Merge branch 'master' into gayberne

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

@@ -81,51 +81,51 @@ class CharmmCrdFile(object):
 
     def _parse(self, fname):
 
-        crdfile = open(fname, 'r')
-        line = crdfile.readline()
-
-        while len(line.strip()) == 0:      # Skip whitespace, as a precaution
-            line = crdfile.readline()
-
-        intitle = True
-
-        while intitle:
-            self.title.append(line.strip())
+        with open(fname, 'r') as crdfile:
             line = crdfile.readline()
-            if len(line.strip()) == 0:
-                intitle = False
-            elif line.strip()[0] != '*':
-                intitle = False
-            else:
-                intitle = True
-
-        while len(line.strip()) == 0:      # Skip whitespace
-            line = crdfile.readline()
-
-        try:
-            self.natom = int(line.strip().split()[0])
-
-            for row in range(self.natom):
-                line = crdfile.readline().strip().split()
-                self.atomno.append(int(line[0]))
-                self.resno.append(int(line[1]))
-                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)
-                self.segid.append(line[7])
-                self.resid.append(int(line[8]))
-                self.weighting.append(float(line[9]))
-
-            if self.natom != len(self.positions):
-                raise CharmmFileError("Error parsing CHARMM .crd file: %d "
-                                      "atoms requires %d positions (not %d)" %
-                                      (self.natom, self.natom,
-                                       len(self.positions))
-                )
-
-        except (ValueError, IndexError) as e:
-            raise CharmmFileError('Error parsing CHARMM coordinate file')
+    
+            while len(line.strip()) == 0:      # Skip whitespace, as a precaution
+                line = crdfile.readline()
+    
+            intitle = True
+    
+            while intitle:
+                self.title.append(line.strip())
+                line = crdfile.readline()
+                if len(line.strip()) == 0:
+                    intitle = False
+                elif line.strip()[0] != '*':
+                    intitle = False
+                else:
+                    intitle = True
+    
+            while len(line.strip()) == 0:      # Skip whitespace
+                line = crdfile.readline()
+    
+            try:
+                self.natom = int(line.strip().split()[0])
+    
+                for row in range(self.natom):
+                    line = crdfile.readline().strip().split()
+                    self.atomno.append(int(line[0]))
+                    self.resno.append(int(line[1]))
+                    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)
+                    self.segid.append(line[7])
+                    self.resid.append(int(line[8]))
+                    self.weighting.append(float(line[9]))
+    
+                if self.natom != len(self.positions):
+                    raise CharmmFileError("Error parsing CHARMM .crd file: %d "
+                                          "atoms requires %d positions (not %d)" %
+                                          (self.natom, self.natom,
+                                           len(self.positions))
+                    )
+    
+            except (ValueError, IndexError) as 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.

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

@@ -178,23 +178,23 @@ class CharmmPsfFile(object):
         if not os.path.exists(psf_name):
             raise IOError('Could not find PSF file %s' % psf_name)
         # Open the PSF and read the first line. It must start with "PSF"
-        psf = open(psf_name, 'r')
-        line = psf.readline()
-        if not line.startswith('PSF'):
-            raise CharmmPSFError('Unrecognized PSF file. First line is %s' %
-                                 line.strip())
-        # Store the flags
-        psf_flags = line.split()[1:]
-        # Now get all of the sections and store them in a dict
-        psf.readline()
-        # Now get all of the sections
-        psfsections = _ZeroDict()
-        while True:
-            try:
-                sec, ptr, data = CharmmPsfFile._parse_psf_section(psf)
-            except CharmmPsfEOF:
-                break
-            psfsections[sec] = (ptr, data)
+        with open(psf_name, 'r') as psf:
+            line = psf.readline()
+            if not line.startswith('PSF'):
+                raise CharmmPSFError('Unrecognized PSF file. First line is %s' %
+                                     line.strip())
+            # Store the flags
+            psf_flags = line.split()[1:]
+            # Now get all of the sections and store them in a dict
+            psf.readline()
+            # Now get all of the sections
+            psfsections = _ZeroDict()
+            while True:
+                try:
+                    sec, ptr, data = CharmmPsfFile._parse_psf_section(psf)
+                except CharmmPsfEOF:
+                    break
+                psfsections[sec] = (ptr, data)
         # store the title
         title = psfsections['NTITLE'][1]
         # Next is the number of atoms
@@ -1217,6 +1217,7 @@ class CharmmPsfFile(object):
             else:
                 raise ValueError('Illegal nonbonded method for use with GBSA')
             gb.setForceGroup(self.GB_FORCE_GROUP)
+            gb.finalize()
             system.addForce(gb)
             force.setReactionFieldDielectric(1.0) # applies to NonbondedForce
 

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

@@ -88,8 +88,7 @@ class DCDReporter(object):
 
         if self._dcd is None:
             self._dcd = DCDFile(self._out, simulation.topology, simulation.integrator.getStepSize(), 0, self._reportInterval)
-        a,b,c = state.getPeriodicBoxVectors()
-        self._dcd.writeModel(state.getPositions(), mm.Vec3(a[0].value_in_unit(nanometer), b[1].value_in_unit(nanometer), c[2].value_in_unit(nanometer))*nanometer)
+        self._dcd.writeModel(state.getPositions(), periodicBoxVectors=state.getPeriodicBoxVectors())
 
     def __del__(self):
         self._out.close()

wrappers/python/simtk/openmm/app/forcefield.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) 2012-2015 Stanford University and the Authors.
+Portions copyright (c) 2012-2016 Stanford University and the Authors.
 Authors: Peter Eastman, Mark Friedrichs
 Contributors:
 
@@ -38,6 +38,8 @@ import itertools
 import xml.etree.ElementTree as etree
 import math
 from math import sqrt, cos
+from copy import deepcopy
+from heapq import heappush, heappop
 import simtk.openmm as mm
 import simtk.unit as unit
 from . import element as elem
@@ -115,6 +117,8 @@ class ForceField(object):
         """
         self._atomTypes = {}
         self._templates = {}
+        self._patches = {}
+        self._templatePatches = {}
         self._templateSignatures = {None:[]}
         self._atomClasses = {'':set()}
         self._forces = []
@@ -175,8 +179,8 @@ class ForceField(object):
                 for residue in tree.getroot().find('Residues').findall('Residue'):
                     resName = residue.attrib['name']
                     template = ForceField._TemplateData(resName)
-                    if 'overload' in residue.attrib:
-                        template.overloadLevel = int(residue.attrib['overload'])
+                    if 'override' in residue.attrib:
+                        template.overrideLevel = int(residue.attrib['override'])
                     atomIndices = {}
                     for atom in residue.findall('Atom'):
                         params = {}
@@ -201,8 +205,81 @@ class ForceField(object):
                             template.addExternalBondByName(bond.attrib['atomName'])
                         else:
                             template.addExternalBond(int(bond.attrib['from']))
+                    for patch in residue.findall('AllowPatch'):
+                        patchName = patch.attrib['name']
+                        if ':' in patchName:
+                            colonIndex = patchName.find(':')
+                            self.registerTemplatePatch(resName, patchName[:colonIndex], int(patchName[colonIndex+1:])-1)
+                        else:
+                            self.registerTemplatePatch(resName, patchName, 0)
                     self.registerResidueTemplate(template)
 
+        # Load the patch defintions.
+
+        for tree in trees:
+            if tree.getroot().find('Patches') is not None:
+                for patch in tree.getroot().find('Patches').findall('Patch'):
+                    patchName = patch.attrib['name']
+                    if 'residues' in patch.attrib:
+                        numResidues = int(patch.attrib['residues'])
+                    else:
+                        numResidues = 1
+                    patchData = ForceField._PatchData(patchName, numResidues)
+                    allAtomNames = set()
+                    for atom in patch.findall('AddAtom'):
+                        params = {}
+                        for key in atom.attrib:
+                            if key not in ('name', 'type'):
+                                params[key] = _convertParameterToNumber(atom.attrib[key])
+                        atomName = atom.attrib['name']
+                        if atomName in allAtomNames:
+                            raise ValueError('Patch '+patchName+' contains multiple atoms named '+atomName)
+                        allAtomNames.add(atomName)
+                        atomDescription = ForceField._PatchAtomData(atomName)
+                        typeName = atom.attrib['type']
+                        patchData.addedAtoms[atomDescription.residue].append(ForceField._TemplateAtomData(atomDescription.name, typeName, self._atomTypes[typeName].element, params))
+                    for atom in patch.findall('ChangeAtom'):
+                        params = {}
+                        for key in atom.attrib:
+                            if key not in ('name', 'type'):
+                                params[key] = _convertParameterToNumber(atom.attrib[key])
+                        atomName = atom.attrib['name']
+                        if atomName in allAtomNames:
+                            raise ValueError('Patch '+patchName+' contains multiple atoms named '+atomName)
+                        allAtomNames.add(atomName)
+                        atomDescription = ForceField._PatchAtomData(atomName)
+                        typeName = atom.attrib['type']
+                        patchData.changedAtoms[atomDescription.residue].append(ForceField._TemplateAtomData(atomDescription.name, typeName, self._atomTypes[typeName].element, params))
+                    for atom in patch.findall('RemoveAtom'):
+                        atomName = atom.attrib['name']
+                        if atomName in allAtomNames:
+                            raise ValueError('Patch '+patchName+' contains multiple atoms named '+atomName)
+                        allAtomNames.add(atomName)
+                        atomDescription = ForceField._PatchAtomData(atomName)
+                        patchData.deletedAtoms.append(atomDescription)
+                    for bond in patch.findall('AddBond'):
+                        atom1 = ForceField._PatchAtomData(bond.attrib['atomName1'])
+                        atom2 = ForceField._PatchAtomData(bond.attrib['atomName2'])
+                        patchData.addedBonds.append((atom1, atom2))
+                    for bond in patch.findall('RemoveBond'):
+                        atom1 = ForceField._PatchAtomData(bond.attrib['atomName1'])
+                        atom2 = ForceField._PatchAtomData(bond.attrib['atomName2'])
+                        patchData.deletedBonds.append((atom1, atom2))
+                    for bond in patch.findall('AddExternalBond'):
+                        atom = ForceField._PatchAtomData(bond.attrib['atomName'])
+                        patchData.addedExternalBonds.append(atom)
+                    for bond in patch.findall('RemoveExternalBond'):
+                        atom = ForceField._PatchAtomData(bond.attrib['atomName'])
+                        patchData.deletedExternalBonds.append(atom)
+                    for residue in patch.findall('ApplyToResidue'):
+                        name = residue.attrib['name']
+                        if ':' in name:
+                            colonIndex = name.find(':')
+                            self.registerTemplatePatch(name[colonIndex+1:], patchName, int(name[:colonIndex])-1)
+                        else:
+                            self.registerTemplatePatch(name, patchName, 0)
+                    self.registerPatch(patchData)
+
         # Load force definitions
 
         for tree in trees:
@@ -247,31 +324,40 @@ class ForceField(object):
 
     def registerResidueTemplate(self, template):
         """Register a new residue template."""
+        if template.name in self._templates:
+            # There is already a template with this name, so check the override levels.
+            
+            existingTemplate = self._templates[template.name]
+            if template.overrideLevel < existingTemplate.overrideLevel:
+                # The existing one takes precedence, so just return.
+                return
+            if template.overrideLevel > existingTemplate.overrideLevel:
+                # We need to delete the existing template.
+                del self._templates[template.name]
+                existingSignature = _createResidueSignature([atom.element for atom in existingTemplate.atoms])
+                self._templateSignatures[existingSignature].remove(existingTemplate)
+            else:
+                raise ValueError('Residue template %s with the same override level %d already exists.' % (template.name, template.overrideLevel))
+        
+        # Register the template.
+        
         self._templates[template.name] = template
         signature = _createResidueSignature([atom.element for atom in template.atoms])
         if signature in self._templateSignatures:
-            registered = False
-            for regtemplate in self._templateSignatures[signature]:
-                if regtemplate.name == template.name:
-                    if regtemplate.overloadLevel > template.overloadLevel:
-                        # ok to break - this is done every time a template is
-                        # registered so there can only be one already existing
-                        # with same name at a time
-                        registered = True
-                        break
-                    elif regtemplate.overloadLevel < template.overloadLevel:
-                        self._templateSignatures[signature].remove(regtemplate)
-                        self._templateSignatures[signature].append(template)
-                        registered = True
-                    else:
-                        raise Exception('Residue template %s with the same overloadLevel %d already exists.' %
-                                         (template.name, template.overloadLevel)
-                                         )
-            if not registered:
-                self._templateSignatures[signature].append(template)
+            self._templateSignatures[signature].append(template)
         else:
             self._templateSignatures[signature] = [template]
 
