinbox.py
@@ -16,10 +16,15 @@
import yaml
from mdfactory import workflows
-from mdfactory.build import _center_in_cubic_box, _ion_counts
+from mdfactory.build import _center_in_cubic_box, _ion_counts, _prepare_protein
from mdfactory.models.composition import ProteinBoxComposition, ProteinMixedBoxComposition
from mdfactory.models.input import BuildInput
-from mdfactory.models.parametrization import CharmmConfig, Pdb2gmxConfig
+from mdfactory.models.parametrization import (
+ AmberConfig,
+ CharmmConfig,
+ Pdb2gmxConfig,
+ SmirnoffConfig,
+)
from mdfactory.models.species import ProteinSpecies, SingleMoleculeSpecies
from mdfactory.prepare import resolve_protein_pdb_path
from mdfactory.setup import protein
@@ -31,6 +36,7 @@
check_forcefield_available,
clean_pdb,
download_forcefield,
+ parse_gmx_version,
run_pdb2gmx,
update_topology_molecules,
)
@@ -835,3 +841,206 @@ def test_ion_counts(self, ions, expected):
for smiles, resname, count in ions
]
assert _ion_counts(species) == expected
+
+
+EXAMPLES_DIR = Path(__file__).resolve().parents[2] / "examples" / "proteinbox"
+
+
+class TestAmberConfig:
+ def test_defaults_and_sage_settings(self):
+ config = AmberConfig()
+ assert (config.forcefield, config.water_model) == ("amber14sb", "tip3p")
+ assert config.ignore_hydrogens is True and config.merge_all is False
+ smirnoff = config.smirnoff_config()
+ assert isinstance(smirnoff, SmirnoffConfig)
+ assert smirnoff.forcefield == SmirnoffConfig().forcefield == config.sage_forcefield
+ assert smirnoff.charge_method == config.charge_method
+
+ def test_smirnoff_config_follows_sage_fields(self):
+ config = AmberConfig(sage_forcefield="openff-2.1.0.offxml", charge_method="am1bcc")
+ smirnoff = config.smirnoff_config()
+ assert (smirnoff.forcefield, smirnoff.charge_method) == ("openff-2.1.0.offxml", "am1bcc")
+
+ def test_frozen(self):
+ with pytest.raises(Exception):
+ AmberConfig().forcefield = "amber19sb"
+
+ @pytest.mark.parametrize(
+ ("overrides", "match"),
+ [
+ ({"forcefield": "amber19sb"}, "Only 'amber14sb'"),
+ ({"forcefield": "charmm36m"}, "Only 'amber14sb'"),
+ ({"water_model": "opc"}, "Only 'tip3p'"),
+ ({"water_model": "spce"}, "Only 'tip3p'"),
+ ],
+ )
+ def test_rejects_unsupported_choices(self, overrides, match):
+ with pytest.raises(ValueError, match=match):
+ AmberConfig(**overrides)
+
+
+class TestAmberInput:
+ @pytest.mark.parametrize("sim_type", PROTEIN_SIM_TYPES)
+ @pytest.mark.parametrize("explicit", [False, True])
+ def test_accepts_amber_for_protein_types(self, sim_type, protein_pdb, explicit):
+ data = protein_input_data(sim_type, protein_pdb, parametrization="amber")
+ if explicit:
+ data["parametrization_config"] = {"type": "amber", "sage_forcefield": "x.offxml"}
+ inp = BuildInput(**data)
+ assert inp.parametrization == "amber"
+ assert isinstance(inp.parametrization_config, AmberConfig)
+ if explicit:
+ assert inp.parametrization_config.sage_forcefield == "x.offxml"
+
+ def test_yaml_round_trip(self, protein_pdb):
+ yaml_str = f"""
+simulation_type: proteinbox
+parametrization: amber
+parametrization_config:
+ type: amber
+ forcefield: amber14sb
+ water_model: tip3p
+system:
+ protein:
+ resname: LYZ
+ pdb_path: {protein_pdb}
+ padding: 12.0
+"""
+ inp = BuildInput(**yaml.safe_load(yaml_str))
+ assert BuildInput.from_data_row(inp.to_data_row()).hash == inp.hash
+
+ def test_rejected_for_mixedbox(self):
+ system = {"species": [{"smiles": "O", "resname": "SOL", "count": 10}]}
+ with pytest.raises(ValueError, match="not valid for simulation type"):
+ BuildInput(simulation_type="mixedbox", parametrization="amber", system=system)
+
+ @pytest.mark.parametrize("simulation_type", ["mixedbox", "bilayer", "lnp"])
+ def test_not_allowed_for_small_molecule_types(self, simulation_type):
+ from mdfactory.models.input import allowed_parametrizations
+
+ assert "amber" not in allowed_parametrizations[simulation_type]
+
+ def test_amber_merge_all_conflicts_with_chains(self, protein_pdb):
+ data = protein_input_data(
+ "proteinbox",
+ protein_pdb,
+ parametrization="amber",
+ protein={"resname": "INS", "chains": ["A", "B"]},
+ )
+ data["parametrization_config"] = {"type": "amber", "merge_all": True}
+ with pytest.raises(ValueError, match="merge_all"):
+ BuildInput(**data)
+
+ def test_example_yaml_and_csv(self):
+ import pandas as pd
+
+ from mdfactory.prepare import df_to_build_input_models
+
