addSolvent now only replaces newly added water molecules with ions (#4104)

* addSolvent now only replaces newly added water molecules with ions

previously pre-existing (i.e. potentially crystallographic waters) were candidates for replacement with an ion.

concentration calculations (i.e. total water molecules) still include these pre-existing water molecules

* only include added water in concentration calc

wrappers/python/openmm/app/modeller.py

@@ -619,7 +619,7 @@ class Modeller(object):
             addedWaters = filteredWaters
 
         # Add the water molecules.
-
+        waterPos = {}
         for index, pos in addedWaters:
             newResidue = newTopology.addResidue(residue.name, newChain)
             residue = pdbResidues[index]
@@ -629,6 +629,8 @@ class Modeller(object):
             for atom in residue.atoms():
                 molAtoms.append(newTopology.addAtom(atom.name, atom.element, newResidue))
                 newPositions.append((pos+pdbPositions[atom.index]-oPos)*nanometer)
+                if atom.element == elem.oxygen:
+                    waterPos[newResidue] = newPositions[-1]
             for atom1 in molAtoms:
                 if atom1.element == elem.oxygen:
                     for atom2 in molAtoms:
@@ -638,16 +640,6 @@ class Modeller(object):
         self.topology = newTopology
         self.positions = newPositions
 
-        # Convert water list to dictionary (residue:position)
-        waterPos = {}
-        _oxygen = elem.oxygen
-        for chain in newTopology.chains():
-            for residue in chain.residues():
-                if residue.name == 'HOH':
-                    for atom in residue.atoms():
-                        if atom.element == _oxygen:
-                            waterPos[residue] = newPositions[atom.index]
-
         # Total number of waters in the box
         numTotalWaters = len(waterPos)