System setup with espaloma (#11)

* Separate solvation and parameter assignment

* Add espaloma model

* Parametrize solute with espaloma

* Linters

devtools/conda-envs/proteinbenchmark-espaloma.yaml

@@ -0,0 +1,35 @@
+name: openff-proteinbenchmark-espaloma
+channels:
+  - conda-forge
+  - openeye
+  - defaults
+dependencies:
+  - black
+  - click
+  - isort
+  - pip
+  - python
+
+  # System setup
+  - pip:
+    - git+https://github.com/deGrootLab/pmx@develop
+    - git+https://github.com/Electrostatics/pdb2pqr@master#egg=pdb2pqr
+
+  # MM calculations
+  - ambertools
+  - cudatoolkit
+  - espaloma>=0.3.2
+  - openeye-toolkits
+  - openff-forcefields
+  - openff-toolkit>=0.13.0
+  - openff-units
+  - openmm>=8.0.0
+  - openmmforcefields>=0.12.0
+  - openmmtools
+
+  # Analysis
+  - loos
+  - pandas
+  - pymol-open-source
+  - seaborn
+

devtools/conda-envs/proteinbenchmark.yaml

@@ -14,7 +14,6 @@ dependencies:
   - pip:
     - git+https://github.com/deGrootLab/pmx@develop
     - git+https://github.com/Electrostatics/pdb2pqr@master#egg=pdb2pqr
-    - git+https://github.com/openmm/openmmforcefields@main
 
   # MM calculations
   - ambertools
@@ -24,6 +23,7 @@ dependencies:
   - openff-toolkit>=0.13.0
   - openff-units
   - openmm>=8.0.0
+  - openmmforcefields>=0.12.0
   - openmmtools
 
   # Analysis

proteinbenchmark/force_fields.py

@@ -8,6 +8,10 @@
 # List of force fields with force field XML file, water model, and water model
 # XML file
 force_fields = {
+    "espaloma-0.3.2-tip3p": {
+        "force_field_file": Path(ff_directory, "espaloma-0.3.2.pt"),
+        "water_model": "tip3p",
+    },
     "ff14sb-opc": {
         "force_field_file": Path(
             ff_directory, "nerenberg_ff14sb_c0ala_c0gly_c0val.xml"

proteinbenchmark/protein_system.py

@@ -15,6 +15,7 @@
 from proteinbenchmark.openmm_simulation import OpenMMSimulation
 from proteinbenchmark.simulation_parameters import *
 from proteinbenchmark.system_setup import (
+    assign_parameters,
     build_initial_coordinates,
     minimize_gmx,
     minimize_openmm,
@@ -168,8 +169,8 @@ def setup(self):
                     'contain one of "aa_sequence" or "initial_pdb"'
                 )
 
-        # Solvate, add ions, and construct parametrized system
-        if not exists_and_not_empty(self.parametrized_system):
+        # Solvate and add ions using Amber ff14SB as a reference force field
+        if not exists_and_not_empty(solvated_pdb):
             print(f"Solvating system {self.system_name}")
 
             # Get parameters for solvation and constructing OpenMM system
@@ -191,8 +192,29 @@ def setup(self):
                 vdw_switch_width = VDW_SWITCH_WIDTH
 
             solvate(
-                simulation_platform=self.simulation_platform,
                 ionic_strength=self.target_parameters["ionic_strength"],
+                protonated_pdb_file=self.protonated_pdb,
+                solvated_pdb_file=solvated_pdb,
+                water_model=self.water_model,
+                solvent_padding=solvent_padding,
+            )
+
+        # Construct parametrized system
+        if not exists_and_not_empty(self.parametrized_system):
+            print(f"Parametrizing system {self.system_name}")
+
+            if "nonbonded_cutoff" in self.target_parameters:
+                nonbonded_cutoff = self.target_parameters["nonbonded_cutoff"]
+            else:
+                nonbonded_cutoff = NONBONDED_CUTOFF
+
+            if "vdw_switch_width" in self.target_parameters:
+                vdw_switch_width = self.target_parameters["vdw_switch_width"]
+            else:
+                vdw_switch_width = VDW_SWITCH_WIDTH
+
+            assign_parameters(
+                simulation_platform=self.simulation_platform,
                 nonbonded_cutoff=nonbonded_cutoff,
                 vdw_switch_width=vdw_switch_width,
                 protonated_pdb_file=self.protonated_pdb,
@@ -201,7 +223,6 @@ def setup(self):
                 water_model=self.water_model,
                 force_field_file=self.force_field_file,
                 water_model_file=self.water_model_file,
-                solvent_padding=solvent_padding,
                 setup_prefix=self.setup_prefix,
             )