Merge remote-tracking branch 'origin/master' into charmm

tools/ci/requirements-conda.txt

+numpy
+cython
+pip
+nose
+

tools/conda-recipe/README.md

+This is a recipe for building the current development package into a conda binary.
+
+The installation on travis-ci is done by building the conda package, installing
+it, running the tests, and then if successful pushing the package to binstar
+(and the docs to AWS S3). The binstar auth token is an encrypted environment
+variable generated using:
+
+binstar auth -n openmm-travis -o omnia --max-age 22896000 -c --scopes api:write
+
+and then saved in the environment variable BINSTAR_TOKEN.
+
+You can set up travis to store an encrypted token via
+
+gem install travis travis encrypt BINSTAR_TOKEN=xx
+
+where xx is the token output by binstar. The final command should print a line (containing 'secure') for inclusion in your .travis.yml file.

tools/conda-recipe/build.sh

+#!/bin/bash
+
+CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$PREFIX"
+
+if [[ "$OSTYPE" == "linux-gnu" ]]; then
+    # setting the rpath so that libOpenMMPME.so finds the right libfftw3
+    CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
+    CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
+    #CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPP/lib/x86_64/libOpenCL.so" # TEST
+
+elif [[ "$OSTYPE" == "darwin"* ]]; then
+    export MACOSX_DEPLOYMENT_TARGET="10.7"
+    CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
+fi
+
+# Set location for FFTW3 on both linux and mac
+CMAKE_FLAGS+=" -DFFTW_INCLUDES=$PREFIX/include"
+if [[ "$OSTYPE" == "linux-gnu" ]]; then
+    CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.so"
+    CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.so"
+elif [[ "$OSTYPE" == "darwin"* ]]; then
+    CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.dylib"
+    CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.dylib"
+fi
+
+# Copy source to current directory.
+cp -r $RECIPE_DIR/../.. .
+
+# Build in subdirectory.
+mkdir build
+cd build
+cmake .. $CMAKE_FLAGS
+make -j4
+make install
+
+# Run C tests.
+# Exclude OpenCL tests because @peastman suspects mesa on travis implementation is broken.
+# @jchodera and @pgrinaway suspect travis is working, but AMD OpenCL tests are actually failing due to a bug.
+ctest -j2 -V -E "[A-Za-z]+OpenCL[A-Za-z]+"
+
+# Install Python wrappers.
+export OPENMM_INCLUDE_PATH=$PREFIX/include
+export OPENMM_LIB_PATH=$PREFIX/lib
+cd python
+$PYTHON setup.py install
+cd ..
+
+# Remove one random file
+#rm $PREFIX/bin/TestReferenceHarmonicBondForce
+
+# Copy all tests to bin directory so they will be distributed with install package.
+cp `find . -name "Test*" -type f -maxdepth 1` $PREFIX/bin
+

tools/conda-recipe/meta.yaml

+package:
+  name: openmm
+  version: !!str dev
+
+requirements:
+  build:
+    - cmake
+    - python
+    - fftw3f
+
+  run:
+    - python
+    - fftw3f
+    - numpy
+
+about:
+  home: https://simtk.org/home/openmm
+  license: GPL

tools/conda-recipe/plugin-dir.patch

+diff --git wrappers/python/simtk/openmm/__init__.py wrappers/python/simtk/openmm/__init__.py
+index 7e47b11..0ef290a 100644
+--- wrappers/python/simtk/openmm/__init__.py
++++ wrappers/python/simtk/openmm/__init__.py
+@@ -13,6 +13,10 @@ import os, os.path
+ from simtk.openmm.openmm import *
+ from simtk.openmm.vec3 import Vec3
+ from simtk.openmm import version
+-if os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(version.openmm_library_path):
++_plugin_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', '..', '..', '..', 'plugins'))
++if os.path.isdir(_plugin_dir):
++    pluginLoadedLibNames = Platform.loadPluginsFromDirectory(_plugin_dir)
++    del _plugin_dir
++elif os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(version.openmm_library_path):
+     pluginLoadedLibNames = Platform.loadPluginsFromDirectory(os.path.join(version.openmm_library_path, 'plugins'))
+ else:
+     pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
\ No newline at end of file

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

@@ -13,7 +13,7 @@ Copyright (c) 2014 the Authors
 
 Author: Jason Deckman
 Contributors: Jason M. Swails
-Date: April 19, 2014
+Date: June 6, 2014
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -64,7 +64,7 @@ class CharmmCrdFile(object):
         self.resname = []                  # Residue name
         self.resid = []                    # Residue ID
         self.attype = []                   # Atom type
-        self.positions = []*u.angstroms    # 3N atomic coordinates
+        self.positions = []                # 3N atomic coordinates
         self.title = []                    # .crd file title block
         self.segid = []                    # Segment ID
         self.weighting = []                # Atom weighting
@@ -105,7 +105,7 @@ class CharmmCrdFile(object):
                 self.resname.append(line[2])
                 self.attype.append(line[3])
                 pos = Vec3(float(line[4]), float(line[5]), float(line[6]))
-                self.positions.append(pos * u.angstroms)
+                self.positions.append(pos)
                 self.segid.append(line[7])
                 self.resid.append(int(line[8]))
                 self.weighting.append(float(line[9]))
@@ -120,6 +120,10 @@ class CharmmCrdFile(object):
         except (ValueError, IndexError), e:
             raise CharmmFileError('Error parsing CHARMM coordinate file')
 
+        # Apply units to the positions now. Do it this way to allow for
+        # (possible) numpy functionality in the future.
+        self.positions = u.Quantity(self.positions, u.angstroms)
+
 class CharmmRstFile(object):
     """
     Reads and parses data, velocities and coordinates from a CHARMM restart
@@ -209,8 +213,9 @@ class CharmmRstFile(object):
         self.velocities = [v * ONE_TIMESCALE for v in self.velocities]
 
         # Add units to positions and velocities
-        self.positions *= u.angstroms
-        self.velocities *= u.angstroms / u.picoseconds
+        self.positions = u.Quantity(self.positions, u.angstroms)
+        self.positionsold = u.Quantity(self.positionsold, u.angstroms)
+        self.velocities = u.Quantity(self.velocities, u.angstroms/u.picoseconds)
 
     def _scan(self, handle, str, r=0): # read lines in file until str is found
         scanning = True

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

@@ -158,10 +158,13 @@ class CharmmPsfFile(object):
         title = list()
         for i in range(ntitle):
             title.append(psf.readline().rstrip())
-        # Skip the blank line
-        psf.readline()
+        # Skip all blank lines. Most of the time there is only 1, but I've seen
+        # a file that has 2
+        line = psf.readline().strip()
+        while not line:
+            line = psf.readline().strip()
         # Next is the number of atoms
-        natom = conv(psf.readline().strip(), int, 'natom')
+        natom = conv(line, int, 'natom')
         # Parse all of the atoms
         residue_list = ResidueList()
         atom_list = AtomList()
@@ -1182,8 +1185,11 @@ class CharmmPsfFile(object):
                 if switchDistance >= nonbondedCutoff:
                     raise ValueError('switchDistance is too large compared '
                                      'to the cutoff!')
-                    force.setUseSwitchingFunction(True)
-                    force.setSwitchingDistance(switchDistance)
+                if abs(switchDistance) != switchDistance:
+                    # Detects negatives for both Quantity and float
+                    raise ValueError('switchDistance must be non-negative!')
+                force.setUseSwitchingFunction(True)
+                force.setSwitchingDistance(switchDistance)
 
         else: # periodic
             # Set up box vectors (from inpcrd if available, or fall back to
@@ -1223,8 +1229,11 @@ class CharmmPsfFile(object):
                 if switchDistance >= nonbondedCutoff:
                     raise ValueError('switchDistance is too large compared '
                                      'to the cutoff!')
-                    force.setUseSwitchingFunction(True)
-                    force.setSwitchingDistance(switchDistance)
+                if abs(switchDistance) != switchDistance:
+                    # Detects negatives for both Quantity and float
+                    raise ValueError('switchDistance must be non-negative!')
+                force.setUseSwitchingFunction(True)
+                force.setSwitchingDistance(switchDistance)
 
             if ewaldErrorTolerance is not None:
                 force.setEwaldErrorTolerance(ewaldErrorTolerance)

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

-#!/bin/env python
-
 """
 element.py: Used for managing elements.
 

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

@@ -40,6 +40,11 @@ import simtk.unit as unit
 import element as elem
 from simtk.openmm.app import Topology
 
+def _convertParameterToNumber(param):
+    if unit.is_quantity(param):
+        return mm.stripUnits((param,))[0]
+    return float(param)
+
 # Enumerated values for nonbonded method
 
 class NoCutoff(object):
@@ -95,8 +100,11 @@ class ForceField(object):
         """Load one or more XML files and create a ForceField object based on them.
 
         Parameters:
-         - files A list of XML files defining the force field.  Each entry may be an absolute file path, a path relative to the
-           current working directory, or a path relative to this module's data subdirectory (for built in force fields).
+         - files A list of XML files defining the force field.  Each entry may
+           be an absolute file path, a path relative to the current working
+           directory, a path relative to this module's data subdirectory
+           (for built in force fields), or an open file-like object with a
+           read() method from which the forcefield XML data can be loaded.
         """
         self._atomTypes = {}
         self._templates = {}
@@ -106,6 +114,7 @@ class ForceField(object):
         self._scripts = []
         for file in files:
             try:
+                # this handles either filenames or open file-like objects
                 tree = etree.parse(file)
             except IOError:
                 tree = etree.parse(os.path.join(os.path.dirname(__file__), 'data', file))
@@ -115,13 +124,7 @@ class ForceField(object):
 
             if tree.getroot().find('AtomTypes') is not None:
                 for type in tree.getroot().find('AtomTypes').findall('Type'):
-                    element = None
-                    if 'element' in type.attrib:
-                        element = elem.get_by_symbol(type.attrib['element'])
-                    name = type.attrib['name']
-                    if name in self._atomTypes:
-                        raise ValueError('Found multiple definitions for atom type: '+name)
-                    self._atomTypes[name] = (type.attrib['class'], float(type.attrib['mass']), element)
+                    self.registerAtomType(type.attrib)
 
             # Load the residue templates.
 
@@ -129,38 +132,17 @@ class ForceField(object):
                 for residue in root.find('Residues').findall('Residue'):
                     resName = residue.attrib['name']
                     template = ForceField._TemplateData(resName)
-                    self._templates[resName] = template
                     for atom in residue.findall('Atom'):
                         template.atoms.append(ForceField._TemplateAtomData(atom.attrib['name'], atom.attrib['type'], self._atomTypes[atom.attrib['type']][2]))
                     for site in residue.findall('VirtualSite'):
                         template.virtualSites.append(ForceField._VirtualSiteData(site))
                     for bond in residue.findall('Bond'):
-                        b = (int(bond.attrib['from']), int(bond.attrib['to']))
-                        template.bonds.append(b)
-                        template.atoms[b[0]].bondedTo.append(b[1])
-                        template.atoms[b[1]].bondedTo.append(b[0])
+                        template.addBond(int(bond.attrib['from']), int(bond.attrib['to']))
                     for bond in residue.findall('ExternalBond'):
                         b = int(bond.attrib['from'])
                         template.externalBonds.append(b)
                         template.atoms[b].externalBonds += 1
-            for template in self._templates.values():
-                signature = _createResidueSignature([atom.element for atom in template.atoms])
-                if signature in self._templateSignatures:
-                    self._templateSignatures[signature].append(template)
-                else:
-                    self._templateSignatures[signature] = [template]
-
-            # Build sets of every atom type belonging to each class
-
-            for type in self._atomTypes:
-                atomClass = self._atomTypes[type][0]
-                if atomClass in self._atomClasses:
-                    typeSet = self._atomClasses[atomClass]
-                else:
-                    typeSet = set()
-                    self._atomClasses[atomClass] = typeSet
-                typeSet.add(type)
-                self._atomClasses[''].add(type)
+                    self.registerResidueTemplate(template)
 
             # Load force definitions
 
@@ -171,12 +153,53 @@ class ForceField(object):
             # Load scripts
 
             for node in tree.getroot().findall('Script'):
-                self._scripts.append(node.text)
+                self.registerScript(node.text)
+
+    def getGenerators(self):
+        """Get the list of all registered generators."""
+        return self._forces
+    
+    def registerGenerator(self, generator):
+        """Register a new generator."""
+        self._forces.append(generator)
+    
+    def registerAtomType(self, parameters):
+        """Register a new atom type."""
+        name = parameters['name']
+        if name in self._atomTypes:
+            raise ValueError('Found multiple definitions for atom type: '+name)
+        atomClass = parameters['class']
+        mass = _convertParameterToNumber(parameters['mass'])
+        element = None
+        if 'element' in parameters:
+            element = parameters['element']
+            if not isinstance(element, elem.Element):
+                element = elem.get_by_symbol(element)
+        self._atomTypes[name] = (atomClass, mass, element)
+        if atomClass in self._atomClasses:
+            typeSet = self._atomClasses[atomClass]
+        else:
+            typeSet = set()
+            self._atomClasses[atomClass] = typeSet
+        typeSet.add(name)
+        self._atomClasses[''].add(name)
+    
+    def registerResidueTemplate(self, template):
+        """Register a new residue template."""
+        self._templates[template.name] = template
+        signature = _createResidueSignature([atom.element for atom in template.atoms])
+        if signature in self._templateSignatures:
+            self._templateSignatures[signature].append(template)
+        else:
+            self._templateSignatures[signature] = [template]
+    
+    def registerScript(self, script):
+        """Register a new script to be executed after building the System."""
+        self._scripts.append(script)
 
-    def _findAtomTypes(self, node, num):
+    def _findAtomTypes(self, attrib, num):
         """Parse the attributes on an XML tag to find the set of atom types for each atom it involves."""
         types = []
-        attrib = node.attrib
         for i in range(num):
             if num == 1:
                 suffix = ''
@@ -186,7 +209,7 @@ class ForceField(object):
             typeAttrib = 'type'+suffix
             if classAttrib in attrib:
                 if typeAttrib in attrib:
-                    raise ValueError('Tag specifies both a type and a class for the same atom: '+etree.tostring(node))
+                    raise ValueError('Specified both a type and a class for the same atom: '+str(attrib))
                 if attrib[classAttrib] not in self._atomClasses:
                     types.append(None) # Unknown atom class
                 else:
@@ -198,18 +221,17 @@ class ForceField(object):
                     types.append([attrib[typeAttrib]])
         return types
 
-    def _parseTorsion(self, node):
+    def _parseTorsion(self, attrib):
         """Parse the node defining a torsion."""
-        types = self._findAtomTypes(node, 4)
+        types = self._findAtomTypes(attrib, 4)
         if None in types:
             return None
         torsion = PeriodicTorsion(types)
-        attrib = node.attrib
         index = 1
         while 'phase%d'%index in attrib:
             torsion.periodicity.append(int(attrib['periodicity%d'%index]))
-            torsion.phase.append(float(attrib['phase%d'%index]))
-            torsion.k.append(float(attrib['k%d'%index]))
+            torsion.phase.append(_convertParameterToNumber(attrib['phase%d'%index]))
+            torsion.k.append(_convertParameterToNumber(attrib['k%d'%index]))
             index += 1
         return torsion
 
@@ -235,6 +257,11 @@ class ForceField(object):
             self.virtualSites = []
             self.bonds = []
             self.externalBonds = []
+        
+        def addBond(self, atom1, atom2):
+            self.bonds.append((atom1, atom2))
+            self.atoms[atom1].bondedTo.append(atom2)
+            self.atoms[atom2].bondedTo.append(atom1)
 
     class _TemplateAtomData:
         """Inner class used to encapsulate data about an atom in a residue template definition."""
@@ -668,23 +695,27 @@ def _findMatchErrors(forcefield, res):
 class HarmonicBondGenerator:
     """A HarmonicBondGenerator constructs a HarmonicBondForce."""
 
-    def __init__(self):
+    def __init__(self, forcefield):
+        self.ff = forcefield
         self.types1 = []
         self.types2 = []
         self.length = []
         self.k = []
+    
+    def registerBond(self, parameters):
+        types = self.ff._findAtomTypes(parameters, 2)
+        if None not in types:
+            self.types1.append(types[0])
+            self.types2.append(types[1])
+            self.length.append(_convertParameterToNumber(parameters['length']))
+            self.k.append(_convertParameterToNumber(parameters['k']))
 
     @staticmethod
     def parseElement(element, ff):
-        generator = HarmonicBondGenerator()
-        ff._forces.append(generator)
+        generator = HarmonicBondGenerator(ff)
+        ff.registerGenerator(generator)
         for bond in element.findall('Bond'):
-            types = ff._findAtomTypes(bond, 2)
-            if None not in types:
-                generator.types1.append(types[0])
-                generator.types2.append(types[1])
-                generator.length.append(float(bond.attrib['length']))
-                generator.k.append(float(bond.attrib['k']))
+            generator.registerBond(bond.attrib)
 
     def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
         existing = [sys.getForce(i) for i in range(sys.getNumForces())]
@@ -715,25 +746,29 @@ parsers["HarmonicBondForce"] = HarmonicBondGenerator.parseElement
 class HarmonicAngleGenerator:
     """A HarmonicAngleGenerator constructs a HarmonicAngleForce."""
 