+    def registerPatch(self, patch):
+        """Register a new patch that can be applied to templates."""
+        self._patches[patch.name] = patch
+    
+    def registerTemplatePatch(self, residue, patch, patchResidueIndex):
+        """Register that a particular patch can be used with a particular residue."""
+        if residue not in self._templatePatches:
+            self._templatePatches[residue] = []
+        self._templatePatches[residue].append((patch, patchResidueIndex))
+
     def registerScript(self, script):
         """Register a new script to be executed after building the System."""
         self._scripts.append(script)
@@ -396,11 +482,21 @@ class ForceField(object):
             """Add a constraint to the system, avoiding duplicate constraints."""
             key = (min(atom1, atom2), max(atom1, atom2))
             if key in self.constraints:
-                if self.constraints(key) != distance:
+                if self.constraints[key] != distance:
                     raise ValueError('Two constraints were specified between atoms %d and %d with different distances' % (atom1, atom2))
             else:
                 self.constraints[key] = distance
                 system.addConstraint(atom1, atom2, distance)
+        
+        def recordMatchedAtomParameters(self, residue, template, matches):
+            """Record parameters for atoms based on having matched a residue to a template."""
+            matchAtoms = dict(zip(matches, residue.atoms()))
+            for atom, match in zip(residue.atoms(), matches):
+                self.atomType[atom] = template.atoms[match].type
+                self.atomParameters[atom] = template.atoms[match].parameters
+                for site in template.virtualSites:
+                    if match == site.index:
+                        self.virtualSites[atom] = (site, [matchAtoms[i].index for i in site.atoms], matchAtoms[site.excludeWith].index)
 
     class _TemplateData(object):
         """Inner class used to encapsulate data about a residue template definition."""
@@ -410,7 +506,7 @@ class ForceField(object):
             self.virtualSites = []
             self.bonds = []
             self.externalBonds = []
-            self.overloadLevel = 0
+            self.overrideLevel = 0
 
         def getAtomIndexByName(self, atom_name):
             """Look up an atom index by atom name, providing a helpful error message if not found."""
@@ -496,6 +592,92 @@ class ForceField(object):
             else:
                 self.excludeWith = self.atoms[0]
 
+    class _PatchData(object):
+        """Inner class used to encapsulate data about a patch definition."""
+        def __init__(self, name, numResidues):
+            self.name = name
+            self.numResidues = numResidues
+            self.addedAtoms = [[] for i in range(numResidues)]
+            self.changedAtoms = [[] for i in range(numResidues)]
+            self.deletedAtoms = []
+            self.addedBonds = []
+            self.deletedBonds = []
+            self.addedExternalBonds = []
+            self.deletedExternalBonds = []
+        
+        def createPatchedTemplates(self, templates):
+            """Apply this patch to a set of templates, creating new modified ones."""
+            if len(templates) != self.numResidues:
+                raise ValueError("Patch '%s' expected %d templates, received %d", (self.name, self.numResidues, len(templates)))
+            
+            # Construct a new version of each template.
+            
+            newTemplates = []
+            for index, template in enumerate(templates):
+                newTemplate = ForceField._TemplateData("%s-%s" % (template.name, self.name))
+                newTemplates.append(newTemplate)
+                
+                # Build the list of atoms in it.
+                
+                for atom in template.atoms:
+                    if not any(deleted.name == atom.name and deleted.residue == index for deleted in self.deletedAtoms):
+                        newTemplate.atoms.append(ForceField._TemplateAtomData(atom.name, atom.type, atom.element, atom.parameters))
+                for atom in self.addedAtoms[index]:
+                    if any(a.name == atom.name for a in newTemplate.atoms):
+                        raise ValueError("Patch '%s' adds an atom with the same name as an existing atom: %s" % (self.name, atom.name))
+                    newTemplate.atoms.append(ForceField._TemplateAtomData(atom.name, atom.type, atom.element, atom.parameters))
+                oldAtomIndex = dict([(atom.name, i) for i, atom in enumerate(template.atoms)])
+                newAtomIndex = dict([(atom.name, i) for i, atom in enumerate(newTemplate.atoms)])
+                for atom in self.changedAtoms[index]:
+                    if atom.name not in newAtomIndex:
+                        raise ValueError("Patch '%s' modifies nonexistent atom '%s' in template '%s'" % (self.name, atom.name, template.name))
+                    newTemplate.atoms[newAtomIndex[atom.name]] = ForceField._TemplateAtomData(atom.name, atom.type, atom.element, atom.parameters)
+                
+                # Copy over the virtual sites, translating the atom indices.
+                
+                indexMap = dict([(oldAtomIndex[name], newAtomIndex[name]) for name in newAtomIndex if name in oldAtomIndex])
+                for site in template.virtualSites:
+                    if site.index in indexMap and all(i in indexMap for i in site.atoms):
+                        newSite = deepcopy(site)
+                        newSite.index = indexMap[site.index]
+                        newSite.atoms = [indexMap[i] for i in site.atoms]
+                        newTemplate.virtualSites.append(newSite)
+                
+                # Build the lists of bonds and external bonds.
+                
+                atomMap = dict([(template.atoms[i], indexMap[i]) for i in indexMap])
+                deletedBonds = [(atom1.name, atom2.name) for atom1, atom2 in self.deletedBonds if atom1.residue == index and atom2.residue == index]
+                for atom1, atom2 in template.bonds:
+                    a1 = template.atoms[atom1]
+                    a2 = template.atoms[atom2]
+                    if a1 in atomMap and a2 in atomMap and (a1.name, a2.name) not in deletedBonds and (a2.name, a1.name) not in deletedBonds:
+                        newTemplate.addBond(atomMap[a1], atomMap[a2])
+                deletedExternalBonds = [atom.name for atom in self.deletedExternalBonds if atom.residue == index]
+                for atom in template.externalBonds:
+                    if template.atoms[atom].name not in deletedExternalBonds:
+                        newTemplate.addExternalBond(indexMap[atom])
+                for atom1, atom2 in self.addedBonds:
+                    if atom1.residue == index and atom2.residue == index:
+                        newTemplate.addBondByName(atom1.name, atom2.name)
+                    elif atom1.residue == index:
+                        newTemplate.addExternalBondByName(atom1.name)
+                    elif atom2.residue == index:
+                        newTemplate.addExternalBondByName(atom2.name)
+                for atom in self.addedExternalBonds:
+                    newTemplate.addExternalBondByName(atom.name)
+            return newTemplates
+            
+    class _PatchAtomData(object):
+        """Inner class used to encapsulate data about an atom in a patch definition."""
+        def __init__(self, description):
+            if ':' in description:
+                colonIndex = description.find(':')
+                self.residue = int(description[:colonIndex])-1
+                self.name = description[colonIndex+1:]
+            else:
+                self.residue = 0
+                self.name = description
+
     class _AtomType(object):
         """Inner class used to record atom types and associated properties."""
         def __init__(self, name, atomClass, mass, element):
@@ -575,7 +757,7 @@ class ForceField(object):
                 raise ValueError('%s: No parameters defined for atom type %s' % (self.forceName, t))
 
 
-    def _getResidueTemplateMatches(self, res, bondedToAtom):
+    def _getResidueTemplateMatches(self, res, bondedToAtom, templateSignatures=None):
         """Return the residue template matches, or None if none are found.
 
         Parameters
@@ -596,10 +778,12 @@ class ForceField(object):
         """
         template = None
         matches = None
+        if templateSignatures is None:
+            templateSignatures = self._templateSignatures
         signature = _createResidueSignature([atom.element for atom in res.atoms()])
-        if signature in self._templateSignatures:
+        if signature in templateSignatures:
             allMatches = []
-            for t in self._templateSignatures[signature]:
+            for t in templateSignatures[signature]:
                 match = _matchResidue(res, t, bondedToAtom)
                 if match is not None:
                     allMatches.append((t, match))
@@ -805,8 +989,8 @@ class ForceField(object):
             data.atomBonds[bond.atom2].append(i)
 
         # Find the template matching each residue and assign atom types.
-        # If no templates are found, attempt to use residue template generators to create new templates (and potentially atom types/parameters).
 
+        unmatchedResidues = []
         for chain in topology.chains():
             for res in chain.residues():
                 if res in residueTemplates:
@@ -819,30 +1003,37 @@ class ForceField(object):
                     # Attempt to match one of the existing templates.
                     [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
                 if matches is None:
-                    # No existing templates match.  Try any registered residue template generators.
-                    for generator in self._templateGenerators:
-                        if generator(self, res):
-                            # This generator has registered a new residue template that should match.
-                            [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
-                            if matches is None:
-                                # Something went wrong because the generated template does not match the residue signature.
-                                raise Exception('The residue handler %s indicated it had correctly parameterized residue %s, but the generated template did not match the residue signature.' % (generator.__class__.__name__, str(res)))
-                            else:
-                                # We successfully generated a residue template.  Break out of the for loop.
-                                break
-
-                # Raise an exception if we have found no templates that match.
-                if matches is None:
-                    raise ValueError('No template found for residue %d (%s).  %s' % (res.index+1, res.name, _findMatchErrors(self, res)))
-
-                # Store parameters for the matched residue template.
-                matchAtoms = dict(zip(matches, res.atoms()))
-                for atom, match in zip(res.atoms(), matches):
-                    data.atomType[atom] = template.atoms[match].type
-                    data.atomParameters[atom] = template.atoms[match].parameters
-                    for site in template.virtualSites:
-                        if match == site.index:
-                            data.virtualSites[atom] = (site, [matchAtoms[i].index for i in site.atoms], matchAtoms[site.excludeWith].index)
+                    unmatchedResidues.append(res)
+                else:
+                    data.recordMatchedAtomParameters(res, template, matches)
+        
+        # Try to apply patches to find matches for any unmatched residues.
+        
+        if len(unmatchedResidues) > 0:
+            unmatchedResidues = _applyPatchesToMatchResidues(self, data, unmatchedResidues, bondedToAtom)
+        
+        # If we still haven't found a match for a residue, attempt to use residue template generators to create
+        # new templates (and potentially atom types/parameters).
+
+        for res in unmatchedResidues:
+            # A template might have been generated on an earlier iteration of this loop.
+            [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
+            if matches is None:
+                # Try all generators.
+                for generator in self._templateGenerators:
+                    if generator(self, res):
+                        # This generator has registered a new residue template that should match.
+                        [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
+                        if matches is None:
+                            # Something went wrong because the generated template does not match the residue signature.
+                            raise Exception('The residue handler %s indicated it had correctly parameterized residue %s, but the generated template did not match the residue signature.' % (generator.__class__.__name__, str(res)))
+                        else:
+                            # We successfully generated a residue template.  Break out of the for loop.
+                            break
+            if matches is None:
+                raise ValueError('No template found for residue %d (%s).  %s' % (res.index+1, res.name, _findMatchErrors(self, res)))
+            else:
+                data.recordMatchedAtomParameters(res, template, matches)
 
         # Create the System and add atoms
 
@@ -1008,6 +1199,32 @@ class ForceField(object):
         return sys
 
 
+def _findBondsForExclusions(data, sys):
+    """Create a list of bonds to use when identifying exclusions."""
+    bondIndices = []
+    for bond in data.bonds:
+        bondIndices.append((bond.atom1, bond.atom2))
+
+    # If a virtual site does *not* share exclusions with another atom, add a bond between it and its first parent atom.
+
+    for i in range(sys.getNumParticles()):
+        if sys.isVirtualSite(i):
+            (site, atoms, excludeWith) = data.virtualSites[data.atoms[i]]
+            if excludeWith is None:
+                bondIndices.append((i, site.getParticle(0)))
+
+    # Certain particles, such as lone pairs and Drude particles, share exclusions with a parent atom.
+    # If the parent atom does not interact with an atom, the child particle does not either.
+
+    for atom1, atom2 in bondIndices:
+        for child1 in data.excludeAtomWith[atom1]:
+            bondIndices.append((child1, atom2))
+            for child2 in data.excludeAtomWith[atom2]:
+                bondIndices.append((child1, child2))
+        for child2 in data.excludeAtomWith[atom2]:
+            bondIndices.append((atom1, child2))
+    return bondIndices
+
 def _countResidueAtoms(elements):
     """Count the number of atoms of each element in a residue."""
     counts = {}
@@ -1054,15 +1271,14 @@ def _matchResidue(res, template, bondedToAtom):
         corresponds to, or None if it does not match the template
     """
     atoms = list(res.atoms())
-    if len(atoms) != len(template.atoms):
+    numAtoms = len(atoms)
+    if numAtoms != len(template.atoms):
         return None
-    matches = len(atoms)*[0]
-    hasMatch = len(atoms)*[False]
 
