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Merge pull request #221 from OpenFreeEnergy/adapt_septop_restraint_settings
Adapt host min/max distance restraints + fix broken notebook
2 parents 8afe723 + 43049c6 commit aba2508

4 files changed

Lines changed: 90 additions & 66 deletions

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‎abfe_tutorial/abfe_json/toluene.json‎

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‎abfe_tutorial/abfe_tutorial.ipynb‎

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@@ -133,7 +133,7 @@
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"Generating charges: 100%|█████████████████████████| 1/1 [00:00<00:00, 1.53it/s]\n"
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"Generating charges: 100%|█████████████████████████| 1/1 [00:00<00:00, 1.42it/s]\n"
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]
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}
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],
@@ -231,17 +231,33 @@
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"execution_count": 7,
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"id": "c31c712b-4844-477b-8aa4-ded6f0c8ca5f",
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Users/hannahbaumann/miniforge3/envs/openfe_dev/lib/python3.12/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
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"\n",
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"Due to the on going maintenance burden of keeping command line application\n",
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"wrappers up to date, we have decided to deprecate and eventually remove these\n",
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"modules.\n",
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"\n",
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"We instead now recommend building your command line and invoking it directly\n",
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"with the subprocess module.\n",
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" warnings.warn(\n"
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]
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}
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],
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"source": [
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"from openfe.protocols.openmm_afe import AbsoluteBindingProtocol;"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"execution_count": 8,
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"id": "fb839094",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"execution_count": 9,
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"id": "8b99f77f-c70c-436d-b4eb-fb462a4b043e",
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"metadata": {
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"scrolled": true
@@ -262,7 +278,7 @@
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"output_type": "stream",
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"text": [
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"{'alchemical_settings': {},\n",
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" 'complex_equil_output_settings': {'checkpoint_interval': <Quantity(250.0, 'picosecond')>,\n",
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" 'complex_equil_output_settings': {'checkpoint_interval': <Quantity(1.0, 'nanosecond')>,\n",
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" 'checkpoint_storage_filename': 'checkpoint.chk',\n",
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" 'equil_npt_structure': 'equil_npt_structure.pdb',\n",
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" 'equil_nvt_structure': 'equil_nvt_structure.pdb',\n",
@@ -367,7 +383,7 @@
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" 0.9,\n",
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" 0.95,\n",
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" 1.0]},\n",
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" 'complex_output_settings': {'checkpoint_interval': <Quantity(250.0, 'picosecond')>,\n",
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" 'complex_output_settings': {'checkpoint_interval': <Quantity(1.0, 'nanosecond')>,\n",
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" 'checkpoint_storage_filename': 'complex_checkpoint.nc',\n",
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" 'forcefield_cache': 'db.json',\n",
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" 'output_filename': 'complex.nc',\n",
@@ -424,11 +440,11 @@
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" 'dssp_filter': True,\n",
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" 'guest_atoms': None,\n",
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" 'host_atoms': None,\n",
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" 'host_max_distance': <Quantity(3, 'nanometer')>,\n",
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" 'host_min_distance': <Quantity(1, 'nanometer')>,\n",
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" 'host_max_distance': <Quantity(3.0, 'nanometer')>,\n",
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" 'host_min_distance': <Quantity(1.0, 'nanometer')>,\n",
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" 'host_selection': 'backbone',\n",
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" 'rmsf_cutoff': <Quantity(0.1, 'nanometer')>},\n",
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" 'solvent_equil_output_settings': {'checkpoint_interval': <Quantity(250.0, 'picosecond')>,\n",
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" 'solvent_equil_output_settings': {'checkpoint_interval': <Quantity(1.0, 'nanosecond')>,\n",
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" 'checkpoint_storage_filename': 'checkpoint.chk',\n",
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" 'equil_npt_structure': 'equil_npt_structure.pdb',\n",
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" 'equil_nvt_structure': 'equil_nvt_structure.pdb',\n",
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" 0.77,\n",
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" 0.85,\n",
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" 1.0]},\n",
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" 'solvent_output_settings': {'checkpoint_interval': <Quantity(250.0, 'picosecond')>,\n",
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" 'solvent_output_settings': {'checkpoint_interval': <Quantity(1.0, 'nanosecond')>,\n",
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" 'checkpoint_storage_filename': 'solvent_checkpoint.nc',\n",
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" 'forcefield_cache': 'db.json',\n",
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" 'output_filename': 'solvent.nc',\n",
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"execution_count": 11,
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"id": "55067780-d228-4661-8c1e-5cb0217fd2dc",
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"metadata": {},
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"outputs": [],
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"source": [
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"from openff.units import unit\n",
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"\n",
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"# change the values\n",
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"# Run only a single repeat\n",
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"settings.protocol_repeats = 1\n",
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"settings.solvent_simulation_settings.equilibration_length = 10 * unit.picosecond\n",
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"settings.solvent_simulation_settings.production_length = 500 * unit.picosecond\n",
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"settings.complex_simulation_settings.equilibration_length = 10 * unit.picosecond\n",
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"settings.complex_simulation_settings.production_length = 500 * unit.picosecond\n",
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"# Change the min and max distance between protein and ligand atoms for Boresch restraints to avoid periodicity issues\n",
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"settings.restraint_settings.host_min_distance = 0.5 * unit.nanometer\n",
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"settings.restraint_settings.host_max_distance = 1.5 * unit.nanometer\n",
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"\n",
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"settings.engine_settings.compute_platform = 'CUDA'"
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]
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},
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},
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{
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"cell_type": "code",
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},
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"cell_type": "code",
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},
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{
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"cell_type": "code",
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"id": "b69efbcd-b888-4afc-a33e-01860889f408",
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"metadata": {},
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"outputs": [],
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"outputs": [
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Users/hannahbaumann/miniforge3/envs/openfe_dev/lib/python3.12/site-packages/gufe/transformations/transformation.py:124: DeprecationWarning: use of this method is deprecated; instead use `to_json`\n",
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" warnings.warn(\n"
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]
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}
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],
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"source": [
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"import pathlib\n",
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"# first we create the directory\n",
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},
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{
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"cell_type": "code",
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"execution_count": 15,
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" 'pint_unit_registry': 'openff_units'}"
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"estimate"
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"metadata": {},
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"source": []
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"metadata": {