-    def __init__(self):
+    def __init__(self, forcefield):
+        self.ff = forcefield
         self.types1 = []
         self.types2 = []
         self.types3 = []
         self.angle = []
         self.k = []
 
+    def registerAngle(self, parameters):
+        types = self.ff._findAtomTypes(parameters, 3)
+        if None not in types:
+            self.types1.append(types[0])
+            self.types2.append(types[1])
+            self.types3.append(types[2])
+            self.angle.append(_convertParameterToNumber(parameters['angle']))
+            self.k.append(_convertParameterToNumber(parameters['k']))
+
     @staticmethod
     def parseElement(element, ff):
-        generator = HarmonicAngleGenerator()
-        ff._forces.append(generator)
+        generator = HarmonicAngleGenerator(ff)
+        ff.registerGenerator(generator)
         for angle in element.findall('Angle'):
-            types = ff._findAtomTypes(angle, 3)
-            if None not in types:
-                generator.types1.append(types[0])
-                generator.types2.append(types[1])
-                generator.types3.append(types[2])
-                generator.angle.append(float(angle.attrib['angle']))
-                generator.k.append(float(angle.attrib['k']))
+            generator.registerAngle(angle.attrib)
 
     def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
         existing = [sys.getForce(i) for i in range(sys.getNumForces())]
@@ -797,23 +832,29 @@ class PeriodicTorsion:
 class PeriodicTorsionGenerator:
     """A PeriodicTorsionGenerator constructs a PeriodicTorsionForce."""
 
-    def __init__(self):
+    def __init__(self, forcefield):
+        self.ff = forcefield
         self.proper = []
         self.improper = []
 
+    def registerProperTorsion(self, parameters):
+        torsion = self.ff._parseTorsion(parameters)
+        if torsion is not None:
+            self.proper.append(torsion)
+
+    def registerImproperTorsion(self, parameters):
+        torsion = self.ff._parseTorsion(parameters)
+        if torsion is not None:
+            self.improper.append(torsion)
+
     @staticmethod
     def parseElement(element, ff):
-        generator = PeriodicTorsionGenerator()
-        generator.ff = ff
-        ff._forces.append(generator)
+        generator = PeriodicTorsionGenerator(ff)
+        ff.registerGenerator(generator)
         for torsion in element.findall('Proper'):
-            torsion = ff._parseTorsion(torsion)
-            if torsion is not None:
-                generator.proper.append(torsion)
+            generator.registerProperTorsion(torsion.attrib)
         for torsion in element.findall('Improper'):
-            torsion = ff._parseTorsion(torsion)
-            if torsion is not None:
-                generator.improper.append(torsion)
+            generator.registerImproperTorsion(torsion.attrib)
 
     def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
         existing = [sys.getForce(i) for i in range(sys.getNumForces())]
@@ -902,21 +943,21 @@ class RBTorsion:
 class RBTorsionGenerator:
     """An RBTorsionGenerator constructs an RBTorsionForce."""
 
-    def __init__(self):
+    def __init__(self, forcefield):
+        self.ff = forcefield
         self.proper = []
         self.improper = []
 
     @staticmethod
     def parseElement(element, ff):
-        generator = RBTorsionGenerator()
-        generator.ff = ff
-        ff._forces.append(generator)
+        generator = RBTorsionGenerator(ff)
+        ff.registerGenerator(generator)
         for torsion in element.findall('Proper'):
-            types = ff._findAtomTypes(torsion, 4)
+            types = ff._findAtomTypes(torsion.attrib, 4)
             if None not in types:
                 generator.proper.append(RBTorsion(types, [float(torsion.attrib['c'+str(i)]) for i in range(6)]))
         for torsion in element.findall('Improper'):
-            types = ff._findAtomTypes(torsion, 4)
+            types = ff._findAtomTypes(torsion.attrib, 4)
             if None not in types:
                 generator.improper.append(RBTorsion(types, [float(torsion.attrib['c'+str(i)]) for i in range(6)]))
 
@@ -1002,15 +1043,15 @@ class CMAPTorsion:
 class CMAPTorsionGenerator:
     """A CMAPTorsionGenerator constructs a CMAPTorsionForce."""
 
-    def __init__(self):
+    def __init__(self, forcefield):
+        self.ff = forcefield
         self.torsions = []
         self.maps = []
 
     @staticmethod
     def parseElement(element, ff):
-        generator = CMAPTorsionGenerator()
-        generator.ff = ff
-        ff._forces.append(generator)
+        generator = CMAPTorsionGenerator(ff)
+        ff.registerGenerator(generator)
         for map in element.findall('Map'):
             values = [float(x) for x in map.text.split()]
             size = sqrt(len(values))
@@ -1018,7 +1059,7 @@ class CMAPTorsionGenerator:
                 raise ValueError('CMAP must have the same number of elements along each dimension')
             generator.maps.append(values)
         for torsion in element.findall('Torsion'):
-            types = ff._findAtomTypes(torsion, 5)
+            types = ff._findAtomTypes(torsion.attrib, 5)
             if None not in types:
                 generator.torsions.append(CMAPTorsion(types, int(torsion.attrib['map'])))
 
@@ -1082,28 +1123,32 @@ parsers["CMAPTorsionForce"] = CMAPTorsionGenerator.parseElement
 class NonbondedGenerator:
     """A NonbondedGenerator constructs a NonbondedForce."""
 
-    def __init__(self, coulomb14scale, lj14scale):
+    def __init__(self, forcefield, coulomb14scale, lj14scale):
+        self.ff = forcefield
         self.coulomb14scale = coulomb14scale
         self.lj14scale = lj14scale
         self.typeMap = {}
 
+    def registerAtom(self, parameters):
+        types = self.ff._findAtomTypes(parameters, 1)
+        if None not in types:
+            values = (_convertParameterToNumber(parameters['charge']), _convertParameterToNumber(parameters['sigma']), _convertParameterToNumber(parameters['epsilon']))
+            for t in types[0]:
+                self.typeMap[t] = values
+
     @staticmethod
     def parseElement(element, ff):
         existing = [f for f in ff._forces if isinstance(f, NonbondedGenerator)]
         if len(existing) == 0:
-            generator = NonbondedGenerator(float(element.attrib['coulomb14scale']), float(element.attrib['lj14scale']))
-            ff._forces.append(generator)
+            generator = NonbondedGenerator(ff, float(element.attrib['coulomb14scale']), float(element.attrib['lj14scale']))
+            ff.registerGenerator(generator)
         else:
             # Multiple <NonbondedForce> tags were found, probably in different files.  Simply add more types to the existing one.
             generator = existing[0]
             if generator.coulomb14scale != float(element.attrib['coulomb14scale']) or generator.lj14scale != float(element.attrib['lj14scale']):
                 raise ValueError('Found multiple NonbondedForce tags with different 1-4 scales')
         for atom in element.findall('Atom'):
-            types = ff._findAtomTypes(atom, 1)
-            if None not in types:
-                values = (float(atom.attrib['charge']), float(atom.attrib['sigma']), float(atom.attrib['epsilon']))
-                for t in types[0]:
-                    generator.typeMap[t] = values
+            generator.registerAtom(atom.attrib)
 
     def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
         methodMap = {NoCutoff:mm.NonbondedForce.NoCutoff,
@@ -1125,6 +1170,8 @@ class NonbondedGenerator:
         force.setCutoffDistance(nonbondedCutoff)
         if 'ewaldErrorTolerance' in args:
             force.setEwaldErrorTolerance(args['ewaldErrorTolerance'])
+        if 'useDispersionCorrection' in args:
+            force.setUseDispersionCorrection(bool(args['useDispersionCorrection']))
         sys.addForce(force)
 
     def postprocessSystem(self, sys, data, args):
@@ -1165,24 +1212,28 @@ parsers["NonbondedForce"] = NonbondedGenerator.parseElement
 class GBSAOBCGenerator:
     """A GBSAOBCGenerator constructs a GBSAOBCForce."""
 
-    def __init__(self):
+    def __init__(self, forcefield):
+        self.ff = forcefield
         self.typeMap = {}
 
+    def registerAtom(self, parameters):
+        types = self.ff._findAtomTypes(parameters, 1)
+        if None not in types:
+            values = (_convertParameterToNumber(parameters['charge']), _convertParameterToNumber(parameters['radius']), _convertParameterToNumber(parameters['scale']))
+            for t in types[0]:
+                self.typeMap[t] = values
+
     @staticmethod
     def parseElement(element, ff):
         existing = [f for f in ff._forces if isinstance(f, GBSAOBCGenerator)]
         if len(existing) == 0:
-            generator = GBSAOBCGenerator()
-            ff._forces.append(generator)
+            generator = GBSAOBCGenerator(ff)
+            ff.registerGenerator(generator)
         else:
             # Multiple <GBSAOBCForce> tags were found, probably in different files.  Simply add more types to the existing one.
             generator = existing[0]
         for atom in element.findall('Atom'):
-            types = ff._findAtomTypes(atom, 1)
-            if None not in types:
-                values = (float(atom.attrib['charge']), float(atom.attrib['radius']), float(atom.attrib['scale']))
-                for t in types[0]:
-                    generator.typeMap[t] = values
+            generator.registerAtom(atom.attrib)
 
     def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
         methodMap = {NoCutoff:mm.NonbondedForce.NoCutoff,
@@ -1222,7 +1273,6 @@ class GBVIGenerator:
     """A GBVIGenerator constructs a GBVIForce."""
 
     def __init__(self,ff):
-
         self.ff = ff
         self.fixedParameters = {}
         self.fixedParameters['soluteDielectric'] = 1.0
@@ -1240,9 +1290,9 @@ class GBVIGenerator:
             if (key in element.attrib):
                 generator.fixedParameters[key] = float(element.attrib[key])
 
-        ff._forces.append(generator)
+        ff.registerGenerator(generator)
         for atom in element.findall('Atom'):
-            types = ff._findAtomTypes(atom, 1)
+            types = ff._findAtomTypes(atom.attrib, 1)
             if None not in types:
                 values = (float(atom.attrib['charge']), float(atom.attrib['radius']), float(atom.attrib['gamma']))
                 for t in types[0]:
@@ -1308,7 +1358,8 @@ parsers["GBVIForce"] = GBVIGenerator.parseElement
 class CustomBondGenerator:
     """A CustomBondGenerator constructs a CustomBondForce."""
 
-    def __init__(self):
+    def __init__(self, forcefield):
+        self.ff = forcefield
         self.types1 = []
         self.types2 = []
         self.globalParams = {}
@@ -1317,15 +1368,15 @@ class CustomBondGenerator:
 
     @staticmethod
     def parseElement(element, ff):
-        generator = CustomBondGenerator()
-        ff._forces.append(generator)
+        generator = CustomBondGenerator(ff)
+        ff.registerGenerator(generator)
         generator.energy = element.attrib['energy']
         for param in element.findall('GlobalParameter'):
             generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
         for param in element.findall('PerBondParameter'):
             generator.perBondParams.append(param.attrib['name'])
         for bond in element.findall('Bond'):
-            types = ff._findAtomTypes(bond, 2)
+            types = ff._findAtomTypes(bond.attrib, 2)
             if None not in types:
                 generator.types1.append(types[0])
                 generator.types2.append(types[1])
@@ -1355,7 +1406,8 @@ parsers["CustomBondForce"] = CustomBondGenerator.parseElement
 class CustomAngleGenerator:
     """A CustomAngleGenerator constructs a CustomAngleForce."""
 
-    def __init__(self):
+    def __init__(self, forcefield):
+        self.ff = forcefield
         self.types1 = []
         self.types2 = []
         self.types3 = []
@@ -1365,15 +1417,15 @@ class CustomAngleGenerator:
 
     @staticmethod
     def parseElement(element, ff):
-        generator = CustomAngleGenerator()
-        ff._forces.append(generator)
+        generator = CustomAngleGenerator(ff)
+        ff.registerGenerator(generator)
         generator.energy = element.attrib['energy']
         for param in element.findall('GlobalParameter'):
             generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
         for param in element.findall('PerAngleParameter'):
             generator.perAngleParams.append(param.attrib['name'])
         for angle in element.findall('Angle'):
-            types = ff._findAtomTypes(angle, 3)
+            types = ff._findAtomTypes(angle.attrib, 3)
             if None not in types:
                 generator.types1.append(types[0])
                 generator.types2.append(types[1])
@@ -1417,7 +1469,8 @@ class CustomTorsion:
 class CustomTorsionGenerator:
     """A CustomTorsionGenerator constructs a CustomTorsionForce."""
 
-    def __init__(self):
+    def __init__(self, forcefield):
+        self.ff = forcefield
         self.proper = []
         self.improper = []
         self.globalParams = {}
@@ -1425,20 +1478,19 @@ class CustomTorsionGenerator:
 
     @staticmethod
     def parseElement(element, ff):
-        generator = CustomTorsionGenerator()
-        generator.ff = ff
-        ff._forces.append(generator)
+        generator = CustomTorsionGenerator(ff)
+        ff.registerGenerator(generator)
         generator.energy = element.attrib['energy']
         for param in element.findall('GlobalParameter'):
             generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
         for param in element.findall('PerTorsionParameter'):
             generator.perTorsionParams.append(param.attrib['name'])
         for torsion in element.findall('Proper'):
-            types = ff._findAtomTypes(torsion, 4)
+            types = ff._findAtomTypes(torsion.attrib, 4)
             if None not in types:
                 generator.proper.append(CustomTorsion(types, [float(torsion.attrib[param]) for param in generator.perTorsionParams]))
         for torsion in element.findall('Improper'):
-            types = ff._findAtomTypes(torsion, 4)
+            types = ff._findAtomTypes(torsion.attrib, 4)
             if None not in types:
                 generator.improper.append(CustomTorsion(types, [float(torsion.attrib[param]) for param in generator.perTorsionParams]))
 
@@ -1508,29 +1560,128 @@ class CustomTorsionGenerator:
 parsers["CustomTorsionForce"] = CustomTorsionGenerator.parseElement
 
 
+## @private
+class CustomNonbondedGenerator:
+    """A CustomNonbondedGenerator constructs a CustomNonbondedForce."""
+
+    def __init__(self, forcefield, energy, bondCutoff):
+        self.ff = forcefield
+        self.energy = energy
+        self.bondCutoff = bondCutoff
+        self.typeMap = {}
+        self.globalParams = {}
+        self.perParticleParams = []
+        self.functions = []
+
+    @staticmethod
+    def parseElement(element, ff):
+        generator = CustomNonbondedGenerator(ff, element.attrib['energy'], int(element.attrib['bondCutoff']))
+        ff.registerGenerator(generator)
+        for param in element.findall('GlobalParameter'):
+            generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
+        for param in element.findall('PerParticleParameter'):
+            generator.perParticleParams.append(param.attrib['name'])
+        for atom in element.findall('Atom'):
+            types = ff._findAtomTypes(atom.attrib, 1)
+            if None not in types:
+                values = [float(atom.attrib[param]) for param in generator.perParticleParams]
+                for t in types[0]:
+                    generator.typeMap[t] = values
+
+    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
+        methodMap = {NoCutoff:mm.CustomNonbondedForce.NoCutoff,
+                     CutoffNonPeriodic:mm.CustomNonbondedForce.CutoffNonPeriodic,
+                     CutoffPeriodic:mm.CustomNonbondedForce.CutoffPeriodic}
+        if nonbondedMethod not in methodMap:
+            raise ValueError('Illegal nonbonded method for CustomNonbondedForce')
+        force = mm.CustomNonbondedForce(self.energy)
+        for param in self.globalParams:
+            force.addGlobalParameter(param, self.globalParams[param])
+        for param in self.perParticleParams:
+            force.addPerParticleParameter(param)
+        for (name, type, values, params) in self.functions:
+            if type == 'Continuous1D':
+                force.addTabulatedFunction(name, mm.Continuous1DFunction(values, params['min'], params['max']))
+            elif type == 'Continuous2D':
+                force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax']))
+            elif type == 'Continuous3D':
+                force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], params['zsize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax'], params['zmin'], params['zmax']))
+            elif type == 'Discrete1D':
+                force.addTabulatedFunction(name, mm.Discrete1DFunction(values))
+            elif type == 'Discrete2D':
+                force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], values))
+            elif type == 'Discrete3D':
+                force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
+        for atom in data.atoms:
+            t = data.atomType[atom]
+            if t in self.typeMap:
+                values = self.typeMap[t]
+                force.addParticle(self.typeMap[t])
+            else:
+                raise ValueError('No CustomNonbonded parameters defined for atom type '+t)
+        force.setNonbondedMethod(methodMap[nonbondedMethod])
+        force.setCutoffDistance(nonbondedCutoff)
+        sys.addForce(force)
+
+    def postprocessSystem(self, sys, data, args):
+        # Create exceptions based on bonds, virtual sites, and Drude particles.
+        if self.bondCutoff == 0:
+            return
+        bondIndices = []
+        for bond in data.bonds:
+            bondIndices.append((bond.atom1, bond.atom2))
+        for i in range(sys.getNumParticles()):
+            if sys.isVirtualSite(i):
+                site = sys.getVirtualSite(i)
+                for j in range(site.getNumParticles()):
+                    bondIndices.append((i, site.getParticle(j)))
+        drude = [f for f in sys.getForces() if isinstance(f, mm.DrudeForce)]
+        if len(drude) > 0:
+            drude = drude[0]
+            # For purposes of creating exceptions, a Drude particle is "bonded" to anything
+            # its parent atom is bonded to.
+            drudeMap = {}
+            for i in range(drude.getNumParticles()):
+                params = drude.getParticleParameters(i)
+                drudeMap[params[1]] = params[0]
+            for atom1, atom2 in bondIndices:
+                drude1 = drudeMap[atom1] if atom1 in drudeMap else None
+                drude2 = drudeMap[atom2] if atom2 in drudeMap else None
+                if drude1 is not None:
+                    bondIndices.append((drude1, atom2))
+                    if drude2 is not None:
+                        bondIndices.append((drude1, drude2))
+                if drude2 is not None:
+                    bondIndices.append((atom1, drude2))
+        nonbonded = [f for f in sys.getForces() if isinstance(f, mm.CustomNonbondedForce)][0]
+        nonbonded.createExclusionsFromBonds(bondIndices, self.bondCutoff)
+
+parsers["CustomNonbondedForce"] = CustomNonbondedGenerator.parseElement
+
+
 ## @private
 class CustomGBGenerator:
     """A CustomGBGenerator constructs a CustomGBForce."""
 
