Generalize LysozymeImplicit
@@ -3415,11 +3415,16 @@ class LysozymeImplicit(TestSystem):
Examples
--------
+ Create T4 lysozyme L99A with p-xylene ligand using OBC1 GBSA.
>>> lysozyme = LysozymeImplicit()
>>> (system, positions) = lysozyme.system, lysozyme.positions
+
+ Create T4 lysozyme L99A with p-xylene ligand using OBC2 GBSA.
+ >>> lysozyme = LysozymeImplicit(implicitSolvent=app.OBC2)
+
"""
- def __init__(self, constraints=app.HBonds, implicitSolvent=app.OBC1, **kwargs):
+ def __init__(self, **kwargs):
TestSystem.__init__(self, **kwargs)
@@ -3428,7 +3433,13 @@ class LysozymeImplicit(TestSystem):
# Initialize system.
prmtop = app.AmberPrmtopFile(prmtop_filename)
- system = prmtop.createSystem(implicitSolvent=app.OBC1, constraints=app.HBonds, nonbondedCutoff=None)
+
+ defaults = { 'implicitSolvent' : app.OBC1,
+ 'constraints' : app.HBonds,
+ 'nonbondedMethod' : app.NoCutoff,
+ }
+ create_system_kwargs = handle_kwargs(prmtop.createSystem, defaults, kwargs)
+ system = prmtop.createSystem(**create_system_kwargs)
# Extract topology
self.topology = prmtop.topology
@@ -3439,7 +3450,6 @@ class LysozymeImplicit(TestSystem):
self.system, self.positions = system, positions
-
class SrcImplicit(TestSystem):
"""Src kinase in implicit AMBER 99sb-ildn with OBC GBSA solvent.