     # Translate from global to local atom indices, and record the bonds for each atom.
 
     renumberAtoms = {}
-    for i in range(len(atoms)):
+    for i in range(numAtoms):
         renumberAtoms[atoms[i].index] = i
     bondedTo = []
     externalBonds = []
@@ -1088,37 +1304,264 @@ def _matchResidue(res, template, bondedToAtom):
         templateTypeCount[key] += 1
     if residueTypeCount != templateTypeCount:
         return None
+        
+    # Identify template atoms that could potentially be matches for each atom.
+    
+    candidates = [[] for i in range(numAtoms)]
+    for i in range(numAtoms):
+        for j, atom in enumerate(template.atoms):
+            if (atom.element is not None and atom.element != atoms[i].element) or (atom.element is None and atom.name != atoms[i].name):
+                continue
+            if len(atom.bondedTo) != len(bondedTo[i]):
+                continue
+            if atom.externalBonds != externalBonds[i]:
+                continue
+            candidates[i].append(j)
+
+    # Find an optimal ordering for matching atoms.  This means 1) start with the one that has the fewest options,
+    # and 2) follow with ones that are bonded to an already matched atom.
+    
+    searchOrder = []
+    atomsToOrder = set(range(numAtoms))
+    efficientAtomSet = set()
+    efficientAtomHeap = []
+    while len(atomsToOrder) > 0:
+        if len(efficientAtomSet) == 0:
+            fewestNeighbors = numAtoms+1
+            for i in atomsToOrder:
+                if len(candidates[i]) < fewestNeighbors:
+                    nextAtom = i
+                    fewestNeighbors = len(candidates[i])
+        else:
+            nextAtom = heappop(efficientAtomHeap)[1]
+            efficientAtomSet.remove(nextAtom)
+        searchOrder.append(nextAtom)
+        atomsToOrder.remove(nextAtom)
+        for i in bondedTo[nextAtom]:
+            if i in atomsToOrder:
+                if i not in efficientAtomSet:
+                    efficientAtomSet.add(i)
+                    heappush(efficientAtomHeap, (len(candidates[i]), i))
+    inverseSearchOrder = [0]*numAtoms
+    for i in range(numAtoms):
+        inverseSearchOrder[searchOrder[i]] = i
+    bondedTo = [[inverseSearchOrder[bondedTo[i][j]] for j in range(len(bondedTo[i]))] for i in searchOrder]
+    candidates = [candidates[i] for i in searchOrder]
 
     # Recursively match atoms.
 
-    if _findAtomMatches(atoms, template, bondedTo, externalBonds, matches, hasMatch, 0):
-        return matches
+    matches = numAtoms*[0]
+    hasMatch = numAtoms*[False]
+    if _findAtomMatches(template, bondedTo, matches, hasMatch, candidates, 0):
+        return [matches[inverseSearchOrder[i]] for i in range(numAtoms)]
     return None
 
 
-def _findAtomMatches(atoms, template, bondedTo, externalBonds, matches, hasMatch, position):
+def _getAtomMatchCandidates(template, bondedTo, matches, candidates, position):
+    """Get a list of template atoms that are potential matches for the next atom."""
+    for bonded in bondedTo[position]:
+        if bonded < position:
+            # This atom is bonded to another one for which we already have a match, so only consider
+            # template atoms that *that* one is bonded to.
+            return template.atoms[matches[bonded]].bondedTo
+    return candidates[position]
+
+
+def _findAtomMatches(template, bondedTo, matches, hasMatch, candidates, position):
     """This is called recursively from inside _matchResidue() to identify matching atoms."""
-    if position == len(atoms):
+    if position == len(matches):
         return True
-    elem = atoms[position].element
-    name = atoms[position].name
-    for i in range(len(atoms)):
+    for i in _getAtomMatchCandidates(template, bondedTo, matches, candidates, position):
         atom = template.atoms[i]
-        if ((atom.element is not None and atom.element == elem) or (atom.element is None and atom.name == name)) and not hasMatch[i] and len(atom.bondedTo) == len(bondedTo[position]) and atom.externalBonds == externalBonds[position]:
+        if not hasMatch[i] and i in candidates[position]:
             # See if the bonds for this identification are consistent
 
             allBondsMatch = all((bonded > position or matches[bonded] in atom.bondedTo for bonded in bondedTo[position]))
             if allBondsMatch:
-                # This is a possible match, so trying matching the rest of the residue.
+                # This is a possible match, so try matching the rest of the residue.
 
                 matches[position] = i
                 hasMatch[i] = True
-                if _findAtomMatches(atoms, template, bondedTo, externalBonds, matches, hasMatch, position+1):
+                if _findAtomMatches(template, bondedTo, matches, hasMatch, candidates, position+1):
                     return True
                 hasMatch[i] = False
     return False
 
 
+def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom):
+    """Try to apply patches to find matches for residues."""
+    # Start by creating all templates than can be created by applying a combination of one-residue patches
+    # to a single template.  The number of these is usually not too large, and they often cover a large fraction
+    # of residues.
+    
+    patchedTemplateSignatures = {}
+    patchedTemplates = {}
+    for name, template in forcefield._templates.items():
+        if name in forcefield._templatePatches:
+            patches = [forcefield._patches[patchName] for patchName, patchResidueIndex in forcefield._templatePatches[name] if forcefield._patches[patchName].numResidues == 1]
+            if len(patches) > 0:
+                newTemplates = []
+                patchedTemplates[name] = newTemplates
+                _generatePatchedSingleResidueTemplates(template, patches, 0, newTemplates)
+                for patchedTemplate in newTemplates:
+                    signature = _createResidueSignature([atom.element for atom in patchedTemplate.atoms])
+                    if signature in patchedTemplateSignatures:
+                        patchedTemplateSignatures[signature].append(patchedTemplate)
+                    else:
+                        patchedTemplateSignatures[signature] = [patchedTemplate]
+    
+    # Now see if any of those templates matches any of the residues.
+    
+    unmatchedResidues = []
+    for res in residues:
+        [template, matches] = forcefield._getResidueTemplateMatches(res, bondedToAtom, patchedTemplateSignatures)
+        if matches is None:
+            unmatchedResidues.append(res)
+        else:
+            data.recordMatchedAtomParameters(res, template, matches)
+    if len(unmatchedResidues) == 0:
+        return []
+    
+    # We need to consider multi-residue patches.  This can easily lead to a combinatorial explosion, so we make a simplifying
+    # assumption: that no residue is affected by more than one multi-residue patch (in addition to any number of single-residue
+    # patches).  Record all multi-residue patches, and the templates they can be applied to.
+    
+    patches = {}
+    maxPatchSize = 0
+    for patch in forcefield._patches.values():
+        if patch.numResidues > 1:
+            patches[patch.name] = [[] for i in range(patch.numResidues)]
+            maxPatchSize = max(maxPatchSize, patch.numResidues)
+    if maxPatchSize == 0:
+        return unmatchedResidues # There aren't any multi-residue patches
+    for templateName in forcefield._templatePatches:
+        for patchName, patchResidueIndex in forcefield._templatePatches[templateName]:
+            if patchName in patches:
+                # The patch should accept this template, *and* all patched versions of it generated above.
+                patches[patchName][patchResidueIndex].append(forcefield._templates[templateName])
+                if templateName in patchedTemplates:
+                    patches[patchName][patchResidueIndex] += patchedTemplates[templateName]
+    
+    # Record which unmatched residues are bonded to each other.
+    
+    bonds = set()
+    topology = residues[0].chain.topology
+    for atom1, atom2 in topology.bonds():
+        if atom1.residue != atom2.residue:
+            res1 = atom1.residue
+            res2 = atom2.residue
+            if res1 in unmatchedResidues and res2 in unmatchedResidues:
+                bond = tuple(sorted((res1, res2), key=lambda x: x.index))
+                if bond not in bonds:
+                    bonds.add(bond)
+    
+    # Identify clusters of unmatched residues that are all bonded to each other.  These are the ones we'll
+    # try to apply multi-residue patches to.
+    
+    clusterSize = 2
+    clusters = bonds
+    while clusterSize <= maxPatchSize:
+        # Try to apply patches to clusters of this size.
+        
+        for patchName in patches:
+            patch = forcefield._patches[patchName]
+            if patch.numResidues == clusterSize:
+                matchedClusters = _matchToMultiResiduePatchedTemplates(data, clusters, patch, patches[patchName], bondedToAtom)
+                for cluster in matchedClusters:
+                    for residue in cluster:
+                        unmatchedResidues.remove(residue)
+                bonds = set(bond for bond in bonds if bond[0] in unmatchedResidues and bond[1] in unmatchedResidues)
+
+        # Now extend the clusters to find ones of the next size up.
+        
+        largerClusters = set()
+        for cluster in clusters:
+            for bond in bonds:
+                if bond[0] in cluster and bond[1] not in cluster:
+                    newCluster = tuple(sorted(cluster+(bond[1],), key=lambda x: x.index))
+                    largerClusters.add(newCluster)
+                elif bond[1] in cluster and bond[0] not in cluster:
+                    newCluster = tuple(sorted(cluster+(bond[0],), key=lambda x: x.index))
+                    largerClusters.add(newCluster)
+        if len(largerClusters) == 0:
+            # There are no clusters of this size or larger
+            break
+        clusters = largerClusters
+        clusterSize += 1
+
+    return unmatchedResidues
+
+
+def _generatePatchedSingleResidueTemplates(template, patches, index, newTemplates):
+    """Apply all possible combinations of a set of single-residue patches to a template."""
+    try:
+        patchedTemplate = patches[index].createPatchedTemplates([template])[0]
+        newTemplates.append(patchedTemplate)
+    except:
+        # This probably means the patch is inconsistent with another one that has already been applied,
+        # so just ignore it.
+        patchedTemplate = None
+    
+    # Call this function recursively to generate combinations of patches.
+    
+    if index+1 < len(patches):
+        _generatePatchedSingleResidueTemplates(template, patches, index+1, newTemplates)
+        if patchedTemplate is not None:
+            _generatePatchedSingleResidueTemplates(patchedTemplate, patches, index+1, newTemplates)
+
+
+def _matchToMultiResiduePatchedTemplates(data, clusters, patch, residueTemplates, bondedToAtom):
+    """Apply a multi-residue patch to templates, then try to match them against clusters of residues."""
+    matchedClusters = []
+    selectedTemplates = [None]*patch.numResidues
+    _applyMultiResiduePatch(data, clusters, patch, residueTemplates, selectedTemplates, 0, matchedClusters, bondedToAtom)
+    return matchedClusters
+
+
+def _applyMultiResiduePatch(data, clusters, patch, candidateTemplates, selectedTemplates, index, matchedClusters, bondedToAtom):
+    """This is called recursively to apply a multi-residue patch to all possible combinations of templates."""
+
+    if index < patch.numResidues:
+        for template in candidateTemplates[index]:
+            selectedTemplates[index] = template
+            _applyMultiResiduePatch(data, clusters, patch, candidateTemplates, selectedTemplates, index+1, matchedClusters, bondedToAtom)
+    else:
+        # We're at the deepest level of the recursion.  We've selected a template for each residue, so apply the patch,
+        # then try to match it against clusters.
+        
+        try:
+            patchedTemplates = patch.createPatchedTemplates(selectedTemplates)
+        except:
+            # This probably means the patch is inconsistent with another one that has already been applied,
+            # so just ignore it.
+            raise
+            return
+        newlyMatchedClusters = []
+        for cluster in clusters:
+            for residues in itertools.permutations(cluster):
+                residueMatches = []
+                for residue, template in zip(residues, patchedTemplates):
+                    matches = _matchResidue(residue, template, bondedToAtom)
+                    if matches is None:
+                        residueMatches = None
+                        break
+                    else:
+                        residueMatches.append(matches)
+                if residueMatches is not None:
+                    # We successfully matched the template to the residues.  Record the parameters.
+                    
+                    for i in range(patch.numResidues):
+                        data.recordMatchedAtomParameters(residues[i], patchedTemplates[i], residueMatches[i])
+                    newlyMatchedClusters.append(cluster)
+                    break
+        
+        # Record which clusters were successfully matched.
+        
+        matchedClusters += newlyMatchedClusters
+        for cluster in newlyMatchedClusters:
+            clusters.remove(cluster)
+        
+
 def _findMatchErrors(forcefield, res):
     """Try to guess why a residue failed to match any template and return an error message."""
     residueCounts = _countResidueAtoms([atom.element for atom in res.atoms()])
@@ -1713,37 +2156,156 @@ class NonbondedGenerator(object):
         sys.addForce(force)
 
     def postprocessSystem(self, sys, data, args):
-        # Create exceptions based on bonds.
+        # Create the exceptions.
 