-    def __init__(self):
+    def __init__(self, forcefield):
+        self.ff = forcefield
         self.typeMap = {}
         self.globalParams = {}
         self.perParticleParams = []
-        self.paramValues = []
         self.computedValues = []
         self.energyTerms = []
         self.functions = []
 
     @staticmethod
     def parseElement(element, ff):
-        generator = CustomGBGenerator()
-        ff._forces.append(generator)
+        generator = CustomGBGenerator(ff)
+        ff.registerGenerator(generator)
         for param in element.findall('GlobalParameter'):
             generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
         for param in element.findall('PerParticleParameter'):
             generator.perParticleParams.append(param.attrib['name'])
         for atom in element.findall('Atom'):
-            types = ff._findAtomTypes(atom, 1)
+            types = ff._findAtomTypes(atom.attrib, 1)
             if None not in types:
                 values = [float(atom.attrib[param]) for param in generator.perParticleParams]
                 for t in types[0]:
@@ -1653,7 +1804,7 @@ class AmoebaBondGenerator:
         generator = AmoebaBondGenerator(float(element.attrib['bond-cubic']), float(element.attrib['bond-quartic']))
         forceField._forces.append(generator)
         for bond in element.findall('Bond'):
-            types = forceField._findAtomTypes(bond, 2)
+            types = forceField._findAtomTypes(bond.attrib, 2)
             if None not in types:
                 generator.types1.append(types[0])
                 generator.types2.append(types[1])
@@ -1766,7 +1917,7 @@ class AmoebaAngleGenerator:
         generator = AmoebaAngleGenerator(forceField, float(element.attrib['angle-cubic']), float(element.attrib['angle-quartic']),  float(element.attrib['angle-pentic']), float(element.attrib['angle-sextic']))
         forceField._forces.append(generator)
         for angle in element.findall('Angle'):
-            types = forceField._findAtomTypes(angle, 3)
+            types = forceField._findAtomTypes(angle.attrib, 3)
             if None not in types:
 
                 generator.types1.append(types[0])
@@ -2251,7 +2402,7 @@ class AmoebaTorsionGenerator:
         # where ti=[amplitude_i,angle_i]
 
         for torsion in element.findall('Torsion'):
-            types = forceField._findAtomTypes(torsion, 4)
+            types = forceField._findAtomTypes(torsion.attrib, 4)
             if None not in types:
 
                 generator.types1.append(types[0])
@@ -2277,10 +2428,10 @@ class AmoebaTorsionGenerator:
 
             else:
                 outputString = "AmoebaTorsionGenerator: error getting types: %s %s %s %s" % (
-                                    stretchBend.attrib['class1'],
-                                    stretchBend.attrib['class2'],
-                                    stretchBend.attrib['class3'],
-                                    stretchBend.attrib['class4'])
+                                    torsion.attrib['class1'],
+                                    torsion.attrib['class2'],
+                                    torsion.attrib['class3'],
+                                    torsion.attrib['class4'])
                 raise ValueError(outputString)
 
     #=============================================================================================
@@ -2362,7 +2513,7 @@ class AmoebaPiTorsionGenerator:
         forceField._forces.append(generator)
 
         for piTorsion in element.findall('PiTorsion'):
-            types = forceField._findAtomTypes(piTorsion, 2)
+            types = forceField._findAtomTypes(piTorsion.attrib, 2)
             if None not in types:
                 generator.types1.append(types[0])
                 generator.types2.append(types[1])
@@ -2481,7 +2632,7 @@ class AmoebaTorsionTorsionGenerator:
         # <TorsionTorsion class1="3" class2="1" class3="2" class4="3" class5="1" grid="0" nx="25" ny="25" />
 
         for torsionTorsion in element.findall('TorsionTorsion'):
-            types = forceField._findAtomTypes(torsionTorsion, 5)
+            types = forceField._findAtomTypes(torsionTorsion.attrib, 5)
             if None not in types:
 
                 generator.types1.append(types[0])
@@ -2719,7 +2870,7 @@ class AmoebaStretchBendGenerator:
         # <StretchBend class1="2" class2="1" class3="4" k1="3.14005676385" k2="3.14005676385" />
 
         for stretchBend in element.findall('StretchBend'):
-            types = forceField._findAtomTypes(stretchBend, 3)
+            types = forceField._findAtomTypes(stretchBend.attrib, 3)
             if None not in types:
 
                 generator.types1.append(types[0])
@@ -2876,7 +3027,7 @@ class AmoebaVdwGenerator:
         # sigma is modified based on radiustype and radiussize
 
         for atom in element.findall('Vdw'):
-            types = forceField._findAtomTypes(atom, 1)
+            types = forceField._findAtomTypes(atom.attrib, 1)
             if None not in types:
 
                 values = [float(atom.attrib['sigma']), float(atom.attrib['epsilon']), float(atom.attrib['reduction'])]
@@ -2963,7 +3114,7 @@ class AmoebaVdwGenerator:
             # dispersion correction
 
             if ('useDispersionCorrection' in args):
-                force.setUseDispersionCorrection(int(args['useDispersionCorrection']))
+                force.setUseDispersionCorrection(bool(args['useDispersionCorrection']))
 
             if (nonbondedMethod == PME):
                 force.setNonbondedMethod(mm.AmoebaVdwForce.CutoffPeriodic)
@@ -3149,7 +3300,7 @@ class AmoebaMultipoleGenerator:
         # set type map: [ kIndices, multipoles, AMOEBA/OpenMM axis type]
 
         for atom in element.findall('Multipole'):
-            types = forceField._findAtomTypes(atom, 1)
+            types = forceField._findAtomTypes(atom.attrib, 1)
             if None not in types:
 
                 # k-indices not provided default to 0
@@ -3206,7 +3357,7 @@ class AmoebaMultipoleGenerator:
         # polarization parameters
 
         for atom in element.findall('Polarize'):
-            types = forceField._findAtomTypes(atom, 1)
+            types = forceField._findAtomTypes(atom.attrib, 1)
             if None not in types:
 
                 classIndex = atom.attrib['type']
@@ -3734,7 +3885,7 @@ class AmoebaWcaDispersionGenerator:
         # typeMap[] = [ radius, epsilon ]
 
         for atom in element.findall('WcaDispersion'):
-            types = forceField._findAtomTypes(atom, 1)
+            types = forceField._findAtomTypes(atom.attrib, 1)
             if None not in types:
 
                 values = [float(atom.attrib['radius']), float(atom.attrib['epsilon'])]
@@ -4078,7 +4229,7 @@ class AmoebaUreyBradleyGenerator:
         generator = AmoebaUreyBradleyGenerator()
         forceField._forces.append(generator)
         for bond in element.findall('UreyBradley'):
-            types = forceField._findAtomTypes(bond, 3)
+            types = forceField._findAtomTypes(bond.attrib, 3)
             if None not in types:
 
                 generator.types1.append(types[0])
@@ -4129,20 +4280,21 @@ parsers["AmoebaUreyBradleyForce"] = AmoebaUreyBradleyGenerator.parseElement
 class DrudeGenerator:
     """A DrudeGenerator constructs a DrudeForce."""
 
-    def __init__(self):
+    def __init__(self, forcefield):
+        self.ff = forcefield
         self.typeMap = {}
 
     @staticmethod
     def parseElement(element, ff):
         existing = [f for f in ff._forces if isinstance(f, DrudeGenerator)]
         if len(existing) == 0:
-            generator = DrudeGenerator()
-            ff._forces.append(generator)
+            generator = DrudeGenerator(ff)
+            ff.registerGenerator(generator)
         else:
             # Multiple <DrudeForce> tags were found, probably in different files.  Simply add more types to the existing one.
             generator = existing[0]
         for particle in element.findall('Particle'):
-            types = ff._findAtomTypes(particle, 5)
+            types = ff._findAtomTypes(particle.attrib, 5)
             if None not in types[:2]:
                 aniso12 = 0.0
                 aniso34 = 0.0

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

@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012-2013 Stanford University and the Authors.
+Portions copyright (c) 2012-2014 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -111,7 +111,7 @@ class GromacsTopFile(object):
                 if len(fields) < 2:
                     raise ValueError('Illegal line in .top file: '+line)
                 name = fields[1]
-                valueStart = stripped.find(name, len(command))+len(name)
+                valueStart = stripped.find(name, len(command))+len(name)+1
                 value = line[valueStart:].strip()
                 self._defines[name] = value
             elif command == '#ifdef':
@@ -745,6 +745,12 @@ class GromacsTopFile(object):
                     atom1params = nb.getParticleParameters(baseAtomIndex+atoms[0])
                     atom2params = nb.getParticleParameters(baseAtomIndex+atoms[1])
                     exceptions.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], atom1params[0]*atom2params[0]*fudgeQQ, params[0], params[1]))
+                for fields in moleculeType.exclusions:
+                    atoms = [int(x)-1 for x in fields]
+                    for atom in atoms[1:]:
+                        if atom > atoms[0]:
+                            exceptions.append((baseAtomIndex+atoms[0], baseAtomIndex+atom, 0, 0, 0))
+                    
 
         # Create nonbonded exceptions.
 

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

@@ -12,9 +12,9 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012-2013 Stanford University and the Authors.
+Portions copyright (c) 2012-2014 Stanford University and the Authors.
 Authors: Randall J. Radmer, John D. Chodera, Peter Eastman
-Contributors: Christoph Klein, Michael R. Shirts
+Contributors: Christoph Klein, Michael R. Shirts, Jason Swails
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -76,6 +76,10 @@ POINTER_LABEL_LIST = POINTER_LABELS.replace(',', '').split()
 VELSCALE = 20.455 # velocity conversion factor to angstroms/picosecond
 TINY = 1.0e-8
 
+class NbfixPresent(Exception):
+    """ Exception raised when NBFIX is used for the Lennard-Jones terms """
+    pass
+
 class PrmtopLoader(object):
     """Parsed AMBER prmtop file.
 
@@ -297,7 +301,11 @@ class PrmtopLoader(object):
         return self.residuePointerDict[iAtom]
 
     def getNonbondTerms(self):
-        """Return list of all rVdw, epsilon pairs for each atom"""
+        """
+        Return list of all rVdw, epsilon pairs for each atom. If off-diagonal
+        elements of the Lennard-Jones A and B coefficient matrices are found,
+        NbfixPresent exception is raised
+        """
         try:
             return self._nonbondTerms
         except AttributeError:
@@ -305,9 +313,10 @@ class PrmtopLoader(object):
         self._nonbondTerms=[]
         lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
         energyConversionFactor = units.kilocalorie_per_mole.conversion_factor_to(units.kilojoule_per_mole)
+        numTypes = self.getNumTypes()
+        atomTypeIndexes=self._getAtomTypeIndexes()
+        type_parameters = [(0, 0) for i in range(numTypes)]
         for iAtom in range(self.getNumAtoms()):
-            numTypes=self.getNumTypes()
-            atomTypeIndexes=self._getAtomTypeIndexes()
             index=(numTypes+1)*(atomTypeIndexes[iAtom]-1)
             nbIndex=int(self._raw_data['NONBONDED_PARM_INDEX'][index])-1
             if nbIndex<0:
@@ -320,9 +329,31 @@ class PrmtopLoader(object):
             except ZeroDivisionError:
                 rMin = 1.0
                 epsilon = 0.0
+            type_parameters[atomTypeIndexes[iAtom]-1] = (rMin/2.0, epsilon)
             rVdw = rMin/2.0*lengthConversionFactor
             epsilon = epsilon*energyConversionFactor
             self._nonbondTerms.append( (rVdw, epsilon) )
+        # Check if we have any off-diagonal modified LJ terms that would require
+        # an NBFIX-like solution
+        for i in range(numTypes):
+            for j in range(numTypes):
+                index = int(self._raw_data['NONBONDED_PARM_INDEX'][numTypes*i+j]) - 1
+                rij = type_parameters[i][0] + type_parameters[j][0]
+                wdij = sqrt(type_parameters[i][1] * type_parameters[j][1])
+                a = float(self._raw_data['LENNARD_JONES_ACOEF'][index])
+                b = float(self._raw_data['LENNARD_JONES_BCOEF'][index])
+                if a == 0 or b == 0:
+                    if a != 0 or b != 0 or (wdij != 0 and rij != 0):
+                        del self._nonbondTerms
+                        raise NbfixPresent('Off-diagonal Lennard-Jones elements'
+                                           ' found. Cannot determine LJ '
+                                           'parameters for individual atoms.')
+                elif (abs((a - (wdij * rij ** 12)) / a) > 1e-6 or
+                      abs((b - (2 * wdij * rij**6)) / b) > 1e-6):
+                    del self._nonbondTerms
+                    raise NbfixPresent('Off-diagonal Lennard-Jones elements '
+                                       'found. Cannot determine LJ parameters '
+                                       'for individual atoms.')
         return self._nonbondTerms
 
     def _getBonds(self, bondPointers):
@@ -429,27 +460,67 @@ class PrmtopLoader(object):
                           +self._raw_data["DIHEDRALS_WITHOUT_HYDROGEN"]
         returnList=[]
         charges=self.getCharges()
-        nonbondTerms = self.getNonbondTerms()
-        for ii in range(0,len(dihedralPointers),5):
-            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 = sqrt(epsilonI*epsilonL)
-                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))
+        try:
+            nonbondTerms = self.getNonbondTerms()
+        except NbfixPresent:
+            # We need to do the unit conversions here, since getNonbondTerms
+            # never finished and it has unit conversions in there
+            length_conv = units.angstrom.conversion_factor_to(units.nanometers)
+            ene_conv = units.kilocalories_per_mole.conversion_factor_to(
+                                units.kilojoules_per_mole)
+            parm_acoef = [float(x) for x in self._raw_data['LENNARD_JONES_ACOEF']]
+            parm_bcoef = [float(x) for x in self._raw_data['LENNARD_JONES_BCOEF']]
+            nbidx = [int(x) for x in self._raw_data['NONBONDED_PARM_INDEX']]
+            numTypes = self.getNumTypes()
+            atomTypeIndexes=self._getAtomTypeIndexes()
+            for ii in range(0, len(dihedralPointers), 5):
+                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]
+                    typ1 = atomTypeIndexes[iAtom] - 1
+                    typ2 = atomTypeIndexes[lAtom] - 1
+                    idx = nbidx[numTypes*typ1+typ2] - 1
+                    a = parm_acoef[idx]
+                    b = parm_bcoef[idx]
+                    try:
+                        epsilon = b * b / (4 * a) * ene_conv
+                        rMin = (2 * a / b) ** (1/6.0) * length_conv
+                    except ZeroDivisionError:
+                        rMin = 1
+                        epsilon = 0
+                    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))
+        else:
+            # This block gets hit if NbfixPresent is _not_ caught
+            for ii in range(0,len(dihedralPointers),5):
+                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 = sqrt(epsilonI*epsilonL)
+                    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):
@@ -782,9 +853,54 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
 