+ inp = BuildInput(**yaml.safe_load((EXAMPLES_DIR / "lysozyme_amber14sb.yaml").read_text()))
+ assert isinstance(inp.parametrization_config, AmberConfig)
+ models, errors = df_to_build_input_models(pd.read_csv(EXAMPLES_DIR / "proteins_amber.csv"))
+ assert errors == {}
+ assert [m.parametrization for m in models] == ["amber"]
+ assert isinstance(models[0].parametrization_config, AmberConfig)
+ assert models[0].system.protein.protonation_states == {"HIS15": "HIE"}
+
+
+class TestGmxVersion:
+ @pytest.mark.parametrize(
+ ("text", "expected"),
+ [
+ ("2026.3-conda_forge", (2026, 3)),
+ ("2024.3", (2024, 3)),
+ ("2026.0-dev-20250101-abcdef", (2026, 0)),
+ ("2026-beta1", (2026, 0)),
+ (
+ " :-) GROMACS - gmx, 2026.3-conda_forge (-:\n\n"
+ "GROMACS version: 2026.3-conda_forge\nPrecision: mixed\n",
+ (2026, 3),
+ ),
+ ],
+ )
+ def test_parse(self, text, expected):
+ assert parse_gmx_version(text) == expected
+
+ @pytest.mark.parametrize("text", ["", "not a version", "GROMACS version: unknown"])
+ def test_parse_garbage_raises(self, text):
+ with pytest.raises(ValueError, match="Could not parse a GROMACS version"):
+ parse_gmx_version(text)
+
+ def test_min_version_from_topology(self, tmp_path):
+ amber = tmp_path / "amber.top"
+ amber.write_text(
+ '#include "amber14sb.ff/forcefield.itp"\n#include "amber14sb.ff/tip3p.itp"\n'
+ )
+ charmm = tmp_path / "charmm.top"
+ charmm.write_text('#include "charmm36-feb2026_cgenff-5.0.ff/forcefield.itp"\n')
+ assert protein.min_gmx_version_for_topology(amber) == (2026, 0)
+ assert protein.min_gmx_version_for_topology(charmm) is None
+ assert protein.min_gmx_version_for_topology(tmp_path / "missing.top") is None
+
+
+def _patch_prepare_protein(monkeypatch, tmp_path, version_output):
+ """Fake clean_pdb, ``gmx --version`` and pdb2gmx; return the ordered list of calls."""
+ calls = []
+ _patch_pdb2gmx(monkeypatch, ["Protein_chain_A"], ["posre.itp"])
+ pdb2gmx_run = protein.subprocess.run
+
+ def fake_run(cmd, **kwargs):
+ if cmd[1:] == ["--version"]:
+ calls.append("version")
+ return SimpleNamespace(returncode=0, stdout=version_output, stderr="")
+ calls.append(cmd[1])
+ return pdb2gmx_run(cmd, **kwargs)
+
+ def fake_clean_pdb(pdb_path, output_path):
+ calls.append("clean_pdb")
+ shutil.copy(pdb_path, output_path)
+ return output_path
+
+ monkeypatch.setattr("mdfactory.setup.protein.subprocess.run", fake_run)
+ monkeypatch.setattr("mdfactory.setup.protein.clean_pdb", fake_clean_pdb)
+ monkeypatch.chdir(tmp_path)
+ return calls
+
+
+class TestPrepareProteinVersionGate:
+ def test_new_gromacs_passes(self, tmp_path, monkeypatch, protein_pdb):
+ calls = _patch_prepare_protein(
+ monkeypatch, tmp_path, "GROMACS version: 2026.3-conda_forge\n"
+ )
+ _prepare_protein(ProteinSpecies(resname="LYZ", pdb_path=protein_pdb), AmberConfig())
+ assert calls == ["version", "clean_pdb", "pdb2gmx"]
+
+ def test_old_gromacs_fails_before_pdb2gmx(self, tmp_path, monkeypatch, protein_pdb):
+ calls = _patch_prepare_protein(monkeypatch, tmp_path, "GROMACS version: 2024.3\n")
+ with pytest.raises(RuntimeError) as exc_info:
+ _prepare_protein(ProteinSpecies(resname="LYZ", pdb_path=protein_pdb), AmberConfig())
+ message = str(exc_info.value)
+ assert "/mock/gmx" in message and "2024.3" in message and ">= 2026" in message
+ assert calls == ["version"]
+
+ @pytest.mark.parametrize("config", [Pdb2gmxConfig(), CharmmConfig()])
+ def test_charmm_configs_skip_gate(self, tmp_path, monkeypatch, protein_pdb, config):
+ calls = _patch_prepare_protein(monkeypatch, tmp_path, "GROMACS version: 2024.3\n")
+ _prepare_protein(ProteinSpecies(resname="LYZ", pdb_path=protein_pdb), config)
+ assert "version" not in calls
+ assert calls[-1] == "pdb2gmx"
+
+
+def test_run_pdb2gmx_amber_passes_forcefield_and_amber_protonation(tmp_path, monkeypatch):
+ pdb = _write_pdb(tmp_path, ("HIS", 15), ("ALA", 16))
+ calls = {}
+ _patch_pdb2gmx(monkeypatch, ["Protein_chain_A"], ["posre.itp"], calls)
+
+ params = _run(tmp_path, pdb, config=AmberConfig(), protonation_states={"HIS15": "HIE"})
+
+ cmd = calls["cmd"]
+ assert cmd[cmd.index("-ff") + 1] == "amber14sb"
+ assert cmd[cmd.index("-water") + 1] == "tip3p"
+ assert "-ignh" in cmd
+ adjusted = Path(cmd[cmd.index("-f") + 1])
+ resnames = [ln[17:20] for ln in adjusted.read_text().splitlines() if ln.startswith("ATOM")]
+ # Amber names pass through unchanged (no CHARMM HSE alias).