-        bondIndices = []
-        for bond in data.bonds:
-            bondIndices.append((bond.atom1, bond.atom2))
+        bondIndices = _findBondsForExclusions(data, sys)
+        nonbonded = [f for f in sys.getForces() if isinstance(f, mm.NonbondedForce)][0]
+        nonbonded.createExceptionsFromBonds(bondIndices, self.coulomb14scale, self.lj14scale)
 
-        # If a virtual site does *not* share exclusions with another atom, add a bond between it and its first parent atom.
+parsers["NonbondedForce"] = NonbondedGenerator.parseElement
 
-        for i in range(sys.getNumParticles()):
-            if sys.isVirtualSite(i):
-                (site, atoms, excludeWith) = data.virtualSites[data.atoms[i]]
-                if excludeWith is None:
-                    bondIndices.append((i, site.getParticle(0)))
 
-        # Certain particles, such as lone pairs and Drude particles, share exclusions with a parent atom.
-        # If the parent atom does not interact with an atom, the child particle does not either.
+## @private
+class LennardJonesGenerator(object):
+    """A NBFix generator to construct the L-J force with NBFIX implemented as a lookup table"""
 
-        for atom1, atom2 in bondIndices:
-            for child1 in data.excludeAtomWith[atom1]:
-                bondIndices.append((child1, atom2))
-                for child2 in data.excludeAtomWith[atom2]:
-                    bondIndices.append((child1, child2))
-            for child2 in data.excludeAtomWith[atom2]:
-                bondIndices.append((atom1, child2))
+    def __init__(self, forcefield, lj14scale):
+        self.ff = forcefield
+        self.nbfixTypes = {}
+        self.lj14scale = lj14scale
+        self.ljTypes = ForceField._AtomTypeParameters(forcefield, 'LennardJonesForce', 'Atom', ('sigma', 'epsilon'))
 
-        # Create the exceptions.
+    def registerNBFIX(self, parameters):
+        types = self.ff._findAtomTypes(parameters, 2)
+        if None not in types:
+            type1 = types[0][0]
+            type2 = types[1][0]
+            epsilon = _convertParameterToNumber(parameters['epsilon'])
+            sigma = _convertParameterToNumber(parameters['sigma'])
+            self.nbfixTypes[(type1, type2)] = [sigma, epsilon]
+            self.nbfixTypes[(type2, type1)] = [sigma, epsilon]
 
-        nonbonded = [f for f in sys.getForces() if isinstance(f, mm.NonbondedForce)][0]
-        nonbonded.createExceptionsFromBonds(bondIndices, self.coulomb14scale, self.lj14scale)
+    def registerLennardJones(self, parameters):
+        self.ljTypes.registerAtom(parameters)
 
-parsers["NonbondedForce"] = NonbondedGenerator.parseElement
+    @staticmethod
+    def parseElement(element, ff):
+        existing = [f for f in ff._forces if isinstance(f, LennardJonesGenerator)]
+        if len(existing) == 0:
+            generator = LennardJonesGenerator(ff, float(element.attrib['lj14scale']))
+            ff.registerGenerator(generator)
+        else:
+            # Multiple <LennardJonesForce> tags were found, probably in different files
+            generator = existing[0]
+            if abs(generator.lj14scale - float(element.attrib['lj14scale'])) > NonbondedGenerator.SCALETOL:
+                raise ValueError('Found multiple LennardJonesForce tags with different 1-4 scales')
+        for LJ in element.findall('Atom'):
+            generator.registerLennardJones(LJ.attrib)
+        for Nbfix in element.findall('NBFixPair'):
+            generator.registerNBFIX(Nbfix.attrib)
+
+    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
+        # First derive the lookup tables
+
+        nbfixTypeSet = set().union(*self.nbfixTypes)
+        ljIndexList = [None]*len(data.atoms)
+        numLjTypes = 0
+        ljTypeList = []
+        typeMap = {}
+        for i, atom in enumerate(data.atoms):
+            atype = data.atomType[atom]
+            values = tuple(self.ljTypes.getAtomParameters(atom, data))
+            if values in typeMap and atype not in nbfixTypeSet:
+                # Only non-NBFIX types can be compressed
+                ljIndexList[i] = typeMap[values]
+            else:
+                typeMap[values] = numLjTypes
+                ljIndexList[i] = numLjTypes
+                numLjTypes += 1
+                ljTypeList.append(atype)
+        reverseMap = [0]*len(typeMap)
+        for typeValue in typeMap:
+            reverseMap[typeMap[typeValue]] = typeValue
+
+        # Now everything is assigned. Create the A- and B-coefficient arrays
+        
+        acoef = [0]*(numLjTypes*numLjTypes)
+        bcoef = acoef[:]
+        for m in range(numLjTypes):
+            for n in range(numLjTypes):
+                pair = (ljTypeList[m], ljTypeList[n])
+                if pair in self.nbfixTypes:
+                    epsilon = self.nbfixTypes[pair][1]
+                    sigma = self.nbfixTypes[pair][0]
+                    sigma6 = sigma**6
+                    acoef[m+numLjTypes*n] = 4*epsilon*sigma6*sigma6
+                    bcoef[m+numLjTypes*n] = 4*epsilon*sigma6
+                    continue
+                else:
+                    sigma = 0.5*(reverseMap[m][0]+reverseMap[n][0])
+                    sigma6 = sigma**6
+                    epsilon = math.sqrt(reverseMap[m][-1]*reverseMap[n][-1])
+                    acoef[m+numLjTypes*n] = 4*epsilon*sigma6*sigma6
+                    bcoef[m+numLjTypes*n] = 4*epsilon*sigma6
+
+        self.force = mm.CustomNonbondedForce('acoef(type1, type2)/r^12 - bcoef(type1, type2)/r^6;')
+        self.force.addTabulatedFunction('acoef', mm.Discrete2DFunction(numLjTypes, numLjTypes, acoef))
+        self.force.addTabulatedFunction('bcoef', mm.Discrete2DFunction(numLjTypes, numLjTypes, bcoef))
+        self.force.addPerParticleParameter('type')
+        if nonbondedMethod in [CutoffPeriodic, Ewald, PME]:
+            self.force.setNonbondedMethod(mm.CustomNonbondedForce.CutoffPeriodic)
+        elif nonbondedMethod is NoCutoff:
+            self.force.setNonbondedMethod(mm.CustomNonbondedForce.NoCutoff)
+        elif nonbondedMethod is CutoffNonPeriodic:
+            self.force.setNonbondedMethod(mm.CustomNonbondedForce.CutoffNonPeriodic)
+        else:
+            raise AssertionError('Unrecognized nonbonded method [%s]' % nonbondedMethod)
+
+        # Add the particles
+
+        for i in ljIndexList:
+            self.force.addParticle((i,))
+        self.force.setUseLongRangeCorrection(True)
+        self.force.setCutoffDistance(nonbondedCutoff)
+        sys.addForce(self.force)
+
+    def postprocessSystem(self, sys, data, args):
+        # Create the exceptions.
+        
+        bondIndices = _findBondsForExclusions(data, sys)
+        if self.lj14scale == 1:
+            # Just exclude the 1-2 and 1-3 interactions.
+            
+            self.force.createExclusionsFromBonds(bondIndices, 2)
+        else:
+            forceCopy = deepcopy(self.force)
+            forceCopy.createExclusionsFromBonds(bondIndices, 2)
+            self.force.createExclusionsFromBonds(bondIndices, 3)
+            if self.force.getNumExclusions() > forceCopy.getNumExclusions() and self.lj14scale != 0:
+                # We need to create a CustomBondForce and use it to implement the scaled 1-4 interactions.
+                
+                bonded = mm.CustomBondForce('%g*epsilon*((sigma/r)^12-(sigma/r)^6)' % (4*self.lj14scale))
+                bonded.addPerBondParameter('sigma')
+                bonded.addPerBondParameter('epsilon')
+                sys.addForce(bonded)
+                skip = set(tuple(forceCopy.getExclusionParticles(i)) for i in range(forceCopy.getNumExclusions()))
+                for i in range(self.force.getNumExclusions()):
+                    p1,p2 = self.force.getExclusionParticles(i)
+                    a1 = data.atoms[p1]
+                    a2 = data.atoms[p2]
+                    if (p1,p2) not in skip and (p2,p1) not in skip:
+                        type1 = data.atomType[a1]
+                        type2 = data.atomType[a2]
+                        if (type1, type2) in self.nbfixTypes:
+                            sigma, epsilon = self.nbfixTypes[(type1, type2)]
+                        else:
+                            values1 = self.ljTypes.getAtomParameters(a1, data)
+                            values2 = self.ljTypes.getAtomParameters(a2, data)
+                            sigma = 0.5*(values1[0]+values2[0])
+                            epsilon = sqrt(values1[1]*values2[1])
+                        bonded.addBond(p1, p2, (sigma, epsilon))
+
+parsers["LennardJonesForce"] = LennardJonesGenerator.parseElement
 
 
 ## @private
@@ -2060,33 +2622,9 @@ class CustomNonbondedGenerator(object):
         sys.addForce(force)
 
     def postprocessSystem(self, sys, data, args):
-        # Create exclusions based on bonds.
-
-        bondIndices = []
-        for bond in data.bonds:
-            bondIndices.append((bond.atom1, bond.atom2))
-
-        # If a virtual site does *not* share exclusions with another atom, add a bond between it and its first parent atom.
-
-        for i in range(sys.getNumParticles()):
-            if sys.isVirtualSite(i):
-                (site, atoms, excludeWith) = data.virtualSites[data.atoms[i]]
-                if excludeWith is None:
-                    bondIndices.append((i, site.getParticle(0)))
-
-        # Certain particles, such as lone pairs and Drude particles, share exclusions with a parent atom.
-        # If the parent atom does not interact with an atom, the child particle does not either.
-
-        for atom1, atom2 in bondIndices:
-            for child1 in data.excludeAtomWith[atom1]:
-                bondIndices.append((child1, atom2))
-                for child2 in data.excludeAtomWith[atom2]:
-                    bondIndices.append((child1, child2))
-            for child2 in data.excludeAtomWith[atom2]:
-                bondIndices.append((atom1, child2))
-
         # Create the exclusions.
 
+        bondIndices = _findBondsForExclusions(data, sys)
         nonbonded = [f for f in sys.getForces() if isinstance(f, mm.CustomNonbondedForce)][0]
         nonbonded.createExclusionsFromBonds(bondIndices, self.bondCutoff)
 
@@ -3504,33 +4042,36 @@ class AmoebaVdwGenerator(object):
         #   <Vdw class="1" sigma="0.371" epsilon="0.46024" reduction="1.0" />
         #   <Vdw class="2" sigma="0.382" epsilon="0.422584" reduction="1.0" />
 
-        generator = AmoebaVdwGenerator(element.attrib['type'], element.attrib['radiusrule'], element.attrib['radiustype'], element.attrib['radiussize'], element.attrib['epsilonrule'],
+        existing = [f for f in forceField._forces if isinstance(f, AmoebaVdwGenerator)]
+        if len(existing) == 0:
+            generator = AmoebaVdwGenerator(element.attrib['type'], element.attrib['radiusrule'], element.attrib['radiustype'], element.attrib['radiussize'], element.attrib['epsilonrule'],
                                         float(element.attrib['vdw-13-scale']), float(element.attrib['vdw-14-scale']), float(element.attrib['vdw-15-scale']))
-        forceField._forces.append(generator)
-        generator.params = ForceField._AtomTypeParameters(forceField, 'AmoebaVdwForce', 'Vdw', ('sigma', 'epsilon', 'reduction'))
+            forceField.registerGenerator(generator)
+            generator.params = ForceField._AtomTypeParameters(forceField, 'AmoebaVdwForce', 'Vdw', ('sigma', 'epsilon', 'reduction'))
+        else:
+            # Multiple <AmoebaVdwForce> tags were found, probably in different files.  Simply add more types to the existing one.
+            generator = existing[0]
+            if abs(generator.vdw13Scale - float(element.attrib['vdw-13-scale'])) > NonbondedGenerator.SCALETOL or \
+                    abs(generator.vdw14Scale - float(element.attrib['vdw-14-scale'])) > NonbondedGenerator.SCALETOL or \
+                    abs(generator.vdw15Scale - float(element.attrib['vdw-15-scale'])) > NonbondedGenerator.SCALETOL:
+                raise ValueError('Found multiple AmoebaVdwForce tags with different scale factors')
+            if generator.radiusrule != element.attrib['radiusrule'] or generator.epsilonrule != element.attrib['epsilonrule'] or \
+                    generator.radiustype != element.attrib['radiustype'] or generator.radiussize != element.attrib['radiussize']:
+                raise ValueError('Found multiple AmoebaVdwForce tags with different combining rules')
         generator.params.parseDefinitions(element)
         two_six = 1.122462048309372
 
     #=============================================================================================
 
-    # Return a set containing the indices of particles bonded to particle with index=particleIndex
-
-    #=============================================================================================
-
     @staticmethod
-    def getBondedParticleSet(particleIndex, data):
-
-        bondedParticleSet = set()
-
-        for bond in data.atomBonds[particleIndex]:
-            atom1 = data.bonds[bond].atom1
-            atom2 = data.bonds[bond].atom2
-            if (atom1 != particleIndex):
-                bondedParticleSet.add(atom1)
-            else:
-                bondedParticleSet.add(atom2)
+    def getBondedParticleSets(sys, data):
 