     # Add per-particle nonbonded parameters.
     sigmaScale = 2**(-1./6.) * 2.0
-    for (charge, (rVdw, epsilon)) in zip(prmtop.getCharges(), prmtop.getNonbondTerms()):
-        sigma = rVdw * sigmaScale
-        force.addParticle(charge, sigma, epsilon)
+    nbfix = False
+    try:
+        nonbondTerms = prmtop.getNonbondTerms()
+    except NbfixPresent:
+        nbfix = True
+        for charge in prmtop.getCharges():
+            force.addParticle(charge, 1.0, 0.0)
+        numTypes = prmtop.getNumTypes()
+        parm_acoef = [float(x) for x in prmtop._raw_data['LENNARD_JONES_ACOEF']]
+        parm_bcoef = [float(x) for x in prmtop._raw_data['LENNARD_JONES_BCOEF']]
+        nbidx = [int(x) for x in prmtop._raw_data['NONBONDED_PARM_INDEX']]
+        acoef = [0 for i in range(numTypes*numTypes)]
+        bcoef = acoef[:] # copy
+        ene_conv = units.kilocalories_per_mole.conversion_factor_to(units.kilojoules_per_mole)
+        length_conv = units.angstroms.conversion_factor_to(units.nanometers)
+        afac = sqrt(ene_conv) * length_conv**6
+        bfac = ene_conv * length_conv**6
+        for i in range(numTypes):
+            for j in range(numTypes):
+                idx = nbidx[numTypes*i+j] - 1
+                acoef[i+numTypes*j] = sqrt(parm_acoef[idx]) * afac
+                bcoef[i+numTypes*j] = parm_bcoef[idx] * bfac
+        cforce = mm.CustomNonbondedForce('(a/r6)^2-b/r6; r6=r^6;'
+                                         'a=acoef(type1, type2);'
+                                         'b=bcoef(type1, type2);')
+        cforce.addTabulatedFunction('acoef',
+                    mm.Discrete2DFunction(numTypes, numTypes, acoef))
+        cforce.addTabulatedFunction('bcoef',
+                    mm.Discrete2DFunction(numTypes, numTypes, bcoef))
+        cforce.addPerParticleParameter('type')
+        for atom in prmtop._getAtomTypeIndexes():
+            cforce.addParticle((atom-1,))
+        # Now set the various properties based on the NonbondedForce object
+        if nonbondedMethod in ('PME', 'Ewald', 'CutoffPeriodic'):
+            cforce.setNonbondedMethod(cforce.CutoffPeriodic)
+            cforce.setCutoffDistance(nonbondedCutoff)
+        elif nonbondedMethod == 'CutoffNonPeriodic':
+            cforce.setNonbondedMethod(cforce.CutoffNonPeriodic)
+            cforce.setCutoffDistance(nonbondedCutoff)
+        elif nonbondedMethod == 'NoCutoff':
+            cforce.setNonbondedMethod(cforce.NoCutoff)
+        else:
+            raise ValueError('Unrecognized cutoff option %s' % nonbondedMethod)
+    else:
+        for (charge, (rVdw, epsilon)) in zip(prmtop.getCharges(), nonbondTerms):
+            sigma = rVdw * sigmaScale
+            force.addParticle(charge, sigma, epsilon)
+
 
     # Add 1-4 Interactions
     excludedAtomPairs = set()
@@ -807,6 +923,13 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
             if min((iAtom, jAtom), (jAtom, iAtom)) in excludedAtomPairs: continue
             force.addException(iAtom, jAtom, excludeParams[0], excludeParams[1], excludeParams[2])
 
+    # Copy the exceptions as exclusions to the CustomNonbondedForce if we have
+    # NBFIX terms
+    if nbfix:
+        for i in range(force.getNumExceptions()):
+            ii, jj, chg, sig, eps = force.getExceptionParameters(i)
+            cforce.addExclusion(ii, jj)
+        system.addForce(cforce)
     system.addForce(force)
 
     # Add virtual sites for water.

wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py

@@ -12,7 +12,7 @@ Copyright (c) 2014 the Authors
 
 Author: Jason M. Swails
 Contributors:
-Date: April 18, 2014
+Date: July 3, 2014
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -421,8 +421,10 @@ class ResidueList(list):
         if self._last_residue is None:
             res = self._last_residue = Residue(resname, resnum)
             list.append(self, res)
-        elif self._last_residue != (resname, resnum):
-            if self._last_residue.idx == resnum:
+        elif (self._last_residue != (resname, resnum) or
+              system != self._last_residue.system):
+            if (self._last_residue.idx == resnum and
+                system == self._last_residue.system):
                 lresname = self._last_residue.resname
                 warnings.warn('Residue %d split into separate residues %s '
                               'and %s' % (resnum, lresname, resname),
@@ -499,7 +501,7 @@ class Angle(object):
         """ See if a bond or an atom is in this angle """
         if isinstance(thing, Bond):
             return self.atom2 in thing and (self.atom1 in thing or
-                                            self.atom2 in thing)
+                                            self.atom3 in thing)
         # Otherwise assume it's an atom
         return self.atom1 is thing or self.atom2 is thing or self.atom3 is thing
 

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

@@ -952,14 +952,14 @@ class Modeller(object):
                                     # This is a virtual site.  Compute its position by the correct rule.
 
                                     if site.type == 'average2':
-                                        position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]]
+                                        position = site.weights[0]*templateAtomPositions[site.atoms[0]] + site.weights[1]*templateAtomPositions[site.atoms[1]]
                                     elif site.type == 'average3':
-                                        position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]] + site.weights[2]*templateAtomPositions[index+site.atoms[2]]
+                                        position = site.weights[0]*templateAtomPositions[site.atoms[0]] + site.weights[1]*templateAtomPositions[site.atoms[1]] + site.weights[2]*templateAtomPositions[site.atoms[2]]
                                     elif site.type == 'outOfPlane':
-                                        v1 = templateAtomPositions[index+site.atoms[1]] - templateAtomPositions[index+site.atoms[0]]
-                                        v2 = templateAtomPositions[index+site.atoms[2]] - templateAtomPositions[index+site.atoms[0]]
+                                        v1 = templateAtomPositions[site.atoms[1]] - templateAtomPositions[site.atoms[0]]
+                                        v2 = templateAtomPositions[site.atoms[2]] - templateAtomPositions[site.atoms[0]]
                                         cross = Vec3(v1[1]*v2[2]-v1[2]*v2[1], v1[2]*v2[0]-v1[0]*v2[2], v1[0]*v2[1]-v1[1]*v2[0])
-                                        position = templateAtomPositions[index+site.atoms[0]] + site.weights[0]*v1 + site.weights[1]*v2 + site.weights[2]*cross
+                                        position = templateAtomPositions[site.atoms[0]] + site.weights[0]*v1 + site.weights[1]*v2 + site.weights[2]*cross
                             if position is None and atom.type in drudeTypeMap:
                                 # This is a Drude particle.  Put it on top of its parent atom.
 

wrappers/python/tests/TestAmberPrmtopFile.py

@@ -5,17 +5,14 @@ from simtk.openmm import *
 from simtk.unit import *
 import simtk.openmm.app.element as elem
 
+prmtop1 = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
+prmtop2 = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
+prmtop3 = AmberPrmtopFile('systems/ff14ipq.parm7')
+inpcrd3 = AmberInpcrdFile('systems/ff14ipq.rst7')
+
 class TestAmberPrmtopFile(unittest.TestCase):
 
     """Test the AmberPrmtopFile.createSystem() method."""
- 
-    def setUp(self):
-        """Set up the tests by loading the input files."""
-
-        # alanine dipeptide with explicit water
-        self.prmtop1 = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
-        # alanine dipeptide with implicit water
-        self.prmtop2 = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
 
     def test_NonbondedMethod(self):
         """Test all five options for the nonbondedMethod parameter."""
@@ -25,7 +22,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
                      CutoffPeriodic:NonbondedForce.CutoffPeriodic, 
                      Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
         for method in methodMap:
-            system = self.prmtop1.createSystem(nonbondedMethod=method)
+            system = prmtop1.createSystem(nonbondedMethod=method)
             forces = system.getForces()
             self.assertTrue(any(isinstance(f, NonbondedForce) and 
                                 f.getNonbondedMethod()==methodMap[method] 
@@ -35,9 +32,9 @@ class TestAmberPrmtopFile(unittest.TestCase):
         """Test to make sure the nonbondedCutoff parameter is passed correctly."""
 
         for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
-            system = self.prmtop1.createSystem(nonbondedMethod=method, 
-                                               nonbondedCutoff=2*nanometer, 
-                                               constraints=HBonds)
+            system = prmtop1.createSystem(nonbondedMethod=method, 
+                                          nonbondedCutoff=2*nanometer, 
+                                          constraints=HBonds)
             cutoff_distance = 0.0*nanometer
             cutoff_check = 2.0*nanometer
             for force in system.getForces():
@@ -49,9 +46,9 @@ class TestAmberPrmtopFile(unittest.TestCase):
         """Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
 
         for method in [Ewald, PME]:
-            system = self.prmtop1.createSystem(nonbondedMethod=method, 
-                                               ewaldErrorTolerance=1e-6, 
-                                               constraints=HBonds)
+            system = prmtop1.createSystem(nonbondedMethod=method, 
+                                          ewaldErrorTolerance=1e-6, 
+                                          constraints=HBonds)
             tolerance = 0
             tolerance_check = 1e-6
             for force in system.getForces():
@@ -63,18 +60,18 @@ class TestAmberPrmtopFile(unittest.TestCase):
         """Test both options (True and False) for the removeCMMotion parameter."""
 
         for b in [True, False]:
-            system = self.prmtop1.createSystem(removeCMMotion=b)
+            system = prmtop1.createSystem(removeCMMotion=b)
             forces = system.getForces()
             self.assertEqual(any(isinstance(f, CMMotionRemover) for f in forces), b)
 
     def test_RigidWaterAndConstraints(self):
         """Test all eight options for the constraints and rigidWater parameters."""
 
-        topology = self.prmtop1.topology
+        topology = prmtop1.topology
         for constraints_value in [None, HBonds, AllBonds, HAngles]:
             for rigidWater_value in [True, False]:
-                system = self.prmtop1.createSystem(constraints=constraints_value, 
-                                                   rigidWater=rigidWater_value)
+                system = prmtop1.createSystem(constraints=constraints_value, 
+                                              rigidWater=rigidWater_value)
                 validateConstraints(self, topology, system, 
                                     constraints_value, rigidWater_value)
 
@@ -84,7 +81,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
 
         """
         for implicitSolvent_value in [HCT, OBC1, OBC2, GBn]:
-            system = self.prmtop2.createSystem(implicitSolvent=implicitSolvent_value)
+            system = prmtop2.createSystem(implicitSolvent=implicitSolvent_value)
             forces = system.getForces()
             if implicitSolvent_value in set([HCT, OBC1, GBn]):
                 force_type = CustomGBForce
@@ -99,7 +96,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
                      CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic}
         for implicitSolvent_value in [HCT, OBC1, OBC2, GBn]:
             for method in methodMap:
-                system = self.prmtop2.createSystem(implicitSolvent=implicitSolvent_value, 
+                system = prmtop2.createSystem(implicitSolvent=implicitSolvent_value, 
                                     solventDielectric=50.0, soluteDielectric=0.9, nonbondedMethod=method)
                 found_matching_solvent_dielectric=False
                 found_matching_solute_dielectric=False
@@ -136,10 +133,10 @@ class TestAmberPrmtopFile(unittest.TestCase):
     def test_HydrogenMass(self):
         """Test that altering the mass of hydrogens works correctly."""
         
-        topology = self.prmtop1.topology
+        topology = prmtop1.topology
         hydrogenMass = 4*amu
-        system1 = self.prmtop1.createSystem()
-        system2 = self.prmtop1.createSystem(hydrogenMass=hydrogenMass)
+        system1 = prmtop1.createSystem()
+        system2 = prmtop1.createSystem(hydrogenMass=hydrogenMass)
         for atom in topology.atoms():
             if atom.element == elem.hydrogen:
                 self.assertNotEqual(hydrogenMass, system1.getParticleMass(atom.index))
@@ -148,5 +145,35 @@ class TestAmberPrmtopFile(unittest.TestCase):
         totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
         self.assertAlmostEqual(totalMass1, totalMass2)
 
+    def test_NBFIX(self):
+        """Test that prmtop files with modified off-diagonal LJ elements are treated properly"""
+        system = prmtop3.createSystem(nonbondedMethod=PME,
+                                      nonbondedCutoff=8*angstroms)
+        # Check the forces
+        has_nonbond_force = has_custom_nonbond_force = False
+        nonbond_exceptions = custom_nonbond_exclusions = 0
+        for force in system.getForces():
+            if isinstance(force, NonbondedForce):
+                has_nonbond_force = True
+                nonbond_exceptions = force.getNumExceptions()
+            elif isinstance(force, CustomNonbondedForce):
+                has_custom_nonbond_force = True
+                custom_nonbond_exceptions = force.getNumExclusions()
+        self.assertTrue(has_nonbond_force)
+        self.assertTrue(has_custom_nonbond_force)
+        self.assertEqual(nonbond_exceptions, custom_nonbond_exceptions)
+        integrator = VerletIntegrator(1.0*femtoseconds)
+        # Use reference platform, since it should always be present and
+        # 'working', and the system is plenty small so this won't be too slow
+        sim = Simulation(prmtop3.topology, system, integrator, Platform.getPlatformByName('Reference'))
+        # Check that the energy is about what we expect it to be
+        sim.context.setPeriodicBoxVectors(*inpcrd3.boxVectors)
+        sim.context.setPositions(inpcrd3.positions)
+        ene = sim.context.getState(getEnergy=True, enforcePeriodicBox=True).getPotentialEnergy()
+        ene = ene.value_in_unit(kilocalories_per_mole)
+        # Make sure the energy is relatively close to the value we get with
+        # Amber using this force field.
+        self.assertAlmostEqual(-7042.3903307/ene, 1, places=3)
+
 if __name__ == '__main__':
     unittest.main()

wrappers/python/tests/TestBytes.py

@@ -8,7 +8,8 @@ class TestBytes(unittest.TestCase):
         system.addParticle(1.0)
         refPositions = [(0,0,0)]
 
-        context = mm.Context(system, mm.VerletIntegrator(0))
+        platform = mm.Platform.getPlatformByName('Reference')
+        context = mm.Context(system, mm.VerletIntegrator(0), platform)
         context.setPositions(refPositions)
         chk = context.createCheckpoint()
         # check that the return value of createCheckpoint is of type bytes (non-unicode)
@@ -22,13 +23,6 @@ class TestBytes(unittest.TestCase):
 
         assert newPositions == refPositions
 
-        # try encoding the checkpoint in utf-8. OpenMM should be able to handle this too
-        context.setPositions([(12345, 12345, 123451)])
-        context.loadCheckpoint(chk.decode('utf-8'))
-        newPositions = context.getState(getPositions=True).getPositions()._value
-
-        assert newPositions == refPositions
-
 
 if __name__ == '__main__':
     unittest.main()

wrappers/python/tests/TestForceField.py

@@ -4,6 +4,7 @@ from simtk.openmm.app import *
 from simtk.openmm import *
 from simtk.unit import *
 import simtk.openmm.app.element as elem
+import simtk.openmm.app.forcefield as forcefield
 
 class TestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method."""
@@ -18,7 +19,8 @@ class TestForceField(unittest.TestCase):
         self.forcefield1 = ForceField('amber99sb.xml', 'tip3p.xml')
         self.topology1 = self.pdb1.topology
         self.topology1.setUnitCellDimensions(Vec3(2, 2, 2))
-        
+
+        # alalnine dipeptide with implicit water
         self.pdb2 = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         self.forcefield2 = ForceField('amber99sb.xml', 'amber99_obc.xml')
 
@@ -38,6 +40,18 @@ class TestForceField(unittest.TestCase):
                                 f.getNonbondedMethod()==methodMap[method] 
                                 for f in forces))
 
+    def test_DispersionCorrection(self):
+        """Test to make sure the nonbondedCutoff parameter is passed correctly."""
+
+        for useDispersionCorrection in [True, False]:
+            system = self.forcefield1.createSystem(self.pdb1.topology,
+                                                   nonbondedCutoff=2*nanometer, 
+                                                   useDispersionCorrection=useDispersionCorrection)
+
+            for force in system.getForces():
+                if isinstance(force, NonbondedForce):
+                    self.assertEqual(useDispersionCorrection, force.getUseDispersionCorrection())
+
     def test_Cutoff(self):
         """Test to make sure the nonbondedCutoff parameter is passed correctly."""
 