‎cookbook/choose_protocol.ipynb‎

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" 'softcore_alpha': 0.85,\n",
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" 'turn_off_core_unique_exceptions': False,\n",
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" 'use_dispersion_correction': False},\n",
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" 'engine_settings': {'compute_platform': None},\n",
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" 'engine_settings': {'compute_platform': None, 'gpu_device_index': None},\n",
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" 'forcefield_settings': {'constraints': 'hbonds',\n",
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" 'forcefields': ['amber/ff14SB.xml',\n",
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" 'amber/tip3p_standard.xml',\n",
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" 'nonbonded_method': 'PME',\n",
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" 'rigid_water': True,\n",
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" 'small_molecule_forcefield': 'openff-2.1.1'},\n",
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" 'integrator_settings': {'barostat_frequency': <Quantity(25, 'timestep')>,\n",
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" 'integrator_settings': {'barostat_frequency': <Quantity(25.0, 'timestep')>,\n",
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" 'constraint_tolerance': 1e-06,\n",
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" 'langevin_collision_rate': <Quantity(1.0, '1 / picosecond')>,\n",
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" 'n_restart_attempts': 20,\n",
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" 'reassign_velocities': False,\n",
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" 'remove_com': False,\n",
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" 'timestep': <Quantity(4, 'femtosecond')>},\n",
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" 'timestep': <Quantity(4.0, 'femtosecond')>},\n",
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" 'lambda_settings': {'lambda_functions': 'default', 'lambda_windows': 11},\n",
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" 'output_settings': {'checkpoint_interval': <Quantity(250, 'picosecond')>,\n",
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" 'output_settings': {'checkpoint_interval': <Quantity(1.0, 'nanosecond')>,\n",
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" 'checkpoint_storage_filename': 'checkpoint.chk',\n",
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" 'forcefield_cache': 'db.json',\n",
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" 'output_filename': 'simulation.nc',\n",
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" 'output_indices': 'not water',\n",
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" 'output_structure': 'hybrid_system.pdb'},\n",
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" 'output_structure': 'hybrid_system.pdb',\n",
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" 'positions_write_frequency': <Quantity(100.0, 'picosecond')>,\n",
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" 'velocities_write_frequency': None},\n",
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" 'partial_charge_settings': {'nagl_model': None,\n",
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" 'minimization_steps': 5000,\n",
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" 'n_replicas': 11,\n",
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" 'production_length': <Quantity(5.0, 'nanosecond')>,\n",
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" 'real_time_analysis_interval': <Quantity(250, 'picosecond')>,\n",
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" 'real_time_analysis_minimum_time': <Quantity(500, 'picosecond')>,\n",
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" 'real_time_analysis_interval': <Quantity(250.0, 'picosecond')>,\n",
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" 'real_time_analysis_minimum_time': <Quantity(500.0, 'picosecond')>,\n",
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" 'sams_flatness_criteria': 'logZ-flatness',\n",
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" 'sams_gamma0': 1.0,\n",
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" 'time_per_iteration': <Quantity(1, 'picosecond')>},\n",
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" 'solvation_settings': {'solvent_model': 'tip3p',\n",
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" 'time_per_iteration': <Quantity(1.0, 'picosecond')>},\n",
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" 'solvation_settings': {'box_shape': 'cube',\n",
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" 'box_size': None,\n",
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" 'box_vectors': None,\n",
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" 'number_of_solvent_molecules': None,\n",
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" 'solvent_model': 'tip3p',\n",
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" 'solvent_padding': <Quantity(1.2, 'nanometer')>},\n",
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" 'thermo_settings': {'ph': None,\n",
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" 'pressure': <Quantity(0.986923267, 'standard_atmosphere')>,\n",
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" solvation_settings=equil_rfe_settings.OpenMMSolvationSettings(\n",
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" solvent_model='tip3p', # Solvent model to generate starting coords\n",
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" solvent_padding=1.2 * unit.nm, # Total distance between periodic image starting coords\n",
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" box_shape = 'cube', # Cubic water box\n",
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" box_size = None, # Size of the water box\n",
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" box_vectors = None, # Box vectors\n",
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" number_of_solvent_molecules = None, # Number of solvent molecules\n",
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" ),\n",
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" partial_charge_settings=equil_rfe_settings.OpenFFPartialChargeSettings(\n",
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" partial_charge_method='am1bcc', # Partial charge method applied - am1bcc\n",
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" checkpoint_storage_filename='checkpoint.chk', # Filename for simulation checkpoints\n",
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" forcefield_cache='db.json', # Cache for small molecule residue templates\n",
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" output_indices='not water', # Do not save water positions\n",
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" checkpoint_interval=250 * unit.ps, # Save a checkpoint every 250 picoseconds\n",
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" checkpoint_interval=1 * unit.ns, # Save a checkpoint every 1 nanoseconds\n",
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" positions_write_frequency=100.0 * unit.picosecond, # Save position every 100 picoseconds\n",
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" velocities_write_frequency = None, # Don't save velocities\n",
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")"
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]
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.4"
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"version": "3.12.10"
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {

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