-        return bondedParticleSet
+        bondedParticleSets = [set() for i in range(len(data.atoms))]
+        bondIndices = _findBondsForExclusions(data, sys)
+        for atom1, atom2 in bondIndices:
+            bondedParticleSets[atom1].add(atom2)
+            bondedParticleSets[atom2].add(atom1)
+        return bondedParticleSets
 
     #=============================================================================================
 
@@ -3539,53 +4080,45 @@ class AmoebaVdwGenerator(object):
         sigmaMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'CUBIC-MEAN':1}
         epsilonMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'HARMONIC':1, 'HHG':1}
 
-        # get or create force depending on whether it has already been added to the system
-
-        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
-        existing = [f for f in existing if type(f) == mm.AmoebaVdwForce]
-        if len(existing) == 0:
-            force = mm.AmoebaVdwForce()
-            sys.addForce(force)
+        force = mm.AmoebaVdwForce()
+        sys.addForce(force)
 
-            # sigma and epsilon combining rules
+        # sigma and epsilon combining rules
 
-            if ('sigmaCombiningRule' in args):
-                sigmaRule = args['sigmaCombiningRule'].upper()
-                if (sigmaRule.upper() in sigmaMap):
-                    force.setSigmaCombiningRule(sigmaRule.upper())
-                else:
-                    stringList = ' ' . join(str(x) for x in sigmaMap.keys())
-                    raise ValueError( "AmoebaVdwGenerator: sigma combining rule %s not recognized; valid values are %s; using default." % (sigmaRule, stringList) )
+        if ('sigmaCombiningRule' in args):
+            sigmaRule = args['sigmaCombiningRule'].upper()
+            if (sigmaRule.upper() in sigmaMap):
+                force.setSigmaCombiningRule(sigmaRule.upper())
             else:
-                force.setSigmaCombiningRule(self.radiusrule)
+                stringList = ' ' . join(str(x) for x in sigmaMap.keys())
+                raise ValueError( "AmoebaVdwGenerator: sigma combining rule %s not recognized; valid values are %s; using default." % (sigmaRule, stringList) )
+        else:
+            force.setSigmaCombiningRule(self.radiusrule)
 
-            if ('epsilonCombiningRule' in args):
-                epsilonRule = args['epsilonCombiningRule'].upper()
-                if (epsilonRule.upper() in epsilonMap):
-                    force.setEpsilonCombiningRule(epsilonRule.upper())
-                else:
-                    stringList = ' ' . join(str(x) for x in epsilonMap.keys())
-                    raise ValueError( "AmoebaVdwGenerator: epsilon combining rule %s not recognized; valid values are %s; using default." % (epsilonRule, stringList) )
+        if ('epsilonCombiningRule' in args):
+            epsilonRule = args['epsilonCombiningRule'].upper()
+            if (epsilonRule.upper() in epsilonMap):
+                force.setEpsilonCombiningRule(epsilonRule.upper())
             else:
-                force.setEpsilonCombiningRule(self.epsilonrule)
-
-            # cutoff
+                stringList = ' ' . join(str(x) for x in epsilonMap.keys())
+                raise ValueError( "AmoebaVdwGenerator: epsilon combining rule %s not recognized; valid values are %s; using default." % (epsilonRule, stringList) )
+        else:
+            force.setEpsilonCombiningRule(self.epsilonrule)
 
-            if ('vdwCutoff' in args):
-                force.setCutoff(args['vdwCutoff'])
-            else:
-                force.setCutoff(nonbondedCutoff)
+        # cutoff
 
-            # dispersion correction
+        if ('vdwCutoff' in args):
+            force.setCutoff(args['vdwCutoff'])
+        else:
+            force.setCutoff(nonbondedCutoff)
 
-            if ('useDispersionCorrection' in args):
-                force.setUseDispersionCorrection(bool(args['useDispersionCorrection']))
+        # dispersion correction
 
-            if (nonbondedMethod == PME):
-                force.setNonbondedMethod(mm.AmoebaVdwForce.CutoffPeriodic)
+        if ('useDispersionCorrection' in args):
+            force.setUseDispersionCorrection(bool(args['useDispersionCorrection']))
 
-        else:
-            force = existing[0]
+        if (nonbondedMethod == PME):
+            force.setNonbondedMethod(mm.AmoebaVdwForce.CutoffPeriodic)
 
         # add particles to force
 
@@ -3614,9 +4147,7 @@ class AmoebaVdwGenerator(object):
         # (1) collect in bondedParticleSets[i], 1-2 indices for all bonded partners of particle i
         # (2) add 1-2,1-3 and self to exclusion set
 
-        bondedParticleSets = []
-        for i in range(len(data.atoms)):
-            bondedParticleSets.append(AmoebaVdwGenerator.getBondedParticleSet(i, data))
+        bondedParticleSets = AmoebaVdwGenerator.getBondedParticleSets(sys, data)
 
         for (i,atom) in enumerate(data.atoms):
 
@@ -3649,34 +4180,8 @@ class AmoebaMultipoleGenerator(object):
 
     #=============================================================================================
 
-    def __init__(self, forceField,
-                       direct11Scale, direct12Scale, direct13Scale, direct14Scale,
-                       mpole12Scale,  mpole13Scale,  mpole14Scale,  mpole15Scale,
-                       mutual11Scale, mutual12Scale, mutual13Scale, mutual14Scale,
-                       polar12Scale,  polar13Scale,  polar14Scale,  polar15Scale):
-
+    def __init__(self, forceField):
         self.forceField = forceField
-
-        self.direct11Scale = direct11Scale
-        self.direct12Scale = direct12Scale
-        self.direct13Scale = direct13Scale
-        self.direct14Scale = direct14Scale
-
-        self.mpole12Scale = mpole12Scale
-        self.mpole13Scale = mpole13Scale
-        self.mpole14Scale = mpole14Scale
-        self.mpole15Scale = mpole15Scale
-
-        self.mutual11Scale = mutual11Scale
-        self.mutual12Scale = mutual12Scale
-        self.mutual13Scale = mutual13Scale
-        self.mutual14Scale = mutual14Scale
-
-        self.polar12Scale = polar12Scale
-        self.polar13Scale = polar13Scale
-        self.polar14Scale = polar14Scale
-        self.polar15Scale = polar15Scale
-
         self.typeMap = {}
 
     #=============================================================================================
@@ -3734,30 +4239,13 @@ class AmoebaMultipoleGenerator(object):
         # <Multipole class="1"    kz="2"    kx="4"    c0="-0.22620" d1="0.08214" d2="0.00000" d3="0.34883" q11="0.11775" q21="0.00000" q22="-1.02185" q31="-0.17555" q32="0.00000" q33="0.90410"  />
         # <Multipole class="2"    kz="1"    kx="3"    c0="-0.15245" d1="0.19517" d2="0.00000" d3="0.19687" q11="-0.20677" q21="0.00000" q22="-0.48084" q31="-0.01672" q32="0.00000" q33="0.68761"  />
 
-        generator = AmoebaMultipoleGenerator(forceField,
-                                              element.attrib['direct11Scale'],
-                                              element.attrib['direct12Scale'],
-                                              element.attrib['direct13Scale'],
-                                              element.attrib['direct14Scale'],
-
-                                              element.attrib['mpole12Scale'],
-                                              element.attrib['mpole13Scale'],
-                                              element.attrib['mpole14Scale'],
-                                              element.attrib['mpole15Scale'],
-
-                                              element.attrib['mutual11Scale'],
-                                              element.attrib['mutual12Scale'],
-                                              element.attrib['mutual13Scale'],
-                                              element.attrib['mutual14Scale'],
-
-                                              element.attrib['polar12Scale'],
-                                              element.attrib['polar13Scale'],
-                                              element.attrib['polar14Scale'],
-                                              element.attrib['polar15Scale'])
-
-
-
-        forceField._forces.append(generator)
+        existing = [f for f in forceField._forces if isinstance(f, AmoebaMultipoleGenerator)]
+        if len(existing) == 0:
+            generator = AmoebaMultipoleGenerator(forceField)
+            forceField.registerGenerator(generator)
+        else:
+            # Multiple <AmoebaMultipoleForce> tags were found, probably in different files.  Simply add more types to the existing one.
+            generator = existing[0]
 
         # set type map: [ kIndices, multipoles, AMOEBA/OpenMM axis type]
 
@@ -3988,45 +4476,37 @@ class AmoebaMultipoleGenerator(object):
         methodMap = {NoCutoff:mm.AmoebaMultipoleForce.NoCutoff,
                      PME:mm.AmoebaMultipoleForce.PME}
 
-        # get or create force depending on whether it has already been added to the system
+        force = mm.AmoebaMultipoleForce()
+        sys.addForce(force)
+        if (nonbondedMethod not in methodMap):
+            raise ValueError( "AmoebaMultipoleForce: input cutoff method not available." )
+        else:
+            force.setNonbondedMethod(methodMap[nonbondedMethod])
+        force.setCutoffDistance(nonbondedCutoff)
 
-        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
-        existing = [f for f in existing if type(f) == mm.AmoebaMultipoleForce]
-        if len(existing) == 0:
-            force = mm.AmoebaMultipoleForce()
-            sys.addForce(force)
-            if (nonbondedMethod not in methodMap):
-                raise ValueError( "AmoebaMultipoleForce: input cutoff method not available." )
-            else:
-                force.setNonbondedMethod(methodMap[nonbondedMethod])
-            force.setCutoffDistance(nonbondedCutoff)
-
-            if ('ewaldErrorTolerance' in args):
-                force.setEwaldErrorTolerance(float(args['ewaldErrorTolerance']))
-
-            if ('polarization' in args):
-                polarizationType = args['polarization']
-                if (polarizationType.lower() == 'direct'):
-                    force.setPolarizationType(mm.AmoebaMultipoleForce.Direct)
-                elif (polarizationType.lower() == 'extrapolated'):
-                    force.setPolarizationType(mm.AmoebaMultipoleForce.Extrapolated)
-                else:
-                    force.setPolarizationType(mm.AmoebaMultipoleForce.Mutual)
+        if ('ewaldErrorTolerance' in args):
+            force.setEwaldErrorTolerance(float(args['ewaldErrorTolerance']))
 
-            if ('aEwald' in args):
-                force.setAEwald(float(args['aEwald']))
+        if ('polarization' in args):
+            polarizationType = args['polarization']
+            if (polarizationType.lower() == 'direct'):
+                force.setPolarizationType(mm.AmoebaMultipoleForce.Direct)
+            elif (polarizationType.lower() == 'extrapolated'):
+                force.setPolarizationType(mm.AmoebaMultipoleForce.Extrapolated)
+            else:
+                force.setPolarizationType(mm.AmoebaMultipoleForce.Mutual)
 
-            if ('pmeGridDimensions' in args):
-                force.setPmeGridDimensions(args['pmeGridDimensions'])
+        if ('aEwald' in args):
+            force.setAEwald(float(args['aEwald']))
 
-            if ('mutualInducedMaxIterations' in args):
-                force.setMutualInducedMaxIterations(int(args['mutualInducedMaxIterations']))
+        if ('pmeGridDimensions' in args):
+            force.setPmeGridDimensions(args['pmeGridDimensions'])
 
-            if ('mutualInducedTargetEpsilon' in args):
-                force.setMutualInducedTargetEpsilon(float(args['mutualInducedTargetEpsilon']))
+        if ('mutualInducedMaxIterations' in args):
+            force.setMutualInducedMaxIterations(int(args['mutualInducedMaxIterations']))
 
-        else:
-            force = existing[0]
+        if ('mutualInducedTargetEpsilon' in args):
+            force.setMutualInducedTargetEpsilon(float(args['mutualInducedTargetEpsilon']))
 
         # add particles to force
         # throw error if particle type not available
@@ -4035,11 +4515,7 @@ class AmoebaMultipoleGenerator(object):
 
         # 1-2
 
-        bonded12ParticleSets = []
-        for i in range(len(data.atoms)):
-            bonded12ParticleSet = AmoebaVdwGenerator.getBondedParticleSet(i, data)
-            bonded12ParticleSet = set(sorted(bonded12ParticleSet))
-            bonded12ParticleSets.append(bonded12ParticleSet)
+        bonded12ParticleSets = AmoebaVdwGenerator.getBondedParticleSets(sys, data)
 
         # 1-3
 
@@ -4627,11 +5103,7 @@ class AmoebaGeneralizedKirkwoodGenerator(object):
 