@@ -119,6 +133,113 @@ class TestForceField(unittest.TestCase):
         totalMass1 = sum([system1.getParticleMass(i) for i in range(system1.getNumParticles())]).value_in_unit(amu)
         totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
         self.assertAlmostEqual(totalMass1, totalMass2)
+    
+    def test_Forces(self):
+        """Compute forces and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""
+        
+        pdb = PDBFile('systems/lysozyme-implicit.pdb')
+        system = self.forcefield2.createSystem(pdb.topology)
+        integrator = VerletIntegrator(0.001)
+        context = Context(system, integrator)
+        context.setPositions(pdb.positions)
+        state1 = context.getState(getForces=True)
+        state2 = XmlSerializer.deserialize(open('systems/lysozyme-implicit-forces.xml').read())
+        numDifferences = 0
+        for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
+            diff = norm(f1-f2)
+            if diff > 0.1 and diff/norm(f1) > 1e-3:
+                numDifferences += 1
+        self.assertTrue(numDifferences < system.getNumParticles()/20) # Tolerate occasional differences from numerical error
+    
+    def test_ProgrammaticForceField(self):
+        """Test building a ForceField programmatically."""
+        
+        # Build the ForceField for TIP3P programmatically.
+        ff = ForceField()
+        ff.registerAtomType({'name':'tip3p-O', 'class':'OW', 'mass':15.99943*daltons, 'element':elem.oxygen})
+        ff.registerAtomType({'name':'tip3p-H', 'class':'HW', 'mass':1.007947*daltons, 'element':elem.hydrogen})
+        residue = ForceField._TemplateData('HOH')
+        residue.atoms.append(ForceField._TemplateAtomData('O', 'tip3p-O', elem.oxygen))
+        residue.atoms.append(ForceField._TemplateAtomData('H1', 'tip3p-H', elem.hydrogen))
+        residue.atoms.append(ForceField._TemplateAtomData('H2', 'tip3p-H', elem.hydrogen))
+        residue.addBond(0, 1)
+        residue.addBond(0, 2)
+        ff.registerResidueTemplate(residue)
+        bonds = forcefield.HarmonicBondGenerator(ff)
+        bonds.registerBond({'class1':'OW', 'class2':'HW', 'length':0.09572*nanometers, 'k':462750.4*kilojoules_per_mole/nanometer})
+        ff.registerGenerator(bonds)
+        angles = forcefield.HarmonicAngleGenerator(ff)
+        angles.registerAngle({'class1':'HW', 'class2':'OW', 'class3':'HW', 'angle':1.82421813418*radians, 'k':836.8*kilojoules_per_mole/radian})
+        ff.registerGenerator(angles)
+        nonbonded = forcefield.NonbondedGenerator(ff, 0.833333, 0.5)
+        nonbonded.registerAtom({'type':'tip3p-O', 'charge':-0.834, 'sigma':0.31507524065751241*nanometers, 'epsilon':0.635968*kilojoules_per_mole})
+        nonbonded.registerAtom({'type':'tip3p-H', 'charge':0.417, 'sigma':1*nanometers, 'epsilon':0*kilojoules_per_mole})
+        ff.registerGenerator(nonbonded)
+        
+        # Build a water box.
+        modeller = Modeller(Topology(), [])
+        modeller.addSolvent(ff, boxSize=Vec3(3, 3, 3)*nanometers)
+        
+        # Create a system using the programmatic force field as well as one from an XML file.
+        system1 = ff.createSystem(modeller.topology)
+        ff2 = ForceField('tip3p.xml')
+        system2 = ff2.createSystem(modeller.topology)
+        self.assertEqual(XmlSerializer.serialize(system1), XmlSerializer.serialize(system2))
+
+class AmoebaTestForceField(unittest.TestCase):
+    """Test the ForceField.createSystem() method with the AMOEBA forcefield."""
+ 
+    def setUp(self):
+        """Set up the tests by loading the input pdb files and force field 
+        xml files.
+
+        """
+
+        self.pdb1 = PDBFile('systems/amoeba-ion-in-water.pdb')
+        self.forcefield1 = ForceField('amoeba2009.xml')
+        self.topology1 = self.pdb1.topology
+
+
+    def test_NonbondedMethod(self):
+        """Test all five options for the nonbondedMethod parameter."""
+
+        methodMap = {NoCutoff:AmoebaMultipoleForce.NoCutoff,
+                     PME:AmoebaMultipoleForce.PME}
+
+        for method in methodMap:
+            system = self.forcefield1.createSystem(self.pdb1.topology,
+                                                  nonbondedMethod=method)
+            forces = system.getForces()
+            self.assertTrue(any(isinstance(f, AmoebaMultipoleForce) and
+                                f.getNonbondedMethod()==methodMap[method]
+                                for f in forces))
+    def test_Cutoff(self):
+        """Test to make sure the nonbondedCutoff parameter is passed correctly."""
+
+        cutoff_distance = 0.7*nanometer
+        for method in [NoCutoff, PME]:
+            system = self.forcefield1.createSystem(self.pdb1.topology,
+                                                   nonbondedMethod=method,
+                                                   nonbondedCutoff=cutoff_distance,
+                                                   constraints=None)
+
+            for force in system.getForces():
+                if isinstance(force, AmoebaVdwForce):
+                    self.assertEqual(force.getCutoff(), cutoff_distance)
+                if isinstance(force, AmoebaMultipoleForce):
+                    self.assertEqual(force.getCutoffDistance(), cutoff_distance)
+
+    def test_DispersionCorrection(self):
+        """Test to make sure the nonbondedCutoff parameter is passed correctly."""
+
+        for useDispersionCorrection in [True, False]:
+            system = self.forcefield1.createSystem(self.pdb1.topology,
+                                                   nonbondedMethod=PME,
+                                                   useDispersionCorrection=useDispersionCorrection)
+
+            for force in system.getForces():
+                if isinstance(force, AmoebaVdwForce):
+                    self.assertEqual(useDispersionCorrection, force.getUseDispersionCorrection())
 
 
 if __name__ == '__main__':