+ assert resnames == ["HIE", "ALA"]
+ assert params.forcefield == "amber14sb"
diff --git a/mdfactory/utils/setup_utilities.py b/mdfactory/utils/setup_utilities.py
index d946071..43fe8eb 100644
--- a/mdfactory/utils/setup_utilities.py
+++ b/mdfactory/utils/setup_utilities.py
@@ -971,8 +971,23 @@ def create_protein_mixedbox_universe(
return merged
-def charmm_native_atom_names(smiles: str) -> list[str] | None:
- """Return canonical CHARMM36m atom names for supported native species."""
+def native_atom_names(smiles: str) -> list[str] | None:
+ """Return the force-field atom names of a supported native water or ion species.
+
+ The bundled CHARMM36m and GROMACS ``amber14sb.ff`` TIP3P water and ion
+ topologies use the same names (``OW``/``HW1``/``HW2``, ``NA``, ``CL``).
+
+ Parameters
+ ----------
+ smiles : str
+ Species SMILES.
+
+ Returns
+ -------
+ list of str or None
+ Atom names in packing order, or None if the species is not native.
+
+ """
return {
"O": ["OW", "HW1", "HW2"],
"[Na+]": ["NA"],
@@ -980,13 +995,20 @@ def charmm_native_atom_names(smiles: str) -> list[str] | None:
}.get(smiles)
+# Kept for existing imports; the native names are not CHARMM-specific.
+charmm_native_atom_names = native_atom_names
+
+
def topology_atom_names(species, parameter_set) -> list[str] | None:
"""Return the atom names the topology expects for a packed solution species.
- Native water and ions use the canonical CHARMM36m names. Small molecules
- with their own ``.itp`` (CGenFF solutes) use that file's ``[ atoms ]`` names,
- so the coordinates match the topology instead of keeping the generic
- element-indexed names from packing.
+ Native water and ions use the force-field names from :func:`native_atom_names`.
+ Small molecules with their own ``.itp`` (CGenFF or SMIRNOFF solutes) use that
+ file's ``[ atoms ]`` names, so the coordinates match the topology instead of
+ keeping the generic element-indexed names from packing. Repeated names
+ (SMIRNOFF names atoms by element only) are numbered with
+ :func:`~mdfactory.utils.topology_utilities.unique_atom_names`, matching the
+ ITP copy that ``generate_gromacs_topology_with_protein`` writes.
Parameters
----------
@@ -1007,13 +1029,13 @@ def topology_atom_names(species, parameter_set) -> list[str] | None:
which would mean the topology and coordinate orders differ.
"""
- native = charmm_native_atom_names(species.smiles)
+ native = native_atom_names(species.smiles)
if native is not None:
return native
if parameter_set.parameter_itp is None:
return None
- from .topology_utilities import read_itp_atoms # noqa: PLC0415
+ from .topology_utilities import read_itp_atoms, unique_atom_names # noqa: PLC0415
itp_atoms = read_itp_atoms(parameter_set.itp)
mol_atoms = list(species.rdkit_molecule.GetAtoms())
@@ -1029,4 +1051,4 @@ def topology_atom_names(species, parameter_set) -> list[str] | None:
f"packed molecule but {name} (mass {itp_mass}) in {parameter_set.itp}; "
"topology and coordinate atom orders differ."
)
- return [name for name, _ in itp_atoms]
+ return unique_atom_names([name for name, _ in itp_atoms])
diff --git a/mdfactory/utils/topology_utilities.py b/mdfactory/utils/topology_utilities.py
index 679e677..5de2d1d 100644
--- a/mdfactory/utils/topology_utilities.py
+++ b/mdfactory/utils/topology_utilities.py
@@ -575,6 +575,88 @@ def read_itp_atoms(itp_path: Path) -> list[tuple[str, float]]:
return atoms
+def unique_atom_names(names: list[str]) -> list[str]:
+ """Return atom names that are unique within one molecule.
+
+ Names that are already unique are returned unchanged (e.g. CGenFF). SMIRNOFF
+ topologies name atoms by element only (``C``, ``C``, ``O``, ``H``, ...);
+ those get a per-name counter (``C1``, ``C2``, ``O1``, ``H1``, ...). PDB
+ readers such as OpenMM's drop atoms whose name repeats within a residue, so
+ coordinates must carry unique names.
+
+ Parameters
+ ----------
+ names : list of str
+ Atom names in topology order.
