Fix for issue choderalab#539

prmtop and incrd updated from https://ambermd.org/Amber20_Benchmark_Suite.tar.gz
mjw99 · May 29, 2022 · 5f6e6b9 · 5f6e6b9
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diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -13,7 +13,6 @@ dependencies:
   - numba
   - numpy
   - openmm >=7.5.0
-  - parmed
   - pip
   - pymbar
   - python

diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
@@ -21,7 +21,6 @@ requirements:
     - numpy
     - scipy
     - openmm >=7.3.1
-    - parmed
     - mdtraj
     - netcdf4 >=1.4.2 # after bugfix: "always return masked array by default, even if there are no masked values"
     - libnetcdf >=4.6.2 # workaround for libssl issues

diff --git a/docs/environment.yml b/docs/environment.yml
@@ -9,7 +9,6 @@ dependencies:
     - cython
     - numpy
     - scipy
-    - parmed
     - mdtraj
     - numpydoc
     - netcdf4 >=1.4.2 # after bugfix: "always return masked array by default, even if there are no masked values"

diff --git a/openmmtools/data/dhfr/JAC.inpcrd b/openmmtools/data/dhfr/JAC.inpcrd
diff --git a/openmmtools/data/dhfr/JAC.prmtop b/openmmtools/data/dhfr/JAC.prmtop
diff --git a/openmmtools/data/dhfr/inpcrd b/openmmtools/data/dhfr/inpcrd
diff --git a/openmmtools/data/dhfr/prmtop b/openmmtools/data/dhfr/prmtop
diff --git a/openmmtools/testsystems.py b/openmmtools/testsystems.py
@@ -3888,17 +3888,11 @@ def __init__(self, constraints=app.HBonds, rigid_water=True, nonbondedCutoff=DEF
 
         TestSystem.__init__(self, **kwargs)
 
-        try:
-            from parmed.amber import AmberParm
-        except ImportError as e:
-            print("DHFR test system requires Parmed (`import parmed`).")
-            raise(e)
-
-        prmtop_filename = get_data_filename("data/dhfr/prmtop")
-        crd_filename = get_data_filename("data/dhfr/inpcrd")
+        prmtop_filename = get_data_filename("data/dhfr/JAC.prmtop")
+        crd_filename = get_data_filename("data/dhfr/JAC.inpcrd")
 
         # Initialize system.
-        self.prmtop = AmberParm(prmtop_filename, crd_filename)
+        self.prmtop = app.AmberPrmtopFile(prmtop_filename)
         system = self.prmtop.createSystem(constraints=constraints, nonbondedMethod=nonbondedMethod, rigidWater=rigid_water, nonbondedCutoff=nonbondedCutoff, hydrogenMass=hydrogenMass)
 
         # Extract topology
@@ -3913,10 +3907,12 @@ def __init__(self, constraints=app.HBonds, rigid_water=True, nonbondedCutoff=DEF
             forces['NonbondedForce'].setUseSwitchingFunction(True)
             forces['NonbondedForce'].setSwitchingDistance(nonbondedCutoff - switch_width)
 
-        positions = self.prmtop.positions
+        # Read positions.
+        inpcrd = app.AmberInpcrdFile(crd_filename)
+        positions = inpcrd.getPositions(asNumpy=True)
 
         # Set box vectors.
-        box_vectors = self.prmtop.box_vectors
+        box_vectors = inpcrd.getBoxVectors(asNumpy=True)
         system.setDefaultPeriodicBoxVectors(box_vectors[0], box_vectors[1], box_vectors[2])
 
         self.system, self.positions = system, positions