wrappers/python/tests/systems/amoeba-ion-in-water.pdb

+TITLE     Generated by filecnv.py : Water Cubic Box (18.643 Ang, 216 AMOEBA)
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   18.640   18.640   18.640  90.00  90.00  90.00 P 1           1
+MODEL        1
+ATOM      1  O   HOH     1       8.039   5.868   0.493  1.00  0.00            
+ATOM      2 H1   HOH     1       7.581   5.023   0.404  1.00  0.00            
+ATOM      3 H2   HOH     1       8.287   6.062  -0.397  1.00  0.00            
+ATOM      4  O   HOH     2       0.115  -8.877   6.446  1.00  0.00            
+ATOM      5 H1   HOH     2       0.959  -8.446   6.405  1.00  0.00            
+ATOM      6 H2   HOH     2       0.247  -9.794   6.138  1.00  0.00            
+ATOM      7  O   HOH     3      -6.576  -0.253   8.105  1.00  0.00            
+ATOM      8 H1   HOH     3      -6.646   0.690   7.896  1.00  0.00            
+ATOM      9 H2   HOH     3      -6.685  -0.401   9.104  1.00  0.00            
+ATOM     10  O   HOH     4       6.583   0.855  -6.669  1.00  0.00            
+ATOM     11 H1   HOH     4       6.260   0.887  -5.765  1.00  0.00            
+ATOM     12 H2   HOH     4       6.169   0.053  -7.054  1.00  0.00            
+ATOM     13  O   HOH     5       5.495   6.436   1.842  1.00  0.00            
+ATOM     14 H1   HOH     5       4.774   6.561   1.208  1.00  0.00            
+ATOM     15 H2   HOH     5       6.254   6.349   1.235  1.00  0.00            
+ATOM     16  O   HOH     6      -4.665  -8.502  -2.653  1.00  0.00            
+ATOM     17 H1   HOH     6      -4.505  -8.388  -3.607  1.00  0.00            
+ATOM     18 H2   HOH     6      -5.565  -8.751  -2.596  1.00  0.00            
+ATOM     19  O   HOH     7      -7.755  -4.661   4.905  1.00  0.00            
+ATOM     20 H1   HOH     7      -7.358  -5.440   5.311  1.00  0.00            
+ATOM     21 H2   HOH     7      -7.076  -4.177   4.404  1.00  0.00            
+ATOM     22  O   HOH     8      -0.282   7.487  -7.686  1.00  0.00            
+ATOM     23 H1   HOH     8      -0.794   7.446  -6.826  1.00  0.00            
+ATOM     24 H2   HOH     8       0.170   8.381  -7.637  1.00  0.00            
+ATOM     25  O   HOH     9      -3.711  -2.262  -1.917  1.00  0.00            
+ATOM     26 H1   HOH     9      -4.424  -2.426  -2.472  1.00  0.00            
+ATOM     27 H2   HOH     9      -4.023  -2.211  -0.972  1.00  0.00            
+ATOM     28  O   HOH    10      -5.812  -5.616   0.835  1.00  0.00            
+ATOM     29 H1   HOH    10      -6.676  -5.712   1.297  1.00  0.00            
+ATOM     30 H2   HOH    10      -5.143  -5.532   1.560  1.00  0.00            
+ATOM     31  O   HOH    11       8.528   5.000   3.444  1.00  0.00            
+ATOM     32 H1   HOH    11       8.866   4.760   4.341  1.00  0.00            
+ATOM     33 H2   HOH    11       7.683   4.540   3.378  1.00  0.00            
+ATOM     34  O   HOH    12       0.063   3.962  -6.445  1.00  0.00            
+ATOM     35 H1   HOH    12      -0.645   4.454  -6.001  1.00  0.00            
+ATOM     36 H2   HOH    12       0.070   3.123  -5.989  1.00  0.00            
+ATOM     37  O   HOH    13       0.169   6.582   6.098  1.00  0.00            
+ATOM     38 H1   HOH    13       0.291   6.371   7.040  1.00  0.00            
+ATOM     39 H2   HOH    13      -0.396   5.942   5.671  1.00  0.00            
+ATOM     40  O   HOH    14       3.739   6.291   8.132  1.00  0.00            
+ATOM     41 H1   HOH    14       4.150   6.101   9.011  1.00  0.00            
+ATOM     42 H2   HOH    14       4.395   5.921   7.527  1.00  0.00            
+ATOM     43  O   HOH    15       3.250   4.562  -2.564  1.00  0.00            
+ATOM     44 H1   HOH    15       3.743   4.531  -3.375  1.00  0.00            
+ATOM     45 H2   HOH    15       2.699   5.379  -2.486  1.00  0.00            
+ATOM     46  O   HOH    16       5.618   5.202   6.376  1.00  0.00            
+ATOM     47 H1   HOH    16       5.619   5.614   5.531  1.00  0.00            
+ATOM     48 H2   HOH    16       5.490   4.269   6.211  1.00  0.00            
+ATOM     49  O   HOH    17      -8.775   6.941  -6.178  1.00  0.00            
+ATOM     50 H1   HOH    17      -8.218   7.319  -5.471  1.00  0.00            
+ATOM     51 H2   HOH    17      -9.036   7.737  -6.649  1.00  0.00            
+ATOM     52  O   HOH    18      -6.941   2.249   7.194  1.00  0.00            
+ATOM     53 H1   HOH    18      -7.367   2.209   6.349  1.00  0.00            
+ATOM     54 H2   HOH    18      -7.415   2.897   7.720  1.00  0.00            
+ATOM     55  O   HOH    19       4.829  -0.184   3.152  1.00  0.00            
+ATOM     56 H1   HOH    19       5.557   0.243   2.724  1.00  0.00            
+ATOM     57 H2   HOH    19       4.135   0.501   3.237  1.00  0.00            
+ATOM     58  O   HOH    20      -2.202  -3.107   9.171  1.00  0.00            
+ATOM     59 H1   HOH    20      -2.320  -4.072   9.247  1.00  0.00            
+ATOM     60 H2   HOH    20      -2.802  -2.935   8.421  1.00  0.00            
+ATOM     61  O   HOH    21       1.689   6.673  -2.435  1.00  0.00            
+ATOM     62 H1   HOH    21       1.972   7.519  -2.054  1.00  0.00            
+ATOM     63 H2   HOH    21       0.874   6.423  -1.954  1.00  0.00            
+ATOM     64  O   HOH    22      -9.080  -6.244  -0.882  1.00  0.00            
+ATOM     65 H1   HOH    22      -8.673  -7.043  -0.480  1.00  0.00            
+ATOM     66 H2   HOH    22      -8.364  -5.814  -1.383  1.00  0.00            
+ATOM     67  O   HOH    23      -8.657  -8.654   0.563  1.00  0.00            
+ATOM     68 H1   HOH    23      -8.178  -9.465   0.842  1.00  0.00            
+ATOM     69 H2   HOH    23      -9.453  -8.686   1.056  1.00  0.00            
+ATOM     70  O   HOH    24      -5.772  -2.632  -4.588  1.00  0.00            
+ATOM     71 H1   HOH    24      -5.457  -3.169  -5.272  1.00  0.00            
+ATOM     72 H2   HOH    24      -5.550  -1.707  -4.739  1.00  0.00            
+ATOM     73  O   HOH    25       7.237  -8.468  -6.950  1.00  0.00            
+ATOM     74 H1   HOH    25       7.990  -8.965  -7.276  1.00  0.00            
+ATOM     75 H2   HOH    25       7.508  -8.173  -6.060  1.00  0.00            
+ATOM     76  O   HOH    26      -2.377  -6.252   1.292  1.00  0.00            
+ATOM     77 H1   HOH    26      -1.831  -6.216   0.487  1.00  0.00            
+ATOM     78 H2   HOH    26      -2.393  -5.371   1.645  1.00  0.00            
+ATOM     79  O   HOH    27       0.833  -5.019   5.432  1.00  0.00            
+ATOM     80 H1   HOH    27       1.092  -5.764   4.863  1.00  0.00            
+ATOM     81 H2   HOH    27       0.148  -5.508   5.955  1.00  0.00            
+ATOM     82  O   HOH    28       7.425  -2.742   0.838  1.00  0.00            
+ATOM     83 H1   HOH    28       6.867  -2.455   1.621  1.00  0.00            
+ATOM     84 H2   HOH    28       7.152  -3.642   0.725  1.00  0.00            
+ATOM     85  O   HOH    29      -0.251   8.631   2.286  1.00  0.00            
+ATOM     86 H1   HOH    29       0.096   9.072   1.496  1.00  0.00            
+ATOM     87 H2   HOH    29       0.451   8.716   2.905  1.00  0.00            
+ATOM     88  O   HOH    30       4.778   9.024   8.252  1.00  0.00            
+ATOM     89 H1   HOH    30       4.396   8.079   8.249  1.00  0.00            
+ATOM     90 H2   HOH    30       4.683   9.287   9.179  1.00  0.00            
+ATOM     91  O   HOH    31       8.220   9.015  -2.508  1.00  0.00            
+ATOM     92 H1   HOH    31       8.519   8.140  -2.217  1.00  0.00            
+ATOM     93 H2   HOH    31       7.640   9.201  -1.814  1.00  0.00            
+ATOM     94  O   HOH    32      -7.944   1.760   4.644  1.00  0.00            
+ATOM     95 H1   HOH    32      -7.921   2.353   3.866  1.00  0.00            
+ATOM     96 H2   HOH    32      -8.706   1.129   4.460  1.00  0.00            
+ATOM     97  O   HOH    33       3.243   3.821  -8.247  1.00  0.00            
+ATOM     98 H1   HOH    33       2.832   4.291  -7.488  1.00  0.00            
+ATOM     99 H2   HOH    33       2.768   2.984  -8.262  1.00  0.00            
+ATOM    100  O   HOH    34       7.558  -8.962   2.368  1.00  0.00            
+ATOM    101 H1   HOH    34       6.660  -8.703   2.710  1.00  0.00            
+ATOM    102 H2   HOH    34       8.154  -9.119   3.115  1.00  0.00            
+ATOM    103  O   HOH    35      -8.425   3.501  -4.439  1.00  0.00            
+ATOM    104 H1   HOH    35      -7.569   3.951  -4.471  1.00  0.00            
+ATOM    105 H2   HOH    35      -8.698   3.546  -5.370  1.00  0.00            
+ATOM    106  O   HOH    36       3.884  -4.850   6.532  1.00  0.00            
+ATOM    107 H1   HOH    36       4.124  -4.040   7.026  1.00  0.00            
+ATOM    108 H2   HOH    36       3.006  -4.640   6.051  1.00  0.00            
+ATOM    109  O   HOH    37       6.206  -5.083   4.954  1.00  0.00            
+ATOM    110 H1   HOH    37       6.896  -5.351   5.633  1.00  0.00            
+ATOM    111 H2   HOH    37       5.366  -5.112   5.464  1.00  0.00            
+ATOM    112  O   HOH    38       7.035  -5.175  -0.739  1.00  0.00            
+ATOM    113 H1   HOH    38       7.853  -5.654  -0.959  1.00  0.00            
+ATOM    114 H2   HOH    38       6.781  -4.792  -1.619  1.00  0.00            
+ATOM    115  O   HOH    39      -4.412  -4.775   3.088  1.00  0.00            
+ATOM    116 H1   HOH    39      -5.065  -4.108   3.116  1.00  0.00            
+ATOM    117 H2   HOH    39      -4.659  -5.257   3.876  1.00  0.00            
+ATOM    118  O   HOH    40      -9.194  -0.001  -2.536  1.00  0.00            
+ATOM    119 H1   HOH    40      -8.589  -0.704  -2.223  1.00  0.00            
+ATOM    120 H2   HOH    40      -8.744   0.832  -2.345  1.00  0.00            
+ATOM    121  O   HOH    41       5.087   2.357   5.594  1.00  0.00            
+ATOM    122 H1   HOH    41       4.145   2.609   5.868  1.00  0.00            
+ATOM    123 H2   HOH    41       5.185   1.494   5.856  1.00  0.00            
+ATOM    124  O   HOH    42      -4.683  -6.147  -1.679  1.00  0.00            
+ATOM    125 H1   HOH    42      -4.869  -5.961  -0.746  1.00  0.00            
+ATOM    126 H2   HOH    42      -4.916  -7.050  -1.813  1.00  0.00            
+ATOM    127  O   HOH    43      -3.179  -0.054  -3.640  1.00  0.00            
+ATOM    128 H1   HOH    43      -2.225  -0.245  -3.524  1.00  0.00            
+ATOM    129 H2   HOH    43      -3.604  -0.351  -2.841  1.00  0.00            
+ATOM    130  O   HOH    44       1.046   2.676  -2.268  1.00  0.00            
+ATOM    131 H1   HOH    44       1.843   3.245  -2.357  1.00  0.00            
+ATOM    132 H2   HOH    44       1.057   2.363  -1.383  1.00  0.00            
+ATOM    133  O   HOH    45      -1.412   4.165  -2.732  1.00  0.00            
+ATOM    134 H1   HOH    45      -0.521   3.698  -2.666  1.00  0.00            
+ATOM    135 H2   HOH    45      -1.383   4.769  -1.944  1.00  0.00            
+ATOM    136  O   HOH    46      -7.660  -2.122  -1.952  1.00  0.00            
+ATOM    137 H1   HOH    46      -8.019  -2.839  -1.356  1.00  0.00            
+ATOM    138 H2   HOH    46      -7.442  -2.604  -2.817  1.00  0.00            
+ATOM    139  O   HOH    47      -1.360   1.967   2.035  1.00  0.00            
+ATOM    140 H1   HOH    47      -1.620   2.869   2.312  1.00  0.00            
+ATOM    141 H2   HOH    47      -2.179   1.451   1.920  1.00  0.00            
+ATOM    142  O   HOH    48       6.290  -4.230  -7.656  1.00  0.00            
+ATOM    143 H1   HOH    48       6.233  -4.447  -6.717  1.00  0.00            
+ATOM    144 H2   HOH    48       6.335  -5.070  -8.050  1.00  0.00            
+ATOM    145  O   HOH    49       9.159  -0.398   3.519  1.00  0.00            
+ATOM    146 H1   HOH    49       9.889  -0.447   2.916  1.00  0.00            
+ATOM    147 H2   HOH    49       8.413  -0.023   2.971  1.00  0.00            
+ATOM    148  O   HOH    50       4.847  -0.826   6.008  1.00  0.00            
+ATOM    149 H1   HOH    50       3.902  -0.629   6.020  1.00  0.00            
+ATOM    150 H2   HOH    50       5.056  -0.799   5.078  1.00  0.00            
+ATOM    151  O   HOH    51      -7.285  -3.465   7.597  1.00  0.00            
+ATOM    152 H1   HOH    51      -7.607  -3.697   6.732  1.00  0.00            
+ATOM    153 H2   HOH    51      -7.133  -2.492   7.565  1.00  0.00            
+ATOM    154  O   HOH    52      -3.090  -3.803   6.552  1.00  0.00            
+ATOM    155 H1   HOH    52      -3.502  -4.557   6.104  1.00  0.00            
+ATOM    156 H2   HOH    52      -2.848  -3.218   5.793  1.00  0.00            
+ATOM    157  O   HOH    53      -0.628  -0.643  -0.688  1.00  0.00            
+ATOM    158 H1   HOH    53      -0.750   0.199  -0.182  1.00  0.00            
+ATOM    159 H2   HOH    53       0.325  -0.889  -0.564  1.00  0.00            
+ATOM    160  O   HOH    54       1.167  -6.679   1.145  1.00  0.00            
+ATOM    161 H1   HOH    54       0.652  -7.308   0.653  1.00  0.00            
+ATOM    162 H2   HOH    54       1.613  -6.178   0.472  1.00  0.00            
+ATOM    163  O   HOH    55       0.886  -7.185   3.758  1.00  0.00            
+ATOM    164 H1   HOH    55       1.236  -8.069   3.709  1.00  0.00            
+ATOM    165 H2   HOH    55       0.920  -6.831   2.841  1.00  0.00            
+ATOM    166  O   HOH    56       2.135   0.084   6.041  1.00  0.00            
+ATOM    167 H1   HOH    56       1.885   0.433   5.160  1.00  0.00            
+ATOM    168 H2   HOH    56       1.679  -0.767   6.079  1.00  0.00            
+ATOM    169  O   HOH    57       0.184   0.302   8.421  1.00  0.00            
+ATOM    170 H1   HOH    57      -0.716   0.418   8.707  1.00  0.00            
+ATOM    171 H2   HOH    57       0.445  -0.630   8.637  1.00  0.00            
+ATOM    172  O   HOH    58      -3.149  -1.997  -5.795  1.00  0.00            
+ATOM    173 H1   HOH    58      -3.232  -1.461  -5.013  1.00  0.00            
+ATOM    174 H2   HOH    58      -3.477  -1.481  -6.557  1.00  0.00            
+ATOM    175  O   HOH    59       2.201  -0.482  -6.617  1.00  0.00            
+ATOM    176 H1   HOH    59       1.368  -0.946  -6.453  1.00  0.00            
+ATOM    177 H2   HOH    59       2.705  -1.216  -6.954  1.00  0.00            
+ATOM    178  O   HOH    60      -1.572  -2.002   4.844  1.00  0.00            
+ATOM    179 H1   HOH    60      -0.747  -2.095   5.356  1.00  0.00            
+ATOM    180 H2   HOH    60      -1.852  -1.078   5.002  1.00  0.00            
+ATOM    181  O   HOH    61       5.400   6.380  -8.004  1.00  0.00            
+ATOM    182 H1   HOH    61       5.037   7.155  -7.526  1.00  0.00            
+ATOM    183 H2   HOH    61       5.148   5.594  -7.490  1.00  0.00            
+ATOM    184  O   HOH    62      -6.338   5.728  -1.743  1.00  0.00            
+ATOM    185 H1   HOH    62      -6.067   4.771  -1.768  1.00  0.00            
+ATOM    186 H2   HOH    62      -5.664   6.129  -2.295  1.00  0.00            
+ATOM    187  O   HOH    63      -2.100  -2.775   0.706  1.00  0.00            
+ATOM    188 H1   HOH    63      -1.406  -3.020   1.364  1.00  0.00            
+ATOM    189 H2   HOH    63      -1.688  -2.182   0.070  1.00  0.00            
+ATOM    190  O   HOH    64      -0.008   5.633   1.418  1.00  0.00            
+ATOM    191 H1   HOH    64      -0.737   5.003   1.551  1.00  0.00            
+ATOM    192 H2   HOH    64      -0.256   6.473   1.771  1.00  0.00            
+ATOM    193  O   HOH    65       3.960  -1.908  -1.971  1.00  0.00            
+ATOM    194 H1   HOH    65       4.389  -1.569  -1.158  1.00  0.00            
+ATOM    195 H2   HOH    65       3.764  -1.183  -2.532  1.00  0.00            
+ATOM    196  O   HOH    66       0.396  -2.409   8.942  1.00  0.00            
+ATOM    197 H1   HOH    66      -0.496  -2.716   8.996  1.00  0.00            
+ATOM    198 H2   HOH    66       0.843  -2.715   9.772  1.00  0.00            
+ATOM    199  O   HOH    67      -5.904  -3.598  -7.198  1.00  0.00            
+ATOM    200 H1   HOH    67      -5.391  -4.021  -7.836  1.00  0.00            
+ATOM    201 H2   HOH    67      -6.856  -3.905  -7.407  1.00  0.00            
+ATOM    202  O   HOH    68       4.776   3.286  -0.543  1.00  0.00            
+ATOM    203 H1   HOH    68       4.503   3.668  -1.420  1.00  0.00            
+ATOM    204 H2   HOH    68       4.308   3.804   0.151  1.00  0.00            
+ATOM    205  O   HOH    69       1.810   1.667  -8.491  1.00  0.00            
+ATOM    206 H1   HOH    69       1.048   1.572  -9.074  1.00  0.00            
+ATOM    207 H2   HOH    69       1.737   0.971  -7.784  1.00  0.00            
+ATOM    208  O   HOH    70      -6.984   8.521   4.996  1.00  0.00            
+ATOM    209 H1   HOH    70      -6.319   9.034   4.547  1.00  0.00            
+ATOM    210 H2   HOH    70      -6.786   7.567   5.127  1.00  0.00            
+ATOM    211  O   HOH    71       8.036  -7.667   5.624  1.00  0.00            
+ATOM    212 H1   HOH    71       8.944  -7.942   5.438  1.00  0.00            
+ATOM    213 H2   HOH    71       8.006  -7.115   6.374  1.00  0.00            
+ATOM    214  O   HOH    72      -2.369   4.402   2.749  1.00  0.00            