+
+ Returns
+ -------
+ list of str
+ Unique atom names in the same order.
+
+ Raises
+ ------
+ ValueError
+ If numbering does not make the names unique.
+
+ """
+ if len(set(names)) == len(names):
+ return list(names)
+ counters: dict[str, int] = defaultdict(int)
+ numbered = []
+ for name in names:
+ counters[name] += 1
+ numbered.append(f"{name}{counters[name]}")
+ if len(set(numbered)) != len(numbered):
+ raise ValueError(f"Could not derive unique atom names from {names}.")
+ return numbered
+
+
+def write_itp_with_atom_names(src: str | Path, dest: str | Path, names: list[str]) -> None:
+ """Copy an ITP, replacing the atom names of its first ``[ atoms ]`` section.
+
+ Parameters
+ ----------
+ src : str or Path
+ Source ``.itp`` with a single-molecule ``[ atoms ]`` section.
+ dest : str or Path
+ Destination path.
+ names : list of str
+ New atom names in topology order; must match the number of atoms.
+
+ Raises
+ ------
+ ValueError
+ If the number of names does not match the ``[ atoms ]`` entries.
+
+ """
+ lines = Path(src).read_text().splitlines(keepends=True)
+ in_atoms = False
+ done = False
+ index = 0
+ for i, raw in enumerate(lines):
+ line = raw.split(";", 1)[0].strip()
+ if done or not line or line.startswith("#"):
+ continue
+ if line.startswith("[") and line.endswith("]"):
+ if in_atoms:
+ done = True
+ continue
+ in_atoms = line[1:-1].strip().lower() == "atoms"
+ continue
+ if in_atoms:
+ if index >= len(names):
+ raise ValueError(f"{src} has more atoms than the {len(names)} names given.")
+ fields = line.split()
+ fields[4] = names[index]
+ comment = raw.split(";", 1)[1].rstrip("\n") if ";" in raw else ""
+ lines[i] = " ".join(fields) + (f" ;{comment}" if comment else "") + "\n"
+ index += 1
+ if index != len(names):
+ raise ValueError(f"{src} has {index} atoms but {len(names)} names were given.")
+ Path(dest).write_text("".join(lines))
+
+
def validate_cgenff_atomtype_compatibility(
prm_files: list[str | Path],
ff_dir: str | Path,
@@ -609,6 +691,156 @@ def validate_cgenff_atomtype_compatibility(
)
+DEFAULTS_FUDGE_TOLERANCE = 1e-6
+
+
+def read_topology_defaults(path: str | Path) -> tuple[int, int, str, float, float] | None:
+ """Return the ``[ defaults ]`` entry of a GROMACS topology or include file.
+
+ Parameters
+ ----------
+ path : str or Path
+ Topology, ``forcefield.itp``, or parameter ``.itp`` file. Includes are
+ not followed.
+
+ Returns
+ -------
+ tuple or None
+ ``(nbfunc, comb_rule, gen_pairs, fudgeLJ, fudgeQQ)``, with ``gen_pairs``
+ lower-cased, or None if the file has no ``[ defaults ]`` section.
+
+ Raises
+ ------
+ ValueError
+ If the ``[ defaults ]`` section has no entry or a malformed one.
+
+ """
+ in_defaults = False
+ with open(path) as fb:
+ for raw in fb:
+ line = raw.split(";", 1)[0].strip()
+ if not line or line.startswith("#"):
+ continue
+ if line.startswith("[") and line.endswith("]"):
+ if in_defaults:
+ break
+ in_defaults = line[1:-1].strip().lower() == "defaults"
+ continue
+ if not in_defaults:
+ continue
+ fields = line.split()
+ if len(fields) < 5:
+ raise ValueError(f"Malformed [ defaults ] entry in {path}: {raw.strip()!r}")
+ try:
+ return (
+ int(fields[0]),
+ int(fields[1]),
+ fields[2].lower(),
+ float(fields[3]),
+ float(fields[4]),
+ )
+ except ValueError as exc:
+ raise ValueError(
+ f"Malformed [ defaults ] entry in {path}: {raw.strip()!r}"
+ ) from exc
+ if in_defaults:
+ raise ValueError(f"[ defaults ] section in {path} has no entry.")
+ return None
+
+
+def check_defaults_compatible(
+ reference_path: str | Path,
+ other_path: str | Path,
+ tolerance: float = DEFAULTS_FUDGE_TOLERANCE,
+) -> None:
+ """Raise unless two files declare equivalent ``[ defaults ]`` entries.
+
+ ``nbfunc``, ``comb-rule`` and ``gen-pairs`` must match exactly; ``fudgeLJ``
+ and ``fudgeQQ`` must agree within *tolerance*, because force fields write
+ the 1-4 scaling with different precision (``0.833333`` versus
+ ``0.83333333333333333``).
+
+ Parameters
+ ----------
+ reference_path : str or Path
+ File whose ``[ defaults ]`` is kept, e.g. the force field's ``forcefield.itp``.
+ other_path : str or Path
+ File whose ``[ defaults ]`` would be dropped, e.g. a SMIRNOFF parameter file.
+ tolerance : float, optional
+ Absolute tolerance for the fudge factors. Default is 1e-6.
