kappa -> implicitSolventKappa

wrappers/python/simtk/openmm/app/amberprmtopfile.py

@@ -142,7 +142,7 @@ class AmberPrmtopFile(object):
 
     def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
                      constraints=None, rigidWater=True, implicitSolvent=None,
-                     kappa=0.0, soluteDielectric=1.0, solventDielectric=78.5,
+                     implicitSolventKappa=0.0, soluteDielectric=1.0, solventDielectric=78.5,
                      removeCMMotion=True, hydrogenMass=None, ewaldErrorTolerance=0.0005):
         """Construct an OpenMM System representing the topology described by this prmtop file.
 
@@ -154,7 +154,7 @@ class AmberPrmtopFile(object):
            Allowed values are None, HBonds, AllBonds, or HAngles.
          - rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
          - implicitSolvent (object=None) If not None, the implicit solvent model to use.  Allowed values are HCT, OBC1, OBC2, GBn, or GBn2.
-         - kappa (float=0.0) The Debye-screening parameter corresponding to ionic strength used for implicit solvent
+         - implicitSolventKappa (float=0.0) The Debye-screening parameter corresponding to ionic strength used for implicit solvent
          - soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model.
          - solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model.
          - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
@@ -198,7 +198,7 @@ class AmberPrmtopFile(object):
             raise ValueError('Illegal value for implicit solvent model')
         sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString, nonbondedCutoff=nonbondedCutoff,
                                                  nonbondedMethod=methodMap[nonbondedMethod], flexibleConstraints=False, gbmodel=implicitString,
-                                                 soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, kappa=kappa,
+                                                 soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, implicitSolventKappa=implicitSolventKappa,
                                                  rigidWater=rigidWater, elements=self.elements)
         if hydrogenMass is not None:
             for atom1, atom2 in self.topology.bonds():

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -566,7 +566,7 @@ class PrmtopLoader(object):
 #=============================================================================================
 
 def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5,
-                    kappa=0.0, nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=None, scnb=None, mm=None, verbose=False,
+                    implicitSolventKappa=0.0, nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=None, scnb=None, mm=None, verbose=False,
                     EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True, elements=None):
     """
     Create an OpenMM System from an Amber prmtop file.
@@ -580,7 +580,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
       gbmodel (String) - if 'OBC', OBC GBSA will be used; if 'GBVI', GB/VI will be used (default: None)
       soluteDielectric (float) - The solute dielectric constant to use in the implicit solvent model (default: 1.0)
       solventDielectric (float) - The solvent dielectric constant to use in the implicit solvent model (default: 78.5)
-      kappa (float) - The Debye screening parameter corresponding to implicit solvent ionic strength
+      implicitSolventKappa (float) - The Debye screening parameter corresponding to implicit solvent ionic strength
       nonbondedCutoff (float) - if specified, will set nonbondedCutoff (default: None)
       scnb (float) - 1-4 Lennard-Jones scaling factor (default: taken from prmtop or 1.2 if not present there)
       scee (float) - 1-4 electrostatics scaling factor (default: taken from prmtop or 2.0 if not present there)
@@ -868,20 +868,20 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
                 cutoff = cutoff.value_in_unit(units.nanometers)
         gb_parms = prmtop.getGBParms(gbmodel, elements)
         if gbmodel == 'HCT':
-            gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff, kappa)
+            gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
         elif gbmodel == 'OBC1':
-            gb = customgb.GBSAOBC1Force(solventDielectric, soluteDielectric, 'ACE', cutoff, kappa)
+            gb = customgb.GBSAOBC1Force(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
         elif gbmodel == 'OBC2':
-            if kappa > 0:
-                gb = customgb.GBSAOBC2Force(solventDielectric, soluteDielectric, 'ACE', cutoff, kappa)
+            if implicitSolventKappa > 0:
+                gb = customgb.GBSAOBC2Force(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
             else:
                 gb = mm.GBSAOBCForce()
                 gb.setSoluteDielectric(soluteDielectric)
                 gb.setSolventDielectric(solventDielectric)
         elif gbmodel == 'GBn':
-            gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, 'ACE', cutoff, kappa)
+            gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
         elif gbmodel == 'GBn2':
-            gb = customgb.GBSAGBn2Force(solventDielectric, soluteDielectric, 'ACE', cutoff, kappa)
+            gb = customgb.GBSAGBn2Force(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
         else:
             raise Exception("Illegal value specified for implicit solvent model")
         for iAtom in range(prmtop.getNumAtoms()):