         # 1-2
 
-        bonded12ParticleSets = []
-        for i in range(len(data.atoms)):
-            bonded12ParticleSet = AmoebaVdwGenerator.getBondedParticleSet(i, data)
-            bonded12ParticleSet = set(sorted(bonded12ParticleSet))
-            bonded12ParticleSets.append(bonded12ParticleSet)
+        bonded12ParticleSets = AmoebaVdwGenerator.getBondedParticleSets(sys, data)
 
         radiusType = 'Bondi'
         for atomIndex in range(0, amoebaMultipoleForce.getNumMultipoles()):

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

@@ -1006,8 +1006,8 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
         for i, (r, s) in enumerate(zip(radii, screen)):
             if abs(r - gb_parms[i][0]) > 1e-4 or abs(s - gb_parms[i][1]) > 1e-4:
                 if not warned:
-                    warnings.warn('Non-optimal GB parameters detected for GB '
-                                  'model %s' % gbmodel)
+                    warnings.warn(
+                        'Non-optimal GB parameters detected for GB model %s' % gbmodel)
                     warned = True
             gb_parms[i][0], gb_parms[i][1] = r, s
 
@@ -1019,7 +1019,13 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
                                 gb_parm[2], gb_parm[3], gb_parm[4]])
             else:
                 gb.addParticle([charge, gb_parm[0], gb_parm[1]])
+
+        # OBC2 with kappa == 0 uses mm.GBSAOBC2Force, which doesn't have
+        # a finalize method
+        if not (gbmodel == 'OBC2' and implicitSolventKappa == 0.):
+            gb.finalize()
         system.addForce(gb)
+
         if nonbondedMethod == 'NoCutoff':
             gb.setNonbondedMethod(mm.NonbondedForce.NoCutoff)
         elif nonbondedMethod == 'CutoffNonPeriodic':

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

@@ -6,9 +6,9 @@ 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) 2012-2015 University of Virginia and the Authors.
+Portions copyright (c) 2012-2016 University of Virginia and the Authors.
 Authors: Christoph Klein, Michael R. Shirts
-Contributors: Jason M. Swails, Peter Eastman
+Contributors: Jason M. Swails, Peter Eastman, Justin L. MacCallum
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -29,19 +29,25 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 
+
 from __future__ import division, absolute_import
 
 from collections import defaultdict
 import copy
 from simtk.openmm.app import element as E
-from simtk.openmm import CustomGBForce, Continuous2DFunction
+from simtk.openmm import CustomGBForce, Discrete2DFunction
 import simtk.unit as u
+from math import floor
+
 
 def strip_unit(value, unit):
+    """Strip off any units and return value in unit"""
     if not u.is_quantity(value):
         return value
     return value.value_in_unit(unit)
 
+
+# GBn and GBn2 lookup tables
 d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
     2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
     3.18854,3.24498,3.30132,3.35752,3.4136,
@@ -106,8 +112,6 @@ d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
     3.6629,3.71694,3.77095,3.82489,3.8788,3.93265,3.98646,4.04022,
     4.09395,4.14762,4.20126,4.25485,4.3084]
 
-
-
 m0=[0.0381511,0.0338587,0.0301776,0.027003,0.0242506,0.0218529,
     0.0197547,0.0179109,0.0162844,0.0148442,0.0135647,0.0124243,
     0.0114047,0.0104906,0.00966876,0.008928,0.0082587,0.00765255,
@@ -192,10 +196,10 @@ m0=[0.0381511,0.0338587,0.0301776,0.027003,0.0242506,0.0218529,
     0.0332033,0.030322,0.0277596,0.0254732,0.0234266,0.0215892,
     0.0199351,0.018442,0.0170909,0.0158654,0.0147514,0.0137365,
     0.0128101,0.0119627,0.0111863]
-# Rescale to nm
-for i in range (len(d0)):
-    d0[i]=d0[i]/10
-    m0[i]=m0[i]*10
+# Rescale to nanometers
+d0 = [d / 10. for d in d0]
+m0 = [m * 10. for m in m0]
+
 
 def _get_bonded_atom_list(topology):
     """ Returns a list of atoms bonded to each other atom in a dict """
@@ -205,6 +209,7 @@ def _get_bonded_atom_list(topology):
         bondeds[a2].append(a1)
     return bondeds
 
+
 def _is_carboxylateO(atom, all_bonds):
     if atom is not E.oxygen: return False
     bondeds = all_bonds[atom]
@@ -224,6 +229,7 @@ def _is_carboxylateO(atom, all_bonds):
     # If we got here, must be a carboxylate
     return True
 
+
 def _bondi_radii(topology):
     """ Sets the bondi radii """
     radii = [0.0 for atom in topology.atoms()]
@@ -250,6 +256,7 @@ def _bondi_radii(topology):
             radii[i] = 1.5
     return radii  # converted to nanometers above
 
+
 def _mbondi_radii(topology):
     """ Sets the mbondi radii """
     radii = [0.0 for atom in topology.atoms()]
@@ -286,6 +293,7 @@ def _mbondi_radii(topology):
             radii[i] = 1.5
     return radii  # converted to nanometers above
 
+
 def _mbondi2_radii(topology):
     """ Sets the mbondi2 radii """
     radii = [0.0 for atom in topology.atoms()]
@@ -320,6 +328,7 @@ def _mbondi2_radii(topology):
             radii[i] = 1.5
     return radii  # Converted to nanometers above
 
+
 def _mbondi3_radii(topology):
     """ Sets the mbondi3 radii """
     radii = _mbondi2_radii(topology)
@@ -333,9 +342,13 @@ def _mbondi3_radii(topology):
                 radii[i] = 1.17
     return radii  # Converted to nanometers above
 
+
 def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, kappa, offset):
-    # Add the energy terms to the CustomGBForce.  These are identical for all the GB models.
+    """Add the energy terms to the CustomGBForce.
+
+    These are identical for all the GB models.
 
+    """
     params = "; solventDielectric=%.16g; soluteDielectric=%.16g; kappa=%.16g; offset=%.16g" % (solventDielectric, soluteDielectric, kappa, offset)
     if cutoff is not None:
         params += "; cutoff=%.16g" % cutoff
@@ -367,6 +380,7 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
             force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");"
                                 "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
 
+
 _SCREEN_PARAMETERS = { # normal, GBn, GBn2
         E.hydrogen : (0.85, 1.09085413633, 1.425952),
         E.carbon : (0.72, 0.48435382330, 1.058554),
@@ -377,33 +391,52 @@ _SCREEN_PARAMETERS = { # normal, GBn, GBn2
         E.sulfur : (0.96, 0.602256336067, -0.703469),
         None : (0.8, 0.5, 0.5) # default
 }
+
 _SCREEN_PARAMETERS[E.deuterium] = _SCREEN_PARAMETERS[E.hydrogen]
 def _screen_parameter(atom):
     if atom.element in _SCREEN_PARAMETERS:
         return _SCREEN_PARAMETERS[atom.element]
     return _SCREEN_PARAMETERS[None]
 
-class CustomAmberGBForce(CustomGBForce):
 
+class CustomAmberGBForceBase(CustomGBForce):
+    """Base class for all of the Amber custom GB forces.
+
+    Should not be instantiated directly, use one of its
+    derived classes instead.
+
+    """
     OFFSET = 0.009
     RADIUS_ARG_POSITION = 1
     SCREEN_POSITION = 2
 
-    def __init__(self, *args, **kwargs):
-        raise NotImplementedError('Cannot instantiate ABC')
+    def __init__(self):
+        CustomGBForce.__init__(self)
+        self.parameters = []
 
     def addParticle(self, params):
-        params = copy.deepcopy(params)
-        params[self.RADIUS_ARG_POSITION] = strip_unit(params[self.RADIUS_ARG_POSITION], u.nanometer) - self.OFFSET
-        params[self.SCREEN_POSITION] *= params[self.RADIUS_ARG_POSITION]
-        CustomGBForce.addParticle(self, params)
-        return params
+        """Add a particle to the force
+
+        Particles are added in order. The number of particles
+        added must match the number of particles in the system.
+
+        Parameters
+        ----------
+        params : list
+            A list of parameters to add to the force. The meaning
+            parameters depends on the model.
 
-    def setParticleParameters(self, idx, params):
+        Returns
+        -------
+        list
+            The list of parameters after stripping off units and
+            modifying SCREEN.
+
+        """
         params = copy.deepcopy(params)
         params[self.RADIUS_ARG_POSITION] = strip_unit(params[self.RADIUS_ARG_POSITION], u.nanometer) - self.OFFSET
         params[self.SCREEN_POSITION] *= params[self.RADIUS_ARG_POSITION]
-        CustomGBForce.addParticle(self, params)
+        self.parameters.append(params)
         return params
 
     @staticmethod
@@ -421,17 +454,50 @@ class CustomAmberGBForce(CustomGBForce):
             List of all parameters needed for this GB model. These can be passed
             to addParticle or setParticleParameters after the charge is inserted
             at the beginning of the list
+
         """
-        raise NotImplementedError('Must override getStandardParameters in subclasses')
+        raise NotImplementedError(
+            'getStandardParameters must be defined in derived classes')
 
-"""
-Amber Equivalent: igb = 1
-"""
-class GBSAHCTForce(CustomAmberGBForce):
+    def finalize(self):
+        """Finalize this force so it can be added to a system.
 
+        This method must be called before the force is added
+        to the system.
+
+        """
+        self._addParticles()
+
+    def _addParticles(self):
+        for params in self.parameters:
+            CustomGBForce.addParticle(self, params)
+
+
+class GBSAHCTForce(CustomAmberGBForceBase):
+    """This class is equivalent to Amber ``igb=1``
+
+    The list of parameters to ``addParticle`` is: ``[q, or, sr]``.
+
+    Parameters
+    ----------
+    solventDielectric: float
+        Dielectric constant for the solvent
+    soluteDielectric: float
+        Dielectric constant for the solute
+    SA: string or None
+        Surface area model to use
+    cutoff: float or Quantity or None
+        Cutoff distance to use. If float, value is in nm. If ``None``,
+        then no cutoffs are used.
+    kappa: float or Quantity
+        Debye kappa parameter related to modelling salt in GB. It has
+        units of 1 / length with 1 / nanometer assumed if a float
+        is given. A value of zero corresponds to zero salt concentration.
+
+    """
     def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
                  cutoff=None, kappa=0.0):
-        CustomGBForce.__init__(self)
+        CustomAmberGBForceBase.__init__(self)
 
         self.addPerParticleParameter("q")
         self.addPerParticleParameter("or") # Offset radius
@@ -447,20 +513,53 @@ class GBSAHCTForce(CustomAmberGBForce):
 
     @staticmethod
     def getStandardParameters(topology):
+        """ Gets list of standard parameters for this GB model based on an input Topology
+
+        Parameters
+        ----------
+        topology : simtk.openmm.app.Topology
+            Topology of the system to get parameters for
+
+        Returns
+        -------
+        list of float
+            List of all parameters needed for this GB model. These can be passed
+            to addParticle or setParticleParameters after the charge is inserted
+            at the beginning of the list
+
+        """
         radii = [[x/10] for x in _mbondi_radii(topology)]
         for i, atom in enumerate(topology.atoms()):
             radii[i].append(_screen_parameter(atom)[0])
         return radii
 
-"""
-Amber Equivalents: igb = 2
-"""
-class GBSAOBC1Force(CustomAmberGBForce):
 
+class GBSAOBC1Force(CustomAmberGBForceBase):
+    """This class is equivalent to Amber ``igb=2``
+
+    The list of parameters to ``addParticle`` is: ``[q, or, sr]``.
+
+    Parameters
+    ----------
+    solventDielectric: float
+        Dielectric constant for the solvent
+    soluteDielectric: float
+        Dielectric constant for the solute
+    SA: string or None
+        Surface area model to use
+    cutoff: float or Quantity or None
+        Cutoff distance to use. If float, value is in nm. If ``None``,
+        then no cutoffs are used.
+    kappa: float or Quantity
+        Debye kappa parameter related to modelling salt in GB. It has
+        units of 1 / length with 1 / nanometer assumed if a float
+        is given. A value of zero corresponds to zero salt concentration.
+
+    """
     def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
                  cutoff=None, kappa=0.0):
 
-        CustomGBForce.__init__(self)
+        CustomAmberGBForceBase.__init__(self)
 
         self.addPerParticleParameter("q")
         self.addPerParticleParameter("or") # Offset radius
@@ -476,20 +575,55 @@ class GBSAOBC1Force(CustomAmberGBForce):
 
     @staticmethod
     def getStandardParameters(topology):
+        """ Gets list of standard parameters for this GB model based on an input Topology
+
+        Parameters
+        ----------
+        topology : simtk.openmm.app.Topology
+            Topology of the system to get parameters for
+
+        Returns
+        -------
+        list of float
+            List of all parameters needed for this GB model. These can be passed
+            to addParticle or setParticleParameters after the charge is inserted
+            at the beginning of the list
+
+        """
         radii = [[x/10] for x in _mbondi2_radii(topology)]
         for i, atom in enumerate(topology.atoms()):
             radii[i].append(_screen_parameter(atom)[0])
         return radii
 
