Change implicitSolentKappa to implicitSolventSaltConc and convert to

implicitSolventKappa the same (black-magic) way that Amber does. I have never
been able to reproduce the prefactor used to convert to kappa in Amber... sigh.

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

@@ -31,6 +31,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
+from math import sqrt
 from simtk.openmm.app import Topology
 from simtk.openmm.app import PDBFile
 from simtk.openmm.app.internal import amber_file_parser
@@ -142,7 +143,7 @@ class AmberPrmtopFile(object):
 
     def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
                      constraints=None, rigidWater=True, implicitSolvent=None,
-                     implicitSolventKappa=0.0*(1/unit.nanometer),
+                     implicitSolventSaltConc=0.0*(unit.moles/unit.liter),
                      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.
@@ -155,7 +156,8 @@ 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.
-         - implicitSolventKappa (float=0.0*1/unit.nanometer) The Debye-screening parameter corresponding to ionic strength used for implicit solvent
+         - implicitSolventSaltConc (float=0.0*unit.moles/unit.liter) The salt concentration for GB 
+                                             calculations (modelled as a debye screening parameter)
          - 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
@@ -197,6 +199,16 @@ class AmberPrmtopFile(object):
             implicitString = 'GBn2'
         else:
             raise ValueError('Illegal value for implicit solvent model')
+        # Use the conversion of ionic strength to kappa used by Amber (external
+        # dielectric of 78.5 -- it's unclear where the 0.10806 comes from
+        # though, although code comments in Amber say 'assuming M salt
+        # concentration, T=298.15, and epsext=78.5')
+        if unit.is_quantity(implicitSolventSaltConc):
+            implicitSolventSaltConc = implicitSolventSaltConc.value_in_unit(unit.moles/unit.liter)
+        # 0.73 to account for ion exclusions. The Amber Debye screening length
+        # units will be in 1/angstrom given these units. Not a pretty way to do
+        # this...
+        implicitSolventKappa = 0.73 * sqrt(0.10806 * implicitSolventSaltConc) / unit.angstrom
         sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString, nonbondedCutoff=nonbondedCutoff,
                                                  nonbondedMethod=methodMap[nonbondedMethod], flexibleConstraints=False, gbmodel=implicitString,
                                                  soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, implicitSolventKappa=implicitSolventKappa,