Take the 1-4 non-bonded scaling parameters from the Amber topology files if

present, defaulting to 1.2 (SCEE) and 2.0 (SCNB) if they're not present. If
values for scee and scnb are provided to readAmberSystem they will override any
values in the topology file, but a warning will be printed (since ignoring the
scaling parameters in the topology file really changes the force field).

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

@@ -41,9 +41,9 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 
 import os
 import os.path
-import copy
 import re
 import math
+import warnings
 
 try:
     import numpy
@@ -431,12 +431,22 @@ class PrmtopLoader(object):
             if int(dihedralPointers[ii+2])>0 and int(dihedralPointers[ii+3])>0:
                 iAtom = int(dihedralPointers[ii])//3
                 lAtom = int(dihedralPointers[ii+3])//3
+                iidx = int(dihedralPointers[ii+4]) - 1
                 chargeProd = charges[iAtom]*charges[lAtom]
                 (rVdwI, epsilonI) = nonbondTerms[iAtom]
                 (rVdwL, epsilonL) = nonbondTerms[lAtom]
                 rMin = (rVdwI+rVdwL)
                 epsilon = math.sqrt(epsilonI*epsilonL)
-                 returnList.append((iAtom, lAtom, chargeProd, rMin, epsilon))
+                try:
+                    iScee = float(self._raw_data["SCEE_SCALE_FACTOR"][iidx])
+                except KeyError:
+                    iScee = 1.2
+                try:
+                    iScnb = float(self._raw_data["SCNB_SCALE_FACTOR"][iidx])
+                except KeyError:
+                    iScnb = 2.0
+
+                returnList.append((iAtom, lAtom, chargeProd, rMin, epsilon, iScee, iScnb))
         return returnList
 
     def getExcludedAtoms(self):
@@ -502,11 +512,15 @@ class PrmtopLoader(object):
                 units.Quantity(y, units.angstrom),
                 units.Quantity(z, units.angstrom))
 
+    @property
+    def has_scee_scnb(self):
+        return ("SCEE_SCALE_FACTOR" in self._raw_data and "SCNB_SCALE_FACTOR" in self._raw_data)
+
 #=============================================================================================
 # AMBER System builder (based on, but not identical to, systemManager from 'zander')
 #=============================================================================================
 
-def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5, nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=1.2, scnb=2.0, mm=None, verbose=False, EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True):
+def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5, nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=None, scnb=None, mm=None, verbose=False, EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True):
     """
     Create an OpenMM System from an Amber prmtop file.
 
@@ -520,8 +534,8 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
       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)
       nonbondedCutoff (float) - if specified, will set nonbondedCutoff (default: None)
-      scnb (float) - 1-4 Lennard-Jones scaling factor (default: 1.2)
-      scee (float) - 1-4 electrostatics scaling factor (default: 2.0)
+      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)
       mm - if specified, this module will be used in place of pyopenmm (default: None)
       verbose (boolean) - if True, print out information on progress (default: False)
       flexibleConstraints (boolean) - if True, flexible bonds will be added in addition ot constrained bonds
@@ -571,6 +585,10 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
     if prmtop.getIfBox()>1:
         raise Exception("only standard periodic boxes are currently supported")
 
+    if prmtop.has_scee_scnb and (scee is not None or scnb is not None):
+        warnings.warn("1-4 scaling parameters in topology file are being ignored. "
+            "This is not recommended unless you know what you are doing.")
+
     # Use pyopenmm implementation of OpenMM by default.
     if mm is None:
         mm = simtk.openmm
@@ -615,7 +633,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
     if shake == 'h-angles':
         numConstrainedBonds = system.getNumConstraints()
         atomConstraints = [[]]*system.getNumParticles()
-        for i in range(system.getNumConstraints()):
+        for i in range(numConstrainedBonds):
             c = system.getConstraintParameters(i)
             distance = c[2].value_in_unit(units.nanometer)
             atomConstraints[c[0]].append((c[1], distance))
@@ -712,9 +730,12 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
     # Add 1-4 Interactions
     excludedAtomPairs = set()
     sigmaScale = 2**(-1./6.)
-    for (iAtom, lAtom, chargeProd, rMin, epsilon) in prmtop.get14Interactions():
-        chargeProd /= scee
-        epsilon /= scnb
+    _scee, _scnb = scee, scnb
+    for (iAtom, lAtom, chargeProd, rMin, epsilon, iScee, iScnb) in prmtop.get14Interactions():
+        if scee is None: _scee = iScee
+        if scnb is None: _scnb = iScnb
+        chargeProd /= _scee
+        epsilon /= _scnb
         sigma = rMin * sigmaScale
         force.addException(iAtom, lAtom, chargeProd, sigma, epsilon)
         excludedAtomPairs.add(min((iAtom, lAtom), (lAtom, iAtom)))