+
+ Raises
+ ------
+ ValueError
+ If either file lacks ``[ defaults ]`` or the entries differ.
+
+ """
+ reference = read_topology_defaults(reference_path)
+ other = read_topology_defaults(other_path)
+ if reference is None or other is None:
+ missing = reference_path if reference is None else other_path
+ raise ValueError(f"No [ defaults ] section found in {missing}.")
+ exact_match = reference[:3] == other[:3]
+ fudge_match = all(abs(a - b) <= tolerance for a, b in zip(reference[3:], other[3:]))
+ if not (exact_match and fudge_match):
+ raise ValueError(
+ "Incompatible [ defaults ] (nbfunc, comb-rule, gen-pairs, fudgeLJ, fudgeQQ): "
+ f"{reference_path} has {reference}, but {other_path} has {other}. "
+ "The small-molecule parameters cannot be combined with this force field."
+ )
+
+
+def check_atomtype_collisions(
+ prm_files: list[str | Path],
+ forcefield_types: dict[str, tuple[str, ...]],
+) -> None:
+ """Reject small-molecule atom types that clash with the force field or each other.
+
+ Unlike CGenFF, whose atom types are meant to be shared with the CHARMM force
+ field, SMIRNOFF atom types are private per molecule. Any name that the force
+ field already defines is therefore a collision. A name defined by two
+ parameter files is accepted only if both give the same parameters.
+
+ Parameters
+ ----------
+ prm_files : list of str or Path
+ Parameter files with an ``[ atomtypes ]`` section.
+ forcefield_types : dict
+ Force-field atom types from :func:`collect_forcefield_atomtype_definitions`.
+
+ Raises
+ ------
+ ValueError
+ On a collision with a force-field atom type, or a name defined with
+ different parameters in two parameter files.
+
+ """
+ seen: dict[str, tuple[tuple[str, ...], str]] = {}
+ for prm in prm_files:
+ *_, sections = extract_reusable_parts_from_cgenff_gmx_top(prm, must_have_moleculetype=False)
+ for section_name, section_text in sections:
+ if section_name != "atomtypes":
+ continue
+ for line in section_text.splitlines():
+ stripped = line.strip()
+ if not stripped or stripped.startswith((";", "[")):
+ continue
+ name = stripped.split()[0]
+ if name in forcefield_types:
+ raise ValueError(
+ f"Atom type '{name}' from {prm} is already defined by the force "
+ "field. Rename the small-molecule residue to avoid the collision."
+ )
+ signature = _atomtype_signature(stripped)
+ previous = seen.get(name)
+ if previous is not None and previous[0] != signature:
+ raise ValueError(
+ f"Atom type '{name}' is defined with different parameters in "
+ f"{previous[1]} and {prm}. Give the species distinct residue names."
+ )
+ seen.setdefault(name, (signature, str(prm)))
+
+
def merge_extra_parameter_itps(
prm_files: list[str | Path],
exclude_atomtypes: Collection[str] | None = None,
diff --git a/pixi.lock b/pixi.lock
index 69da3b8..70d7493 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -16,6 +16,14 @@ platforms:
- __unix=0=0
- __osx=13.0
- __archspec=0=m1
+- name: p1
+ subdir: linux-64
+ virtual-packages:
+ - __cuda=12
+ - __unix=0=0
+ - __linux=4.18
+ - __glibc=2.28
+ - __archspec=0=x86_64
environments:
default:
channels:
@@ -3216,7 +3224,1031 @@ environments:
- pypi: https://files.pythonhosted.org/packages/87/01/6ec7210775ea5e4989a10d89eda6c5ea7ff06caa614231ad533d74fecac8/cyclopts-4.8.0-py3-none-any.whl
- pypi: https://files.pythonhosted.org/packages/9a/4b/4166bb5abbfe6f750fc60ad337c43ecf61340fa52ab386da6e8dbf9e63c4/pyarrow-23.0.1-cp312-cp312-macosx_12_0_arm64.whl
- pypi: https://files.pythonhosted.org/packages/f0/b4/50940504466689cda65680c9e9a1e518e5750c10490639fa687489ac7013/setproctitle-1.3.7-cp312-cp312-macosx_11_0_arm64.whl
+ gmx:
+ channels:
+ - url: https://conda.anaconda.org/conda-forge/
+ indexes:
+ - https://pypi.org/simple
+ packages:
+ linux-64:
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.2.1-h505cf86_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.2.1-h9908984_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_10.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.6-h3c89d7e_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/charset-normalizer-3.5.2-h1114479_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.4.0-py313h2551ef2_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/cuda-nvrtc-13.4.92-hd2095e1_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/cyrus-sasl-2.1.28-hac629b4_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/eigen-abi-5.0.1.80-hf414acd_3.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.11-nompi_h3b011a4_100.