-"""
-Amber Equivalents: igb = 5
-"""
-class GBSAOBC2Force(GBSAOBC1Force):
 
+class GBSAOBC2Force(GBSAOBC1Force):
+    """This class is equivalent to Amber ``igb=5``
+
+    The list of parameters to ``addParticle`` is: ``[q, or, sr]``.
+
+    Parameters
+    ----------
+    solventDielectric: float
+        Dielectric constant for the solvent
+    soluteDielectric: float
+        Dielectric constant for the solute
+    SA: string or None
+        Surface area model to use
+    cutoff: float or Quantity or None
+        Cutoff distance to use. If float, value is in nm. If ``None``,
+        then no cutoffs are used.
+    kappa: float or Quantity
+        Debye kappa parameter related to modelling salt in GB. It has
+        units of 1 / length with 1 / nanometer assumed if a float
+        is given. A value of zero corresponds to zero salt concentration.
+
+    """
     def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
                  cutoff=None, kappa=0.0):
 
-        CustomGBForce.__init__(self)
+        # Note that this is not GBSAOBC1Force, as our initialization
+        # is different. We inherit for getStandardParameters.
+        CustomAmberGBForceBase.__init__(self)
 
         self.addPerParticleParameter("q")
         self.addPerParticleParameter("or") # Offset radius
@@ -503,90 +637,185 @@ class GBSAOBC2Force(GBSAOBC1Force):
                                      "psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
         _createEnergyTerms(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
 
-"""
-Amber Equivalents: igb = 7
-"""
-class GBSAGBnForce(CustomAmberGBForce):
-
-    def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
-                 cutoff=None, kappa=0.0):
-
-        CustomGBForce.__init__(self)
-
-        self.addPerParticleParameter("q")
-        self.addPerParticleParameter("or") # Offset radius
-        self.addPerParticleParameter("sr") # Scaled offset radius
 
-        self.addTabulatedFunction("getd0", Continuous2DFunction(21, 21, d0, 0.1, 0.2, 0.1, 0.2))
-        self.addTabulatedFunction("getm0", Continuous2DFunction(21, 21, m0, 0.1, 0.2, 0.1, 0.2))
+class GBSAGBnForce(CustomAmberGBForceBase):
+    """This class is equivalent to Amber ``igb=7``
+
+    The list of parameters to ``addParticle`` is: ``[q, or, sr]``.
+
+    Parameters
+    ----------
+    solventDielectric: float
+        Dielectric constant for the solvent
+    soluteDielectric: float
+        Dielectric constant for the solute
+    SA: string or None
+        Surface area model to use
+    cutoff: float or Quantity or None
+        Cutoff distance to use. If float, value is in nm. If ``None``,
+        then no cutoffs are used.
+    kappa: float or Quantity
+        Debye kappa parameter related to modelling salt in GB. It has
+        units of 1 / length with 1 / nanometer assumed if a float
+        is given. A value of zero corresponds to zero salt concentration.
+
+    """
+    OFFSET = 0.009
 
-        self.addComputedValue("I",  "Ivdw+neckScale*Ineck;"
-                                    "Ineck=step(radius1+radius2+neckCut-r)*getm0(radius1,radius2)/(1+100*(r-getd0(radius1,radius2))^2+0.3*1000000*(r-getd0(radius1,radius2))^6);"
-                                    "Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
-                                    "U=r+sr2;"
-                                    "L=max(or1, D);"
-                                    "D=abs(r-sr2);"
-                                    "radius1=or1+offset; radius2=or2+offset;"
-                                    "neckScale=0.361825; neckCut=0.68; offset=0.009", CustomGBForce.ParticlePairNoExclusions)
+    def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None, kappa=0.0):
 
-        self.addComputedValue("B", "1/(1/or-tanh(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);"
-                                  "psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
-        _createEnergyTerms(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
+        CustomAmberGBForceBase.__init__(self)
+        self.solventDielectric = solventDielectric
+        self.soluteDielectric = soluteDielectric
+        self.SA = SA
+        self.cutoff = cutoff
+        self.kappa = kappa
+        self._uniqueRadii = None
+        self._radiusToIndex = None
 
     def addParticle(self, parameters):
-        parameters = CustomAmberGBForce.addParticle(self, parameters)
+        parameters = CustomAmberGBForceBase.addParticle(self, parameters)
         if parameters[1] + self.OFFSET < 0.1 or parameters[1] + self.OFFSET > 0.2:
             raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
 
-    def setParticleParameters(self, idx, parameters):
-        parameters = CustomAmberGBForce.setParticleParameters(self, idx, parameters)
-        if parameters[1] < 0.1 or parameters[1] > 0.2:
-            raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
+    def finalize(self):
+        self._findUniqueRadii()
+        self._createRadiusToIndexMap()
+        self._addEnergyTerms()
+        self._addParticles()
 
     @staticmethod
     def getStandardParameters(topology):
+        """ Gets list of standard parameters for this GB model based on an input Topology
+
+        Parameters
+        ----------
+        topology : simtk.openmm.app.Topology
+            Topology of the system to get parameters for
+
+        Returns
+        -------
+        list of float
+            List of all parameters needed for this GB model. These can be passed
+            to addParticle or setParticleParameters after the charge is inserted
+            at the beginning of the list
+
+        """
         radii = [[x/10] for x in _bondi_radii(topology)]
         for i, atom in enumerate(topology.atoms()):
             radii[i].append(_screen_parameter(atom)[1])
         return radii
 
-"""
-Amber Equivalents: igb = 8
-"""
-class GBSAGBn2Force(GBSAGBnForce):
-
-    OFFSET = 0.0195141
-
-    def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
-                 cutoff=None, kappa=0.0):
-
-        CustomGBForce.__init__(self)
-
+    def _findUniqueRadii(self):
+        radii = [p[self.RADIUS_ARG_POSITION] for p in self.parameters]
+        self._uniqueRadii = list(sorted(set(radii)))
+
+    def _createRadiusToIndexMap(self):
+        self._radiusToIndex = {r: i for i, r in enumerate(self._uniqueRadii)}
+
+    def _createUniqueTable(self, fullTable):
+        tablePositions = [(r+self.OFFSET-0.1)*200 for r in self._uniqueRadii]
+        numRadii = len(self._uniqueRadii)
+        index1 = [0]*numRadii
+        index2 = [0]*numRadii
+        weight1 = [0]*numRadii
+        weight2 = [0]*numRadii
+        for i,p in enumerate(tablePositions):
+            if p <= 0:
+                weight1[i] = 1.0
+            elif p >= 20:
+                index1[i] = 20
+                weight1[i] = 1.0
+            else:
+                index1[i] = int(floor(p))
+                index2[i] = index1[i]+1
+                weight1[i] = index2[i]-p
+                weight2[i] = 1.0-weight1[i]
+        table = []
+        for i in range(numRadii):
+            for j in range(numRadii):
+                table.append(weight1[i]*weight1[j]*fullTable[index1[i]*21+index1[j]] +
+                              weight1[i]*weight2[j]*fullTable[index1[i]*21+index2[j]] +
+                              weight2[i]*weight1[j]*fullTable[index2[i]*21+index1[j]] +
+                              weight2[i]*weight2[j]*fullTable[index2[i]*21+index2[j]])
+        return table
+
+    def _addParticles(self):
+        for p in self.parameters:
+            radIndex = self._radiusToIndex[p[self.RADIUS_ARG_POSITION]]
+            CustomGBForce.addParticle(self, p + [radIndex])
+
+    def _addEnergyTerms(self):
         self.addPerParticleParameter("q")
         self.addPerParticleParameter("or") # Offset radius
         self.addPerParticleParameter("sr") # Scaled offset radius
-        self.addPerParticleParameter("alpha")
-        self.addPerParticleParameter("beta")
-        self.addPerParticleParameter("gamma")
+        self.addPerParticleParameter("radindex")
+
+        n = len(self._uniqueRadii)
+        m0Table = self._createUniqueTable(m0)
+        d0Table = self._createUniqueTable(d0)
+        self.addTabulatedFunction("getd0", Discrete2DFunction(n, n, d0Table))
+        self.addTabulatedFunction("getm0", Discrete2DFunction(n, n, m0Table))
+
+        self.addComputedValue("I", "Ivdw+neckScale*Ineck;"
+                                   "Ineck=step(radius1+radius2+neckCut-r)*getm0(radindex1,radindex2)/(1+100*(r-getd0(radindex1,radindex2))^2+"
+                                   "0.3*1000000*(r-getd0(radindex1,radindex2))^6);"
+                                   "Ivdw=select(step(r+sr2-or1), 0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r), 0);"
+                                   "U=r+sr2;"
+                                   "L=max(or1, D);"
+                                   "D=abs(r-sr2);"
+                                   "radius1=or1+offset; radius2=or2+offset;"
+                                   "neckScale=0.361825; neckCut=0.68; offset=0.009", CustomGBForce.ParticlePairNoExclusions)
 
-        self.addTabulatedFunction("getd0", Continuous2DFunction(21, 21, d0, 0.1, 0.2, 0.1, 0.2))
-        self.addTabulatedFunction("getm0", Continuous2DFunction(21, 21, m0, 0.1, 0.2, 0.1, 0.2))
+        self.addComputedValue("B", "1/(1/or-tanh(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);"
+                                  "psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
+        _createEnergyTerms(self, self.solventDielectric, self.soluteDielectric, self.SA, self.cutoff, self.kappa, self.OFFSET)
 
-        self.addComputedValue("I",  "Ivdw+neckScale*Ineck;"
-                                    "Ineck=step(radius1+radius2+neckCut-r)*getm0(radius1,radius2)/(1+100*(r-getd0(radius1,radius2))^2+0.3*1000000*(r-getd0(radius1,radius2))^6);"
-                                    "Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
-                                    "U=r+sr2;"
-                                    "L=max(or1, D);"
-                                    "D=abs(r-sr2);"
-                                    "radius1=or1+offset; radius2=or2+offset;"
-                                    "neckScale=0.826836; neckCut=0.68; offset=0.0195141", CustomGBForce.ParticlePairNoExclusions)
 
-        self.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
-                                     "psi=I*or; radius=or+offset; offset=0.0195141", CustomGBForce.SingleParticle)
-        _createEnergyTerms(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.0195141)
+class GBSAGBn2Force(GBSAGBnForce):
+    """This class is equivalent to Amber ``igb=8``
+
+    The list of parameters to ``addParticle`` is: ``[q, or, sr, alpha, beta, gamma]``.
+
+    Parameters
+    ----------
+    solventDielectric: float
+        Dielectric constant for the solvent
+    soluteDielectric: float
+        Dielectric constant for the solute
+    SA: string or None
+        Surface area model to use
+    cutoff: float or Quantity or None
+        Cutoff distance to use. If float, value is in nm. If ``None``,
+        then no cutoffs are used.
+    kappa: float or Quantity
+        Debye kappa parameter related to modelling salt in GB. It has
+        units of 1 / length with 1 / nanometer assumed if a float
+        is given. A value of zero corresponds to zero salt concentration.
+
+    """
+    OFFSET = 0.0195141
+
+    def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None, kappa=0.0):
+        GBSAGBnForce.__init__(self, solventDielectric, soluteDielectric, SA, cutoff, kappa)
 
     @staticmethod
     def getStandardParameters(topology):
+        """ Gets list of standard parameters for this GB model based on an input Topology
+
+        Parameters
+        ----------
+        topology : simtk.openmm.app.Topology
+            Topology of the system to get parameters for
+
+        Returns
+        -------
+        list of float
+            List of all parameters needed for this GB model. These can be passed
+            to addParticle or setParticleParameters after the charge is inserted
+            at the beginning of the list
+
+        """
         radii = [[x/10] for x in _mbondi3_radii(topology)]
         for i, atom in enumerate(topology.atoms()):
             radii[i].append(_screen_parameter(atom)[2])
@@ -603,3 +832,32 @@ class GBSAGBn2Force(GBSAGBnForce):
             else:
                 radii[i].extend([0.8, 4.85, 0.5])
         return radii
+
+    def _addEnergyTerms(self):
+        self.addPerParticleParameter("q")
+        self.addPerParticleParameter("or") # Offset radius
+        self.addPerParticleParameter("sr") # Scaled offset radius
+        self.addPerParticleParameter("alpha")
+        self.addPerParticleParameter("beta")
+        self.addPerParticleParameter("gamma")
+        self.addPerParticleParameter("radindex")
+
+        n = len(self._uniqueRadii)
+        m0Table = self._createUniqueTable(m0)
+        d0Table = self._createUniqueTable(d0)
+        self.addTabulatedFunction("getd0", Discrete2DFunction(n, n, d0Table))
+        self.addTabulatedFunction("getm0", Discrete2DFunction(n, n, m0Table))
+
+        self.addComputedValue("I", "Ivdw+neckScale*Ineck;"
+                                   "Ineck=step(radius1+radius2+neckCut-r)*getm0(radindex1,radindex2)/(1+100*(r-getd0(radindex1,radindex2))^2+"
+                                   "0.3*1000000*(r-getd0(radindex1,radindex2))^6);"
+                                   "Ivdw=select(step(r+sr2-or1), 0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r), 0);"
+                                   "U=r+sr2;"
+                                   "L=max(or1, D);"
+                                   "D=abs(r-sr2);"
+                                   "radius1=or1+offset; radius2=or2+offset;"
+                                   "neckScale=0.826836; neckCut=0.68; offset=0.0195141", CustomGBForce.ParticlePairNoExclusions)
+
+        self.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
+                                     "psi=I*or; radius=or+offset; offset=0.0195141", CustomGBForce.SingleParticle)
+        _createEnergyTerms(self, self.solventDielectric, self.soluteDielectric, self.SA, self.cutoff, self.kappa, self.OFFSET)