+ATOM    215 H1   HOH    72      -2.101   4.193   3.659  1.00  0.00            
+ATOM    216 H2   HOH    72      -3.291   4.630   2.773  1.00  0.00            
+ATOM    217  O   HOH    73       7.332   0.910   8.635  1.00  0.00            
+ATOM    218 H1   HOH    73       6.493   0.534   8.784  1.00  0.00            
+ATOM    219 H2   HOH    73       7.141   1.869   8.632  1.00  0.00            
+ATOM    220  O   HOH    74       0.369   1.474   4.008  1.00  0.00            
+ATOM    221 H1   HOH    74      -0.105   1.445   4.853  1.00  0.00            
+ATOM    222 H2   HOH    74      -0.369   1.533   3.336  1.00  0.00            
+ATOM    223  O   HOH    75       5.767  -9.208   5.731  1.00  0.00            
+ATOM    224 H1   HOH    75       5.445  -9.395   6.580  1.00  0.00            
+ATOM    225 H2   HOH    75       6.702  -8.805   5.685  1.00  0.00            
+ATOM    226  O   HOH    76       4.162  -2.372   0.781  1.00  0.00            
+ATOM    227 H1   HOH    76       4.495  -2.247   1.647  1.00  0.00            
+ATOM    228 H2   HOH    76       3.609  -3.133   0.711  1.00  0.00            
+ATOM    229  O   HOH    77      -1.983  -6.868  -7.665  1.00  0.00            
+ATOM    230 H1   HOH    77      -1.149  -6.836  -8.203  1.00  0.00            
+ATOM    231 H2   HOH    77      -2.094  -5.962  -7.318  1.00  0.00            
+ATOM    232  O   HOH    78      -4.374  -7.889   1.779  1.00  0.00            
+ATOM    233 H1   HOH    78      -3.642  -7.300   1.538  1.00  0.00            
+ATOM    234 H2   HOH    78      -5.071  -7.407   1.392  1.00  0.00            
+ATOM    235  O   HOH    79       5.161   6.852   4.554  1.00  0.00            
+ATOM    236 H1   HOH    79       5.392   7.675   4.897  1.00  0.00            
+ATOM    237 H2   HOH    79       5.444   6.815   3.631  1.00  0.00            
+ATOM    238  O   HOH    80      -9.138   9.041  -8.058  1.00  0.00            
+ATOM    239 H1   HOH    80      -8.630   9.855  -7.946  1.00  0.00            
+ATOM    240 H2   HOH    80      -9.127   8.772  -9.011  1.00  0.00            
+ATOM    241  O   HOH    81      -5.687  -0.393   5.354  1.00  0.00            
+ATOM    242 H1   HOH    81      -6.067   0.366   4.992  1.00  0.00            
+ATOM    243 H2   HOH    81      -5.831  -0.447   6.338  1.00  0.00            
+ATOM    244  O   HOH    82       1.031   2.281   0.575  1.00  0.00            
+ATOM    245 H1   HOH    82       0.182   2.216   1.029  1.00  0.00            
+ATOM    246 H2   HOH    82       1.469   3.073   0.944  1.00  0.00            
+ATOM    247  O   HOH    83      -5.344  -9.069  -7.701  1.00  0.00            
+ATOM    248 H1   HOH    83      -6.076  -8.559  -8.046  1.00  0.00            
+ATOM    249 H2   HOH    83      -5.531  -9.974  -8.022  1.00  0.00            
+ATOM    250  O   HOH    84       1.744  -4.694  -7.741  1.00  0.00            
+ATOM    251 H1   HOH    84       1.332  -4.686  -6.836  1.00  0.00            
+ATOM    252 H2   HOH    84       2.349  -3.997  -7.787  1.00  0.00            
+ATOM    253  O   HOH    85       5.038   8.639  -6.175  1.00  0.00            
+ATOM    254 H1   HOH    85       5.785   9.177  -6.374  1.00  0.00            
+ATOM    255 H2   HOH    85       5.210   8.228  -5.345  1.00  0.00            
+ATOM    256  O   HOH    86      -0.023   8.844  -3.570  1.00  0.00            
+ATOM    257 H1   HOH    86      -0.459   9.203  -4.426  1.00  0.00            
+ATOM    258 H2   HOH    86       0.776   8.381  -3.782  1.00  0.00            
+ATOM    259  O   HOH    87      -1.668  -9.035  -5.632  1.00  0.00            
+ATOM    260 H1   HOH    87      -1.508  -8.745  -6.515  1.00  0.00            
+ATOM    261 H2   HOH    87      -2.505  -8.575  -5.447  1.00  0.00            
+ATOM    262  O   HOH    88      -1.025  -4.139   2.924  1.00  0.00            
+ATOM    263 H1   HOH    88      -1.638  -3.581   3.380  1.00  0.00            
+ATOM    264 H2   HOH    88      -0.344  -4.419   3.603  1.00  0.00            
+ATOM    265  O   HOH    89       6.772  -9.275  -0.062  1.00  0.00            
+ATOM    266 H1   HOH    89       6.321  -8.407   0.016  1.00  0.00            
+ATOM    267 H2   HOH    89       7.220  -9.351   0.768  1.00  0.00            
+ATOM    268  O   HOH    90      -5.260   5.074   2.814  1.00  0.00            
+ATOM    269 H1   HOH    90      -5.317   5.651   2.001  1.00  0.00            
+ATOM    270 H2   HOH    90      -5.953   4.419   2.667  1.00  0.00            
+ATOM    271  O   HOH    91       0.439  -7.109  -3.006  1.00  0.00            
+ATOM    272 H1   HOH    91       0.122  -6.760  -2.168  1.00  0.00            
+ATOM    273 H2   HOH    91       0.300  -8.047  -3.005  1.00  0.00            
+ATOM    274  O   HOH    92       4.754   0.068  -8.893  1.00  0.00            
+ATOM    275 H1   HOH    92       4.497  -0.819  -8.504  1.00  0.00            
+ATOM    276 H2   HOH    92       3.924   0.546  -9.098  1.00  0.00            
+ATOM    277  O   HOH    93       8.453  -3.238   4.470  1.00  0.00            
+ATOM    278 H1   HOH    93       8.534  -2.386   4.151  1.00  0.00            
+ATOM    279 H2   HOH    93       9.380  -3.622   4.525  1.00  0.00            
+ATOM    280  O   HOH    94      -8.562  -3.354  -5.396  1.00  0.00            
+ATOM    281 H1   HOH    94      -8.983  -3.218  -6.264  1.00  0.00            
+ATOM    282 H2   HOH    94      -7.657  -3.008  -5.367  1.00  0.00            
+ATOM    283  O   HOH    95      -4.087  -7.007   9.259  1.00  0.00            
+ATOM    284 H1   HOH    95      -4.504  -7.764   9.701  1.00  0.00            
+ATOM    285 H2   HOH    95      -3.209  -6.941   9.653  1.00  0.00            
+ATOM    286  O   HOH    96      -2.961   2.902  -4.614  1.00  0.00            
+ATOM    287 H1   HOH    96      -3.009   1.975  -4.316  1.00  0.00            
+ATOM    288 H2   HOH    96      -2.450   3.376  -3.907  1.00  0.00            
+ATOM    289  O   HOH    97      -8.496  -3.305   0.422  1.00  0.00            
+ATOM    290 H1   HOH    97      -8.208  -3.909   1.155  1.00  0.00            
+ATOM    291 H2   HOH    97      -9.382  -3.162   0.529  1.00  0.00            
+ATOM    292  O   HOH    98      -8.646   7.535   1.955  1.00  0.00            
+ATOM    293 H1   HOH    98      -9.207   6.758   1.900  1.00  0.00            
+ATOM    294 H2   HOH    98      -8.931   7.852   2.808  1.00  0.00            
+ATOM    295  O   HOH    99       5.325   0.684  -1.143  1.00  0.00            
+ATOM    296 H1   HOH    99       6.163   0.574  -0.698  1.00  0.00            
+ATOM    297 H2   HOH    99       4.928   1.523  -0.792  1.00  0.00            
+ATOM    298  O   HOH   100      -0.302   3.603  -9.202  1.00  0.00            
+ATOM    299 H1   HOH   100       0.254   4.336  -9.458  1.00  0.00            
+ATOM    300 H2   HOH   100      -0.128   3.520  -8.233  1.00  0.00            
+ATOM    301  O   HOH   101      -7.609  -7.414  -7.642  1.00  0.00            
+ATOM    302 H1   HOH   101      -7.583  -6.832  -8.402  1.00  0.00            
+ATOM    303 H2   HOH   101      -7.817  -6.856  -6.873  1.00  0.00            
+ATOM    304  O   HOH   102      -7.162  -0.866  -7.830  1.00  0.00            
+ATOM    305 H1   HOH   102      -6.916  -1.664  -7.366  1.00  0.00            
+ATOM    306 H2   HOH   102      -8.117  -0.865  -7.738  1.00  0.00            
+ATOM    307  O   HOH   103       8.628  -2.873  -7.501  1.00  0.00            
+ATOM    308 H1   HOH   103       8.430  -2.014  -7.969  1.00  0.00            
+ATOM    309 H2   HOH   103       7.755  -3.342  -7.575  1.00  0.00            
+ATOM    310  O   HOH   104       0.296  -6.725  -9.137  1.00  0.00            
+ATOM    311 H1   HOH   104       0.011  -6.271  -9.953  1.00  0.00            
+ATOM    312 H2   HOH   104       0.802  -5.981  -8.711  1.00  0.00            
+ATOM    313  O   HOH   105      -2.283   4.666   7.799  1.00  0.00            
+ATOM    314 H1   HOH   105      -2.473   5.640   7.876  1.00  0.00            
+ATOM    315 H2   HOH   105      -1.790   4.332   8.562  1.00  0.00            
+ATOM    316  O   HOH   106      -5.132  -2.648   0.721  1.00  0.00            
+ATOM    317 H1   HOH   106      -4.418  -2.848   1.417  1.00  0.00            
+ATOM    318 H2   HOH   106      -5.583  -3.451   0.568  1.00  0.00            
+ATOM    319  O   HOH   107       3.597  -7.110  -8.571  1.00  0.00            
+ATOM    320 H1   HOH   107       3.557  -6.612  -7.707  1.00  0.00            
+ATOM    321 H2   HOH   107       2.931  -6.774  -9.116  1.00  0.00            
+ATOM    322  O   HOH   108      -8.608  -8.319   3.526  1.00  0.00            
+ATOM    323 H1   HOH   108      -7.992  -8.997   3.888  1.00  0.00            
+ATOM    324 H2   HOH   108      -8.438  -8.243   2.566  1.00  0.00            
+ATOM    325  O   HOH   109      -6.941   8.524  -4.898  1.00  0.00            
+ATOM    326 H1   HOH   109      -6.037   8.201  -4.795  1.00  0.00            
+ATOM    327 H2   HOH   109      -6.826   9.016  -5.706  1.00  0.00            
+ATOM    328  O   HOH   110      -8.618   2.117   0.328  1.00  0.00            
+ATOM    329 H1   HOH   110      -9.507   2.587   0.268  1.00  0.00            
+ATOM    330 H2   HOH   110      -8.802   1.370   0.915  1.00  0.00            
+ATOM    331  O   HOH   111      -6.703  -7.096   5.720  1.00  0.00            
+ATOM    332 H1   HOH   111      -6.345  -7.797   5.144  1.00  0.00            
+ATOM    333 H2   HOH   111      -7.115  -7.623   6.408  1.00  0.00            
+ATOM    334  O   HOH   112      -4.243   1.635  -7.536  1.00  0.00            
+ATOM    335 H1   HOH   112      -3.372   1.373  -7.866  1.00  0.00            
+ATOM    336 H2   HOH   112      -4.520   2.387  -8.161  1.00  0.00            
+ATOM    337  O   HOH   113      -4.209  -8.163  -5.306  1.00  0.00            
+ATOM    338 H1   HOH   113      -4.273  -7.181  -5.411  1.00  0.00            
+ATOM    339 H2   HOH   113      -4.501  -8.381  -6.200  1.00  0.00            
+ATOM    340  O   HOH   114       6.037   3.308  -8.447  1.00  0.00            
+ATOM    341 H1   HOH   114       5.046   3.370  -8.401  1.00  0.00            
+ATOM    342 H2   HOH   114       6.249   2.483  -8.061  1.00  0.00            
+ATOM    343  O   HOH   115       1.855  -0.633   0.513  1.00  0.00            
+ATOM    344 H1   HOH   115       2.810  -0.778   0.512  1.00  0.00            
+ATOM    345 H2   HOH   115       1.713   0.210   0.906  1.00  0.00            
+ATOM    346  O   HOH   116      -0.350  -0.799  -3.447  1.00  0.00            
+ATOM    347 H1   HOH   116      -0.639  -0.602  -2.521  1.00  0.00            
+ATOM    348 H2   HOH   116      -0.468  -1.735  -3.577  1.00  0.00            
+ATOM    349  O   HOH   117       2.557   6.236   4.285  1.00  0.00            
+ATOM    350 H1   HOH   117       1.909   6.451   4.910  1.00  0.00            
+ATOM    351 H2   HOH   117       3.454   6.494   4.590  1.00  0.00            
+ATOM    352  O   HOH   118      -7.374  -8.763  -2.641  1.00  0.00            
+ATOM    353 H1   HOH   118      -7.322  -9.154  -3.510  1.00  0.00            
+ATOM    354 H2   HOH   118      -7.997  -9.286  -2.168  1.00  0.00            
+ATOM    355  O   HOH   119       5.102  -2.717   7.917  1.00  0.00            
+ATOM    356 H1   HOH   119       5.105  -2.075   7.214  1.00  0.00            
+ATOM    357 H2   HOH   119       5.997  -3.082   7.930  1.00  0.00            
+ATOM    358  O   HOH   120       0.617  -6.049  -5.430  1.00  0.00            
+ATOM    359 H1   HOH   120       0.065  -6.639  -5.953  1.00  0.00            
+ATOM    360 H2   HOH   120       0.625  -6.347  -4.518  1.00  0.00            
+ATOM    361  O   HOH   121      -5.018   6.814  -8.879  1.00  0.00            
+ATOM    362 H1   HOH   121      -4.047   6.554  -8.848  1.00  0.00            
+ATOM    363 H2   HOH   121      -5.495   6.325  -8.167  1.00  0.00            
+ATOM    364  O   HOH   122      -3.571   8.179   1.037  1.00  0.00            
+ATOM    365 H1   HOH   122      -4.358   7.666   0.884  1.00  0.00            
+ATOM    366 H2   HOH   122      -3.813   9.131   1.289  1.00  0.00            
+ATOM    367  O   HOH   123      -1.089   6.429  -1.100  1.00  0.00            
+ATOM    368 H1   HOH   123      -0.958   6.512  -0.129  1.00  0.00            
+ATOM    369 H2   HOH   123      -1.425   7.353  -1.265  1.00  0.00            
+ATOM    370  O   HOH   124      -8.068   3.899  -9.306  1.00  0.00            
+ATOM    371 H1   HOH   124      -8.429   4.769  -9.587  1.00  0.00            
+ATOM    372 H2   HOH   124      -7.407   4.106  -8.627  1.00  0.00            
+ATOM    373  O   HOH   125      -7.322  -0.835   1.865  1.00  0.00            
+ATOM    374 H1   HOH   125      -6.633  -0.258   1.516  1.00  0.00            
+ATOM    375 H2   HOH   125      -7.594  -1.468   1.181  1.00  0.00            
+ATOM    376  O   HOH   126       6.137  -3.751  -2.944  1.00  0.00            
+ATOM    377 H1   HOH   126       5.314  -3.197  -2.837  1.00  0.00            
+ATOM    378 H2   HOH   126       6.747  -3.054  -3.268  1.00  0.00            
+ATOM    379  O   HOH   127       2.833   7.012   0.636  1.00  0.00            
+ATOM    380 H1   HOH   127       2.330   7.844   0.881  1.00  0.00            
+ATOM    381 H2   HOH   127       2.160   6.335   0.437  1.00  0.00            
+ATOM    382  O   HOH   128       3.405  -5.843  -5.838  1.00  0.00            
+ATOM    383 H1   HOH   128       4.240  -5.687  -5.479  1.00  0.00            
+ATOM    384 H2   HOH   128       2.799  -5.627  -5.149  1.00  0.00            
+ATOM    385  O   HOH   129       4.865   3.938  -5.085  1.00  0.00            
+ATOM    386 H1   HOH   129       4.895   2.983  -5.154  1.00  0.00            
+ATOM    387 H2   HOH   129       5.751   4.278  -4.809  1.00  0.00            
+ATOM    388  O   HOH   130      -4.993  -8.656   4.141  1.00  0.00            
+ATOM    389 H1   HOH   130      -4.097  -9.036   4.154  1.00  0.00            
+ATOM    390 H2   HOH   130      -5.019  -8.186   3.285  1.00  0.00            
+ATOM    391  O   HOH   131      -9.292  -0.951   7.718  1.00  0.00            
+ATOM    392 H1   HOH   131     -10.069  -0.492   8.136  1.00  0.00            
+ATOM    393 H2   HOH   131      -8.538  -0.352   7.799  1.00  0.00            
+ATOM    394  O   HOH   132       5.820  -2.735   3.218  1.00  0.00            
+ATOM    395 H1   HOH   132       5.911  -2.123   3.919  1.00  0.00            
+ATOM    396 H2   HOH   132       6.270  -3.544   3.552  1.00  0.00            
+ATOM    397  O   HOH   133      -4.387   7.103  -3.444  1.00  0.00            
+ATOM    398 H1   HOH   133      -3.580   6.680  -3.829  1.00  0.00            
+ATOM    399 H2   HOH   133      -3.958   7.858  -3.002  1.00  0.00            
+ATOM    400  O   HOH   134       3.032   2.055   3.352  1.00  0.00            
+ATOM    401 H1   HOH   134       2.047   2.003   3.380  1.00  0.00            
+ATOM    402 H2   HOH   134       3.178   2.614   4.097  1.00  0.00            
+ATOM    403  O   HOH   135       7.314   1.186   2.187  1.00  0.00            
+ATOM    404 H1   HOH   135       6.925   2.076   2.385  1.00  0.00            
+ATOM    405 H2   HOH   135       7.425   1.106   1.167  1.00  0.00            
+ATOM    406  O   HOH   136       3.077  -6.778  -0.693  1.00  0.00            
+ATOM    407 H1   HOH   136       3.016  -7.565  -1.263  1.00  0.00            
+ATOM    408 H2   HOH   136       3.761  -6.920  -0.021  1.00  0.00            
+ATOM    409  O   HOH   137       0.482   1.499  -4.856  1.00  0.00            
+ATOM    410 H1   HOH   137       0.708   1.788  -4.008  1.00  0.00            
+ATOM    411 H2   HOH   137      -0.146   0.779  -4.804  1.00  0.00            
+ATOM    412  O   HOH   138       2.657  -0.480  -3.924  1.00  0.00            
+ATOM    413 H1   HOH   138       2.571  -0.270  -4.891  1.00  0.00            
+ATOM    414 H2   HOH   138       1.808  -0.171  -3.595  1.00  0.00            
+ATOM    415  O   HOH   139       7.359   3.219   0.063  1.00  0.00            
+ATOM    416 H1   HOH   139       7.531   3.124  -0.908  1.00  0.00            
+ATOM    417 H2   HOH   139       6.413   3.324   0.053  1.00  0.00            
+ATOM    418  O   HOH   140      -0.072  -2.194  -6.704  1.00  0.00            
+ATOM    419 H1   HOH   140      -0.799  -2.260  -7.333  1.00  0.00            
+ATOM    420 H2   HOH   140      -0.033  -2.956  -6.170  1.00  0.00            
+ATOM    421  O   HOH   141       8.018   3.334  -2.584  1.00  0.00            
+ATOM    422 H1   HOH   141       8.927   3.176  -2.999  1.00  0.00            
+ATOM    423 H2   HOH   141       7.714   4.088  -3.149  1.00  0.00            
+ATOM    424  O   HOH   142      -3.175   0.372   5.085  1.00  0.00            
+ATOM    425 H1   HOH   142      -3.328   1.279   5.414  1.00  0.00            
+ATOM    426 H2   HOH   142      -4.044  -0.022   5.216  1.00  0.00            
+ATOM    427  O   HOH   143       7.709  -1.775  -4.109  1.00  0.00            
+ATOM    428 H1   HOH   143       8.092  -0.993  -3.608  1.00  0.00            
+ATOM    429 H2   HOH   143       8.479  -2.226  -4.429  1.00  0.00            
+ATOM    430  O   HOH   144      -5.099   6.527   5.166  1.00  0.00            