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.18.3-h4db4eae_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.68.0-py313h6cd9899_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.3-ha770c72_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.18-h7cc23a3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-hfd2156b_3.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/gmpy2-2.3.2-py313ha4a6282_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.15-h54a6638_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/gromacs-2026.3-nompi_h26635d9_100.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-py310h44b86e0_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-h7cc23a3_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.5.1-py313h2551ef2_3.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.22.2-hbc21106_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.20-h9073bf1_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.46.1-default_hbd61a6d_103.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.3.0-he78707d_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libabseil-20240722.0-cxx17_hbbce691_4.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-11_h4a7cf45_openblas.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libboost-1.90.0-h1101c1b_3.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libboost-python-1.90.0-py313hcc39c74_3.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.2.1-h39a168f_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.2.1-ha411449_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.2.1-h018ffa1_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-11_h0358290_openblas.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libcufft-12.4.0.43-hd2095e1_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.25-hd45a770_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20260512-pl5321h373387f_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.9.0-hd2095e1_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.7.0-h81df57d_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.3-ha770c72_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.3-h5e6c136_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-16.2.0-ha9f2e26_7.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-16.2.0-h69a702a_7.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-16.2.0-h69a702a_7.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-16.2.0-h6b99dfc_7.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libglib-2.90.0-h569388d_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-16.2.0-he0feb66_7.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libharfbuzz-15.0.0-h23af247_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.13.0-default_he001693_1000.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h0cb94f2_3.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.2.1-h7cc23a3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-11_h47877c9_openblas.conda
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+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.54.1-h13e7031_0.conda
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- pypi: https://files.pythonhosted.org/packages/d0/99/71630546b9395b095f4082be41165d1078204d1696c2d9baade3de3202d0/setproctitle-1.3.7-cp312-cp312-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
name: setproctitle
version: 1.3.7
@@ -13487,6 +23685,27 @@ packages:
requires_dist:
- pytest ; extra == 'test'
requires_python: '>=3.8'
+- pypi: https://files.pythonhosted.org/packages/d1/4e/716b42bf066e180c1235783b46f095a5d871d05dca7006d2295aac29c491/rich_rst-2.2.0-py3-none-any.whl
+ name: rich-rst
+ version: 2.2.0
+ sha256: 1ea1c43813dc4a8d86475fce27ffb74e0ada3d4656c9f8130ba2a59868055fe9
+ requires_dist:
+ - rich>=12.0.0
+ - pygments>=2.0.0
+ - docutils ; extra == 'docs'
+ - sphinx ; extra == 'docs'
+ - sphinx-copybutton ; extra == 'docs'
+ - sphinx-rtd-theme ; extra == 'docs'
+ - pytest ; extra == 'tests'
+ - pytest-cov ; extra == 'tests'
+ - ruff ; extra == 'dev'
+ - mypy ; extra == 'dev'
+ - pre-commit ; extra == 'dev'
+- pypi: https://files.pythonhosted.org/packages/d3/79/e2fc9b1317b7a21e7bcd57eb035cac3fe72f47af3efe2ec3b4dea9a08a04/pyarrow-26.0.1-cp312-cp312-manylinux_2_28_x86_64.whl
+ name: pyarrow
+ version: 26.0.1
+ sha256: c718bf97a92a6dea97fd1062c3b9f9e2e83cb9cc926e752289fa4ffff41738f9
+ requires_python: '>=3.11'
- pypi: https://files.pythonhosted.org/packages/d4/24/a372aaf5c9b7208e7112038812994107bc65a84cd00e0354a88c2c77a617/pytest-9.0.3-py3-none-any.whl
name: pytest
version: 9.0.3
@@ -13507,11 +23726,88 @@ packages:
- setuptools ; extra == 'dev'
- xmlschema ; extra == 'dev'
requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/d9/0e/7cd8f39c2c342d6f1037b7045cf41fe15b3558bad5497ff51ba1734df64b/parsl-2026.11.2-py3-none-any.whl
+ name: parsl
+ version: 2026.11.2
+ sha256: 347144b4360e6e633cd91e0f33914ff38ea5648d1b559d8d61a0a16698ac9c5e
+ requires_dist:
+ - pyzmq>=17.1.2
+ - typeguard>=4,<5
+ - typing-extensions>=4.6,<5
+ - dill
+ - tblib
+ - requests
+ - sortedcontainers
+ - psutil>=5.5.1
+ - setproctitle
+ - filelock>=3.13,<5
+ - sqlalchemy>=2,<2.1 ; extra == 'monitoring'
+ - pydot>=1.4.2 ; extra == 'visualization'
+ - networkx>=3.2,<3.3 ; extra == 'visualization'
+ - flask>=1.0.2 ; extra == 'visualization'
+ - flask-sqlalchemy ; extra == 'visualization'
+ - pandas>=2.2,<3 ; extra == 'visualization'
+ - plotly>=5.19,<7 ; extra == 'visualization'
+ - python-daemon ; extra == 'visualization'
+ - boto3 ; extra == 'aws'
+ - kubernetes ; extra == 'kubernetes'
+ - ipython<=8.6.0 ; extra == 'docs'
+ - nbsphinx ; extra == 'docs'
+ - sphinx>=7.4,<8 ; extra == 'docs'
+ - sphinx-rtd-theme ; extra == 'docs'
+ - google-auth ; extra == 'google-cloud'
+ - google-api-python-client ; extra == 'google-cloud'
+ - python-gssapi ; extra == 'gssapi'
+ - azure<=4 ; extra == 'azure'
+ - msrestazure ; extra == 'azure'
+ - work-queue ; extra == 'workqueue'
+ - pyyaml ; extra == 'flux'
+ - cffi ; extra == 'flux'
+ - jsonschema ; extra == 'flux'
+ - proxystore ; extra == 'proxystore'
+ - radical-pilot==1.90 ; extra == 'radical-pilot'
+ - radical-utils==1.90 ; extra == 'radical-pilot'
+ - globus-compute-sdk>=2.34.0 ; extra == 'globus-compute'
+ - globus-sdk ; extra == 'globus-transfer'
+ - sqlalchemy>=2,<2.1 ; extra == 'all'
+ - pydot>=1.4.2 ; extra == 'all'
+ - networkx>=3.2,<3.3 ; extra == 'all'
+ - flask>=1.0.2 ; extra == 'all'
+ - flask-sqlalchemy ; extra == 'all'
+ - pandas>=2.2,<3 ; extra == 'all'
+ - plotly>=5.19,<7 ; extra == 'all'
+ - python-daemon ; extra == 'all'
+ - boto3 ; extra == 'all'
+ - kubernetes ; extra == 'all'
+ - ipython<=8.6.0 ; extra == 'all'
+ - nbsphinx ; extra == 'all'
+ - sphinx>=7.4,<8 ; extra == 'all'
+ - sphinx-rtd-theme ; extra == 'all'
+ - google-auth ; extra == 'all'
+ - google-api-python-client ; extra == 'all'
+ - python-gssapi ; extra == 'all'
+ - azure<=4 ; extra == 'all'
+ - msrestazure ; extra == 'all'
+ - work-queue ; extra == 'all'
+ - pyyaml ; extra == 'all'
+ - cffi ; extra == 'all'
+ - jsonschema ; extra == 'all'
+ - proxystore ; extra == 'all'
+ - radical-pilot==1.90 ; extra == 'all'
+ - radical-utils==1.90 ; extra == 'all'
+ - globus-compute-sdk>=2.34.0 ; extra == 'all'
+ - globus-sdk ; extra == 'all'
+ requires_python: '>=3.10.0'
- pypi: https://files.pythonhosted.org/packages/db/3c/33bac158f8ab7f89b2e59426d5fe2e4f63f7ed25df84c036890172b412b5/cfgv-3.5.0-py2.py3-none-any.whl
name: cfgv
version: 3.5.0
sha256: a8dc6b26ad22ff227d2634a65cb388215ce6cc96bbcc5cfde7641ae87e8dacc0
requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/de/48/999f6e30323e2e95a4439180b62f6308023970e4a37d31497080ea2a1a78/pyarrow-26.0.1-cp314-cp314-macosx_12_0_arm64.whl
+ name: pyarrow
+ version: 26.0.1
+ sha256: 15435b595c14583f6ac8495c3ef89ac3fed6bc94f168467bfd3b6ba53ad3a643
+ requires_python: '>=3.11'
- pypi: https://files.pythonhosted.org/packages/e0/f9/0595336914c5619e5f28a1fb793285925a8cd4b432c9da0a987836c7f822/shellingham-1.5.4-py2.py3-none-any.whl
name: shellingham
version: 1.5.4
@@ -13547,6 +23843,50 @@ packages:
- uv>=0.5.23
- virtualenv>=21
requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/e7/36/5ee6e05c9bd427237b11b3937ad82bb8ad2752d72c6969314590dd0c2f6e/psutil-7.2.2-cp36-abi3-macosx_10_9_x86_64.whl
+ name: psutil
+ version: 7.2.2
+ sha256: ed0cace939114f62738d808fdcecd4c869222507e266e574799e9c0faa17d486
+ requires_dist:
+ - psleak ; extra == 'dev'
+ - pytest ; extra == 'dev'
+ - pytest-instafail ; extra == 'dev'
+ - pytest-xdist ; extra == 'dev'
+ - setuptools ; extra == 'dev'
+ - abi3audit ; extra == 'dev'
+ - black ; extra == 'dev'
+ - check-manifest ; extra == 'dev'
+ - coverage ; extra == 'dev'
+ - packaging ; extra == 'dev'
+ - pylint ; extra == 'dev'
+ - pyperf ; extra == 'dev'
+ - pypinfo ; extra == 'dev'
+ - pytest-cov ; extra == 'dev'
+ - requests ; extra == 'dev'
+ - rstcheck ; extra == 'dev'
+ - ruff ; extra == 'dev'
+ - sphinx ; extra == 'dev'
+ - sphinx-rtd-theme ; extra == 'dev'
+ - toml-sort ; extra == 'dev'
+ - twine ; extra == 'dev'
+ - validate-pyproject[all] ; extra == 'dev'
+ - virtualenv ; extra == 'dev'
+ - vulture ; extra == 'dev'
+ - wheel ; extra == 'dev'
+ - colorama ; os_name == 'nt' and extra == 'dev'
+ - pyreadline3 ; os_name == 'nt' and extra == 'dev'
+ - pywin32 ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'dev'
+ - wheel ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'dev'
+ - wmi ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'dev'
+ - psleak ; extra == 'test'
+ - pytest ; extra == 'test'
+ - pytest-instafail ; extra == 'test'
+ - pytest-xdist ; extra == 'test'
+ - setuptools ; extra == 'test'
+ - pywin32 ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'test'
+ - wheel ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'test'
+ - wmi ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'test'
+ requires_python: '>=3.6'
- pypi: https://files.pythonhosted.org/packages/e8/3d/1087453384dbde46a8c7f9356eead2c58be8a7bf156bca40243377c85715/more_itertools-11.1.0-py3-none-any.whl
name: more-itertools
version: 11.1.0
@@ -13596,6 +23936,54 @@ packages:
- pytest-enabler>=3.4 ; extra == 'enabler'
- pytest-mypy>=1.0.1 ; platform_python_implementation != 'PyPy' and extra == 'type'
requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/f9/f7/77dfbdccd25561e6a800ce86266a82af9bb6e4e408881b6600916ce8ccca/mdanalysis-2.11.0-cp314-cp314-macosx_10_15_x86_64.whl
+ name: mdanalysis
+ version: 2.11.0
+ sha256: 7ae0438b14a461012fe777cc5383f4fe295b604bfbb94d27dbf1d91427aa81f8
+ requires_dist:
+ - numpy>=1.26.0
+ - griddataformats>=0.4.0
+ - mmtf-python>=1.0.0
+ - joblib>=0.12
+ - scipy>=1.5.0
+ - matplotlib>=1.5.1
+ - tqdm>=4.43.0
+ - threadpoolctl
+ - packaging
+ - filelock
+ - mda-xdrlib
+ - netcdf4>=1.0 ; extra == 'extra-formats'
+ - h5py>=2.10 ; extra == 'extra-formats'
+ - chemfiles>=0.10 ; extra == 'extra-formats'
+ - parmed ; extra == 'extra-formats'
+ - pooch ; extra == 'extra-formats'
+ - pyedr>=0.7.0 ; extra == 'extra-formats'
+ - pytng>=0.2.3 ; extra == 'extra-formats'
+ - gsd>3.0.0 ; extra == 'extra-formats'
+ - gemmi>=0.7.5 ; extra == 'extra-formats'
+ - rdkit>=2022.9.1 ; extra == 'extra-formats'
+ - imdclient>=0.2.2 ; extra == 'extra-formats'
+ - biopython>=1.80 ; extra == 'analysis'
+ - seaborn ; extra == 'analysis'
+ - scikit-learn ; extra == 'analysis'
+ - tidynamics>=1.0.0 ; extra == 'analysis'
+ - networkx>=2.0 ; extra == 'analysis'
+ - waterdynamics ; extra == 'analysis'
+ - pathsimanalysis ; extra == 'analysis'
+ - mdahole2 ; extra == 'analysis'
+ - sphinx ; extra == 'doc'
+ - sphinx-sitemap ; extra == 'doc'
+ - mdanalysis-sphinx-theme>=1.3.0 ; extra == 'doc'
+ - sphinxcontrib-bibtex ; extra == 'doc'
+ - pybtex ; extra == 'doc'
+ - pybtex-docutils ; extra == 'doc'
+ - dask ; extra == 'parallel'
+ requires_python: '>=3.11'
+- pypi: https://files.pythonhosted.org/packages/fa/e8/0485850748dfdba9443f4151c7b2442cfa4987ba6cd871038eb5d6b8eca9/wcwidth-0.9.4-cp310-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
+ name: wcwidth
+ version: 0.9.4
+ sha256: b185c8b927b23af2721be1783499d1cfa5c028b098b0858951b4ae224477f1c2
+ requires_python: '>=3.9'
- pypi: https://files.pythonhosted.org/packages/fb/f0/2dc88e842077719d7384d86cc47403e5102810492b33680e7dadcee64cd8/setproctitle-1.3.7-cp312-cp312-macosx_10_13_universal2.whl
name: setproctitle
version: 1.3.7
diff --git a/pyproject.toml b/pyproject.toml
index 8a7fa27..7facfc9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -119,10 +119,28 @@ docs-dev = { cmd = "bun run dev", cwd = "docs", depends-on = ["docs-fumapy"] }
docs-build = { cmd = "bun run build", cwd = "docs", depends-on = ["docs-fumapy"] }
docs-generate = { cmd = "bun run docs:generate", cwd = "docs", depends-on = ["docs-fumapy"] }
+# GROMACS >= 2026 (ships amber14sb.ff) for the open-source `amber` parametrization.
+# Kept out of the default solve group so CI and existing environments are not
+# re-solved. Packmol is listed explicitly because newer openff-interchange
+# releases no longer pull in the binary.
+[tool.pixi.feature.gmx.dependencies]
+gromacs = { version = ">=2026", build = "nompi_h*" }
+packmol = "*"
+
+[tool.pixi.feature.gmx-cuda]
+platforms = ["linux-64"]
+system-requirements = { cuda = "12" }
+
+[tool.pixi.feature.gmx-cuda.dependencies]
+gromacs = { version = ">=2026", build = "nompi_cuda_h*" }
+packmol = "*"
+
[tool.pixi.environments]
default = { solve-group = "default" }
dev = { features = ["dev"], solve-group = "default" }
docs = { features = ["docs"], solve-group = "default" }
+gmx = { features = ["gmx"] }
+gmx-cuda = { features = ["gmx-cuda"] }
# --- Ruff linter/formatter ---------------------------------------------------