+ATOM    431 H1   HOH   144      -4.189   6.950   5.093  1.00  0.00            
+ATOM    432 H2   HOH   144      -5.207   6.061   4.289  1.00  0.00            
+ATOM    433  O   HOH   145       8.893  -0.159  -7.906  1.00  0.00            
+ATOM    434 H1   HOH   145       8.405   0.225  -7.122  1.00  0.00            
+ATOM    435 H2   HOH   145       8.639   0.460  -8.570  1.00  0.00            
+ATOM    436  O   HOH   146      -4.263  -5.454  -5.270  1.00  0.00            
+ATOM    437 H1   HOH   146      -3.405  -5.209  -5.564  1.00  0.00            
+ATOM    438 H2   HOH   146      -4.911  -5.251  -5.952  1.00  0.00            
+ATOM    439  O   HOH   147       8.883   7.851   4.742  1.00  0.00            
+ATOM    440 H1   HOH   147       9.674   8.080   5.221  1.00  0.00            
+ATOM    441 H2   HOH   147       8.345   7.269   5.297  1.00  0.00            
+ATOM    442  O   HOH   148      -0.309  -5.404  -0.774  1.00  0.00            
+ATOM    443 H1   HOH   148       0.249  -4.705  -0.532  1.00  0.00            
+ATOM    444 H2   HOH   148      -1.094  -5.121  -1.264  1.00  0.00            
+ATOM    445  O   HOH   149       5.072  -8.090   3.321  1.00  0.00            
+ATOM    446 H1   HOH   149       5.125  -8.433   4.296  1.00  0.00            
+ATOM    447 H2   HOH   149       4.846  -7.155   3.366  1.00  0.00            
+ATOM    448  O   HOH   150       0.710  -8.627  -7.212  1.00  0.00            
+ATOM    449 H1   HOH   150       0.882  -8.127  -7.970  1.00  0.00            
+ATOM    450 H2   HOH   150       1.486  -8.744  -6.660  1.00  0.00            
+ATOM    451  O   HOH   151      -2.726   8.212   4.098  1.00  0.00            
+ATOM    452 H1   HOH   151      -1.889   7.861   4.444  1.00  0.00            
+ATOM    453 H2   HOH   151      -2.726   8.156   3.075  1.00  0.00            
+ATOM    454  O   HOH   152      -2.367   7.081   9.006  1.00  0.00            
+ATOM    455 H1   HOH   152      -1.709   7.028   9.733  1.00  0.00            
+ATOM    456 H2   HOH   152      -2.233   8.060   8.705  1.00  0.00            
+ATOM    457  O   HOH   153       6.090  -5.347  -5.159  1.00  0.00            
+ATOM    458 H1   HOH   153       6.663  -6.118  -4.931  1.00  0.00            
+ATOM    459 H2   HOH   153       6.130  -4.741  -4.369  1.00  0.00            
+ATOM    460  O   HOH   154      -6.943   5.559  -7.275  1.00  0.00            
+ATOM    461 H1   HOH   154      -6.852   5.143  -6.441  1.00  0.00            
+ATOM    462 H2   HOH   154      -7.722   6.088  -7.135  1.00  0.00            
+ATOM    463  O   HOH   155      -6.554   5.680   7.665  1.00  0.00            
+ATOM    464 H1   HOH   155      -5.985   5.815   6.863  1.00  0.00            
+ATOM    465 H2   HOH   155      -6.073   6.260   8.297  1.00  0.00            
+ATOM    466  O   HOH   156      -1.773  -7.513   4.829  1.00  0.00            
+ATOM    467 H1   HOH   156      -1.111  -7.160   4.268  1.00  0.00            
+ATOM    468 H2   HOH   156      -1.281  -8.206   5.239  1.00  0.00            
+ATOM    469  O   HOH   157       5.088  -1.778  -5.553  1.00  0.00            
+ATOM    470 H1   HOH   157       4.758  -1.676  -4.673  1.00  0.00            
+ATOM    471 H2   HOH   157       6.001  -1.657  -5.464  1.00  0.00            
+ATOM    472  O   HOH   158       7.974  -0.053  -0.228  1.00  0.00            
+ATOM    473 H1   HOH   158       7.544  -0.925  -0.027  1.00  0.00            
+ATOM    474 H2   HOH   158       8.404  -0.258  -1.091  1.00  0.00            
+ATOM    475  O   HOH   159       2.481  -4.518  -2.565  1.00  0.00            
+ATOM    476 H1   HOH   159       2.654  -5.131  -1.870  1.00  0.00            
+ATOM    477 H2   HOH   159       2.866  -3.653  -2.218  1.00  0.00            
+ATOM    478  O   HOH   160       8.941   6.414  -2.284  1.00  0.00            
+ATOM    479 H1   HOH   160       8.639   5.765  -2.912  1.00  0.00            
+ATOM    480 H2   HOH   160       9.870   6.369  -2.209  1.00  0.00            
+ATOM    481  O   HOH   161      -5.030   3.860  -9.133  1.00  0.00            
+ATOM    482 H1   HOH   161      -4.276   4.457  -8.996  1.00  0.00            
+ATOM    483 H2   HOH   161      -5.711   4.362  -9.608  1.00  0.00            
+ATOM    484  O   HOH   162      -5.791   3.147  -1.317  1.00  0.00            
+ATOM    485 H1   HOH   162      -6.436   2.378  -1.382  1.00  0.00            
+ATOM    486 H2   HOH   162      -5.191   2.984  -0.504  1.00  0.00            
+ATOM    487  O   HOH   163      -2.329  -4.533  -2.630  1.00  0.00            
+ATOM    488 H1   HOH   163      -3.171  -5.058  -2.576  1.00  0.00            
+ATOM    489 H2   HOH   163      -2.499  -3.672  -2.246  1.00  0.00            
+ATOM    490  O   HOH   164       7.390   6.060   8.753  1.00  0.00            
+ATOM    491 H1   HOH   164       6.851   5.658   8.039  1.00  0.00            
+ATOM    492 H2   HOH   164       6.789   6.249   9.485  1.00  0.00            
+ATOM    493  O   HOH   165      -1.734  -4.483  -6.269  1.00  0.00            
+ATOM    494 H1   HOH   165      -1.212  -4.704  -5.518  1.00  0.00            
+ATOM    495 H2   HOH   165      -2.176  -3.710  -5.905  1.00  0.00            
+ATOM    496  O   HOH   166      -0.979   4.105   5.515  1.00  0.00            
+ATOM    497 H1   HOH   166      -1.509   4.308   6.292  1.00  0.00            
+ATOM    498 H2   HOH   166      -0.221   3.585   5.863  1.00  0.00            
+ATOM    499  O   HOH   167      -2.925   4.250  -7.055  1.00  0.00            
+ATOM    500 H1   HOH   167      -2.386   3.828  -7.713  1.00  0.00            
+ATOM    501 H2   HOH   167      -2.854   3.619  -6.304  1.00  0.00            
+ATOM    502  O   HOH   168      -4.193  -1.077  -8.101  1.00  0.00            
+ATOM    503 H1   HOH   168      -4.551  -1.839  -8.506  1.00  0.00            
+ATOM    504 H2   HOH   168      -4.698  -0.329  -8.425  1.00  0.00            
+ATOM    505  O   HOH   169      -8.302  -5.937  -5.244  1.00  0.00            
+ATOM    506 H1   HOH   169      -8.357  -5.005  -5.460  1.00  0.00            
+ATOM    507 H2   HOH   169      -7.765  -5.968  -4.487  1.00  0.00            
+ATOM    508  O   HOH   170       0.475   2.499   7.103  1.00  0.00            
+ATOM    509 H1   HOH   170       0.053   2.668   8.005  1.00  0.00            
+ATOM    510 H2   HOH   170       0.928   1.639   7.275  1.00  0.00            
+ATOM    511  O   HOH   171       0.983  -2.483   6.222  1.00  0.00            
+ATOM    512 H1   HOH   171       0.714  -2.387   7.103  1.00  0.00            
+ATOM    513 H2   HOH   171       1.073  -3.395   5.953  1.00  0.00            
+ATOM    514  O   HOH   172      -1.739   6.386  -4.380  1.00  0.00            
+ATOM    515 H1   HOH   172      -1.086   7.088  -4.202  1.00  0.00            
+ATOM    516 H2   HOH   172      -1.618   5.678  -3.708  1.00  0.00            
+ATOM    517  O   HOH   173      -8.338  -7.832   7.971  1.00  0.00            
+ATOM    518 H1   HOH   173      -8.660  -8.718   7.769  1.00  0.00            
+ATOM    519 H2   HOH   173      -9.133  -7.191   7.981  1.00  0.00            
+ATOM    520  O   HOH   174       3.012   4.410   1.775  1.00  0.00            
+ATOM    521 H1   HOH   174       3.088   3.596   2.267  1.00  0.00            
+ATOM    522 H2   HOH   174       2.920   5.066   2.466  1.00  0.00            
+ATOM    523  O   HOH   175       3.835  -2.844  -8.396  1.00  0.00            
+ATOM    524 H1   HOH   175       4.123  -2.941  -9.341  1.00  0.00            
+ATOM    525 H2   HOH   175       4.550  -3.355  -7.864  1.00  0.00            
+ATOM    526  O   HOH   176       5.454   1.225  -4.087  1.00  0.00            
+ATOM    527 H1   HOH   176       6.075   1.634  -3.481  1.00  0.00            
+ATOM    528 H2   HOH   176       4.836   0.886  -3.441  1.00  0.00            
+ATOM    529  O   HOH   177       1.364  -3.319   1.034  1.00  0.00            
+ATOM    530 H1   HOH   177       1.576  -2.519   1.568  1.00  0.00            
+ATOM    531 H2   HOH   177       0.786  -3.846   1.612  1.00  0.00            
+ATOM    532  O   HOH   178       8.425   3.808  -6.918  1.00  0.00            
+ATOM    533 H1   HOH   178       9.075   3.928  -7.729  1.00  0.00            
+ATOM    534 H2   HOH   178       7.505   3.888  -7.275  1.00  0.00            
+ATOM    535  O   HOH   179       2.777  -8.590  -5.314  1.00  0.00            
+ATOM    536 H1   HOH   179       2.839  -7.702  -5.632  1.00  0.00            
+ATOM    537 H2   HOH   179       3.489  -9.124  -5.685  1.00  0.00            
+ATOM    538  O   HOH   180       2.682  -7.850   6.993  1.00  0.00            
+ATOM    539 H1   HOH   180       3.382  -8.376   7.384  1.00  0.00            
+ATOM    540 H2   HOH   180       3.009  -6.910   7.029  1.00  0.00            
+ATOM    541  O   HOH   181       0.959   5.976   8.842  1.00  0.00            
+ATOM    542 H1   HOH   181       1.908   5.889   8.681  1.00  0.00            
+ATOM    543 H2   HOH   181       0.701   6.300   9.762  1.00  0.00            
+ATOM    544  O   HOH   182      -3.269  -0.095   2.168  1.00  0.00            
+ATOM    545 H1   HOH   182      -3.261  -0.142   3.146  1.00  0.00            
+ATOM    546 H2   HOH   182      -2.758  -0.845   1.881  1.00  0.00            
+ATOM    547  O   HOH   183      -8.343  -5.520   2.186  1.00  0.00            
+ATOM    548 H1   HOH   183      -8.240  -5.469   3.127  1.00  0.00            
+ATOM    549 H2   HOH   183      -9.326  -5.545   1.936  1.00  0.00            
+ATOM    550  O   HOH   184      -3.748   2.251   7.121  1.00  0.00            
+ATOM    551 H1   HOH   184      -4.751   2.368   7.191  1.00  0.00            
+ATOM    552 H2   HOH   184      -3.334   3.091   7.210  1.00  0.00            
+ATOM    553  O   HOH   185       5.491  -6.805   0.724  1.00  0.00            
+ATOM    554 H1   HOH   185       6.053  -6.670   1.517  1.00  0.00            
+ATOM    555 H2   HOH   185       5.861  -6.118   0.175  1.00  0.00            
+ATOM    556  O   HOH   186      -2.313   9.029  -1.341  1.00  0.00            
+ATOM    557 H1   HOH   186      -2.862   9.567  -1.983  1.00  0.00            
+ATOM    558 H2   HOH   186      -2.931   8.715  -0.682  1.00  0.00            
+ATOM    559  O   HOH   187      -5.479   0.699   0.492  1.00  0.00            
+ATOM    560 H1   HOH   187      -4.847   0.137   0.967  1.00  0.00            
+ATOM    561 H2   HOH   187      -5.594   0.350  -0.404  1.00  0.00            
+ATOM    562  O   HOH   188      -4.084  -6.161   5.301  1.00  0.00            
+ATOM    563 H1   HOH   188      -3.506  -6.799   4.940  1.00  0.00            
+ATOM    564 H2   HOH   188      -4.630  -6.788   5.863  1.00  0.00            
+ATOM    565  O   HOH   189       4.659   7.875  -1.282  1.00  0.00            
+ATOM    566 H1   HOH   189       5.386   8.309  -0.774  1.00  0.00            
+ATOM    567 H2   HOH   189       4.055   7.498  -0.619  1.00  0.00            
+ATOM    568  O   HOH   190      -0.166  -3.706  -3.657  1.00  0.00            
+ATOM    569 H1   HOH   190      -0.908  -4.138  -3.272  1.00  0.00            
+ATOM    570 H2   HOH   190       0.514  -4.377  -3.440  1.00  0.00            
+ATOM    571  O   HOH   191      -5.951   0.171  -2.277  1.00  0.00            
+ATOM    572 H1   HOH   191      -5.823   0.714  -3.060  1.00  0.00            
+ATOM    573 H2   HOH   191      -6.282  -0.633  -2.620  1.00  0.00            
+ATOM    574  O   HOH   192      -4.764  -4.232   8.960  1.00  0.00            
+ATOM    575 H1   HOH   192      -5.480  -4.134   8.313  1.00  0.00            
+ATOM    576 H2   HOH   192      -4.642  -5.206   8.983  1.00  0.00            
+ATOM    577  O   HOH   193       0.145  -8.934  -0.348  1.00  0.00            
+ATOM    578 H1   HOH   193      -0.693  -9.106  -0.806  1.00  0.00            
+ATOM    579 H2   HOH   193       0.881  -9.152  -0.962  1.00  0.00            
+ATOM    580  O   HOH   194      -6.024   6.817   0.677  1.00  0.00            
+ATOM    581 H1   HOH   194      -6.335   6.594  -0.147  1.00  0.00            
+ATOM    582 H2   HOH   194      -6.795   7.026   1.255  1.00  0.00            
+ATOM    583  O   HOH   195      -7.976  -4.857  -8.808  1.00  0.00            
+ATOM    584 H1   HOH   195      -7.659  -4.428  -9.586  1.00  0.00            
+ATOM    585 H2   HOH   195      -8.826  -4.435  -8.650  1.00  0.00            
+ATOM    586  O   HOH   196       6.091   7.506  -3.794  1.00  0.00            
+ATOM    587 H1   HOH   196       6.896   8.024  -3.504  1.00  0.00            
+ATOM    588 H2   HOH   196       5.535   7.536  -2.967  1.00  0.00            
+ATOM    589  O   HOH   197       7.449   5.304  -4.471  1.00  0.00            
+ATOM    590 H1   HOH   197       7.018   6.181  -4.365  1.00  0.00            
+ATOM    591 H2   HOH   197       8.016   5.286  -5.241  1.00  0.00            
+ATOM    592  O   HOH   198      -6.900  -5.901  -2.927  1.00  0.00            
+ATOM    593 H1   HOH   198      -7.154  -6.838  -2.857  1.00  0.00            
+ATOM    594 H2   HOH   198      -5.932  -5.822  -2.739  1.00  0.00            
+ATOM    595  O   HOH   199      -2.077  -9.026   8.256  1.00  0.00            
+ATOM    596 H1   HOH   199      -1.233  -9.035   7.789  1.00  0.00            
+ATOM    597 H2   HOH   199      -2.467  -8.111   8.140  1.00  0.00            
+ATOM    598  O   HOH   200      -5.977  -2.535   3.782  1.00  0.00            
+ATOM    599 H1   HOH   200      -5.780  -1.850   4.378  1.00  0.00            
+ATOM    600 H2   HOH   200      -6.306  -1.917   3.065  1.00  0.00            
+ATOM    601  O   HOH   201       2.576  -9.098  -2.268  1.00  0.00            
+ATOM    602 H1   HOH   201       3.391  -9.612  -2.195  1.00  0.00            
+ATOM    603 H2   HOH   201       2.529  -8.810  -3.194  1.00  0.00            
+ATOM    604  O   HOH   202      -5.798   4.562  -4.805  1.00  0.00            
+ATOM    605 H1   HOH   202      -5.028   4.024  -4.763  1.00  0.00            
+ATOM    606 H2   HOH   202      -5.523   5.503  -4.645  1.00  0.00            
+ATOM    607  O   HOH   203       2.642   3.615   5.573  1.00  0.00            
+ATOM    608 H1   HOH   203       1.851   3.465   6.145  1.00  0.00            
+ATOM    609 H2   HOH   203       2.533   4.499   5.175  1.00  0.00            
+ATOM    610  O   HOH   204       8.011  -7.394  -4.619  1.00  0.00            
+ATOM    611 H1   HOH   204       8.169  -7.901  -3.820  1.00  0.00            
+ATOM    612 H2   HOH   204       8.830  -6.924  -4.810  1.00  0.00            
+ATOM    613  O   HOH   205      -5.863   0.151  -5.281  1.00  0.00            
+ATOM    614 H1   HOH   205      -5.088   0.587  -5.588  1.00  0.00            
+ATOM    615 H2   HOH   205      -6.450   0.191  -6.017  1.00  0.00            
+ATOM    616  O   HOH   206       7.645  -5.999   2.880  1.00  0.00            
+ATOM    617 H1   HOH   206       7.086  -5.401   3.352  1.00  0.00            
+ATOM    618 H2   HOH   206       7.945  -6.726   3.484  1.00  0.00            
+ATOM    619  O   HOH   207      -4.127   6.816  -6.252  1.00  0.00            
+ATOM    620 H1   HOH   207      -3.484   6.105  -6.419  1.00  0.00            
+ATOM    621 H2   HOH   207      -3.581   7.596  -6.033  1.00  0.00            
+ATOM    622  O   HOH   208      -2.387   0.594   9.139  1.00  0.00            
+ATOM    623 H1   HOH   208      -2.910  -0.143   9.526  1.00  0.00            
+ATOM    624 H2   HOH   208      -2.860   1.041   8.365  1.00  0.00            
+ATOM    625  O   HOH   209       6.291  -6.637  -8.831  1.00  0.00            
+ATOM    626 H1   HOH   209       5.331  -6.682  -8.839  1.00  0.00            
+ATOM    627 H2   HOH   209       6.669  -7.204  -8.167  1.00  0.00            
+ATOM    628  O   HOH   210       2.510  -8.884   2.290  1.00  0.00            
+ATOM    629 H1   HOH   210       2.430  -8.169   1.697  1.00  0.00            
+ATOM    630 H2   HOH   210       3.446  -8.960   2.484  1.00  0.00            
+ATOM    631  O   HOH   211      -9.142   8.039   7.883  1.00  0.00            
+ATOM    632 H1   HOH   211      -8.383   7.421   7.829  1.00  0.00            
+ATOM    633 H2   HOH   211      -9.916   7.561   8.297  1.00  0.00            
+ATOM    634  O   HOH   212       7.971  -3.288   7.179  1.00  0.00            
+ATOM    635 H1   HOH   212       8.561  -2.572   7.494  1.00  0.00            
+ATOM    636 H2   HOH   212       7.985  -3.225   6.216  1.00  0.00            
+ATOM    637  O   HOH   213       7.974  -6.006   7.682  1.00  0.00            
+ATOM    638 H1   HOH   213       8.211  -5.090   7.590  1.00  0.00            
+ATOM    639 H2   HOH   213       7.297  -6.051   8.386  1.00  0.00            
+ATOM    640  O   HOH   214      -1.174  -5.931   7.038  1.00  0.00            
+ATOM    641 H1   HOH   214      -1.529  -6.552   6.343  1.00  0.00            
+ATOM    642 H2   HOH   214      -1.604  -5.078   6.850  1.00  0.00            
+ATOM    643  O   HOH   215       5.857   3.613   3.066  1.00  0.00            
+ATOM    644 H1   HOH   215       5.145   4.238   2.616  1.00  0.00            
+ATOM    645 H2   HOH   215       5.360   3.257   3.827  1.00  0.00            
+ATOM    646  Ca  Ca    216      -7.511   3.594   2.437  1.00  0.00            
+TER
+ENDMDL

wrappers/python/tests/systems/ff14ipq.rst7

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