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

@@ -345,8 +345,11 @@ class Modeller(object):
         elif padding is not None:
             if is_quantity(padding):
                 padding = padding.value_in_unit(nanometer)
-            maxSize = max(max((pos[i] for pos in self.positions))-min((pos[i] for pos in self.positions)) for i in range(3))
-            maxSize = maxSize.value_in_unit(nanometer)
+            if len(self.positions) == 0:
+                maxSize = 0
+            else:
+                maxSize = max(max((pos[i] for pos in self.positions))-min((pos[i] for pos in self.positions)) for i in range(3))
+                maxSize = maxSize.value_in_unit(nanometer)
             box = (maxSize+2*padding)*Vec3(1, 1, 1)
             vectors = (Vec3(maxSize+2*padding, 0, 0), Vec3(0, maxSize+2*padding, 0), Vec3(0, 0, maxSize+2*padding))
         else:

wrappers/python/simtk/openmm/mtsintegrator.py

@@ -90,7 +90,7 @@ class MTSIntegrator(CustomIntegrator):
 
     def _createSubsteps(self, parentSubsteps, groups):
         group, substeps = groups[0]
-        stepsPerParentStep = substeps/parentSubsteps
+        stepsPerParentStep = substeps//parentSubsteps
         if stepsPerParentStep < 1 or stepsPerParentStep != int(stepsPerParentStep):
             raise ValueError("The number for substeps for each group must be a multiple of the number for the previous group")
         if group < 0 or group > 31:

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -124,6 +124,8 @@ NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'),
                   ('AmoebaMultipoleForce', 'setCovalentMap', 'covalentAtoms'),
                   ('AmoebaMultipoleForce', 'getElectrostaticPotential', 'context'),
                   ('AmoebaMultipoleForce', 'getInducedDipoles', 'context'),
+                  ('AmoebaMultipoleForce', 'getLabFramePermanentDipoles', 'context'),
+                  ('AmoebaMultipoleForce', 'getTotalDipoles', 'context'),
 ]
 
 # SWIG assumes the target language shadow class owns the C++ class
@@ -274,6 +276,8 @@ UNITS = {
 #("AmoebaMultipoleForce",                 "getElectrostaticPotential")                     :  ( ('unit.kilojoule_per_mole'), ()),
 ("AmoebaMultipoleForce",                 "getElectrostaticPotential")                     :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getInducedDipoles")                             :  ( None, ()),
+("AmoebaMultipoleForce",                 "getLabFramePermanentDipoles")                   :  ( None, ()),
+("AmoebaMultipoleForce",                 "getTotalDipoles")                               :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getSystemMultipoleMoments")                     :  ( None, ()),
 
 ("AmoebaOutOfPlaneBendForce",            "getNumOutOfPlaneBends")                         :  ( None, ()),

wrappers/python/tests/TestCharmmFiles.py

@@ -165,7 +165,8 @@ class TestCharmmFiles(unittest.TestCase):
             #out = open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml', 'w')
             #out.write(XmlSerializer.serialize(state1))
             #out.close()
-            state2 = XmlSerializer.deserialize(open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml').read())
+            with open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml') as xml:
+                state2 = XmlSerializer.deserialize(xml.read())
             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)
                 self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-4)

wrappers/python/tests/TestForceField.py

@@ -11,6 +11,7 @@ try:
 except ImportError:
     from io import StringIO
 import os
+import warnings
 
 class TestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method."""
@@ -569,8 +570,8 @@ class TestForceField(unittest.TestCase):
         # confirm charge
         self.assertEqual(sys.getForce(0).getParticleParameters(0)[0]._value, 3.0)
 
-    def test_ResidueOverloading(self):
-        """Test residue overloading via overload tag in the XML"""
+    def test_ResidueOverriding(self):
+        """Test residue overriding via override tag in the XML"""
 
         ffxml1 = """<ForceField>
  <AtomTypes>
@@ -607,7 +608,7 @@ class TestForceField(unittest.TestCase):
   <Type name="Fe2+_tip3p_standard" class="Fe2+_tip3p_standard" element="Fe" mass="55.85"/>
  </AtomTypes>
  <Residues>
-  <Residue name="FE2" overload="1">
+  <Residue name="FE2" override="1">
    <Atom name="FE2" type="Fe2+_tip3p_standard" charge="2.0"/>
   </Residue>
  </Residues>
@@ -625,6 +626,128 @@ class TestForceField(unittest.TestCase):
         self.assertEqual(ff._templates['FE2'].atoms[0].type, 'Fe2+_tip3p_standard')
         ff.createSystem(pdb.topology)
 
+    def test_LennardJonesGenerator(self):
+        """ Test the LennardJones generator"""
+        warnings.filterwarnings('ignore', category=CharmmPSFWarning)
+        psf = CharmmPsfFile('systems/ions.psf')
+        pdb = PDBFile('systems/ions.pdb')
+        params = CharmmParameterSet('systems/toppar_water_ions.str'
+                                    )
+
+        # Box dimensions (found from bounding box)
+        psf.setBox(12.009*angstroms,   12.338*angstroms,   11.510*angstroms)
+
+        # Turn off charges so we only test the Lennard-Jones energies
+        for a in psf.atom_list:
+            a.charge = 0.0
+
+        # Now compute the full energy
+        plat = Platform.getPlatformByName('Reference')
+        system = psf.createSystem(params, nonbondedMethod=PME,
+                                  nonbondedCutoff=5*angstroms)
+
+        con = Context(system, VerletIntegrator(2*femtoseconds), plat)
+        con.setPositions(pdb.positions)
+
+        # Now set up system from ffxml.
+        xml = """
+<ForceField>
+ <AtomTypes>
+  <Type name="SOD" class="SOD" element="Na" mass="22.98977"/>
+  <Type name="CLA" class="CLA" element="Cl" mass="35.45"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="CLA">
+   <Atom name="CLA" type="CLA"/>
+  </Residue>
+  <Residue name="SOD">
+   <Atom name="SOD" type="SOD"/>
+  </Residue>
+ </Residues>
+ <LennardJonesForce lj14scale="1.0">
+  <Atom type="CLA" sigma="0.404468018036" epsilon="0.6276"/>
+  <Atom type="SOD" sigma="0.251367073323" epsilon="0.1962296"/>
+  <NBFixPair type1="CLA" type2="SOD" sigma="0.33239431" epsilon="0.350933"/>
+ </LennardJonesForce>
+</ForceField> """
+        ff = ForceField(StringIO(xml))
+        system2 = ff.createSystem(pdb.topology, nonbondedMethod=PME,
+                                  nonbondedCutoff=5*angstroms)
+        con2 = Context(system2, VerletIntegrator(2*femtoseconds), plat)
+        con2.setPositions(pdb.positions)
+
+        state = con.getState(getEnergy=True, enforcePeriodicBox=True)
+        ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
+        state2 = con2.getState(getEnergy=True, enforcePeriodicBox=True)
+        ene2 = state2.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
+        self.assertAlmostEqual(ene, ene2)
+
+    def test_NBFix(self):
+        """Test using LennardJonesGenerator to implement NBFix terms."""
+        # Create a chain of five atoms.
+        
+        top = Topology()
+        chain = top.addChain()
+        res = top.addResidue('RES', chain)
+        top.addAtom('A', elem.oxygen, res)
+        top.addAtom('B', elem.carbon, res)
+        top.addAtom('C', elem.carbon, res)
+        top.addAtom('D', elem.carbon, res)
+        top.addAtom('E', elem.nitrogen, res)
+        atoms = list(top.atoms())
+        top.addBond(atoms[0], atoms[1])
+        top.addBond(atoms[1], atoms[2])
+        top.addBond(atoms[2], atoms[3])
+        top.addBond(atoms[3], atoms[4])
+        
+        # Create the force field and system.
+        
+        xml = """
+<ForceField>
+ <AtomTypes>
+  <Type name="A" class="A" element="O" mass="1"/>
+  <Type name="B" class="B" element="C" mass="1"/>
+  <Type name="C" class="C" element="C" mass="1"/>
+  <Type name="D" class="D" element="C" mass="1"/>
+  <Type name="E" class="E" element="N" mass="1"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="RES">
+   <Atom name="A" type="A"/>
+   <Atom name="B" type="B"/>
+   <Atom name="C" type="C"/>
+   <Atom name="D" type="D"/>
+   <Atom name="E" type="E"/>
+   <Bond atomName1="A" atomName2="B"/>
+   <Bond atomName1="B" atomName2="C"/>
+   <Bond atomName1="C" atomName2="D"/>
+   <Bond atomName1="D" atomName2="E"/>
+  </Residue>
+ </Residues>
+ <LennardJonesForce lj14scale="0.3">
+  <Atom type="A" sigma="1" epsilon="0.1"/>
+  <Atom type="B" sigma="2" epsilon="0.2"/>
+  <Atom type="C" sigma="3" epsilon="0.3"/>
+  <Atom type="D" sigma="4" epsilon="0.4"/>
+  <Atom type="E" sigma="5" epsilon="0.5"/>
+  <NBFixPair type1="A" type2="D" sigma="2.5" epsilon="1.1"/>
+  <NBFixPair type1="A" type2="E" sigma="3.5" epsilon="1.5"/>
+ </LennardJonesForce>
+</ForceField> """
+        ff = ForceField(StringIO(xml))
+        system = ff.createSystem(top)
+        
+        # Check that it produces the correct energy.
+        
+        integrator = VerletIntegrator(0.001)
+        context = Context(system, integrator, Platform.getPlatform(0))
+        positions = [Vec3(i, 0, 0) for i in range(5)]*nanometers
+        context.setPositions(positions)
+        def ljEnergy(sigma, epsilon, r):
+            return 4*epsilon*((sigma/r)**12-(sigma/r)**6)
+        expected = 0.3*ljEnergy(2.5, 1.1, 3)  + 0.3*ljEnergy(3.5, sqrt(0.1), 3) + ljEnergy(3.5, 1.5, 4)
+        self.assertAlmostEqual(expected, context.getState(getEnergy=True).getPotentialEnergy().value_in_unit(kilojoules_per_mole))
+
 class AmoebaTestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method with the AMOEBA forcefield."""
 

wrappers/python/tests/TestPatches.py

+import unittest
+from simtk.openmm.app import *
+from simtk.openmm import *
+from simtk.unit import *
+import simtk.openmm.app.forcefield as forcefield
+import math
+try:
+    from cStringIO import StringIO
+except ImportError:
+    from io import StringIO
+import os
+
+class TestPatches(unittest.TestCase):
+    """Test ForceFields that use patches."""
+
+    def testParsePatch(self):
+        """Test parsing a <Patch> tag."""
+
+        xml = """
+<ForceField>
+ <AtomTypes>
+  <Type name="A type" class="A class" element="O" mass="15.99943"/>
+  <Type name="B type" class="B class" element="H" mass="1.007947"/>
+ </AtomTypes>
+ <Patches>
+  <Patch name="Test">
+    <AddAtom name="A" type="A type"/>
+    <ChangeAtom name="B" type="B type"/>
+    <RemoveAtom name="C"/>
+    <AddBond atomName1="A" atomName2="B"/>
+    <RemoveBond atomName1="B" atomName2="C"/>
+    <AddExternalBond atomName="A"/>
+    <RemoveExternalBond atomName="C"/>
+    <ApplyToResidue name="RES"/>
+  </Patch>
+ </Patches>
+</ForceField>"""
+        ff = ForceField(StringIO(xml))
+        self.assertEqual(1, len(ff._patches))
+        patch = ff._patches['Test']
+        self.assertEqual(1, len(patch.addedAtoms))
+        self.assertEqual(1, len(patch.addedAtoms[0]))
+        self.assertEqual(1, len(patch.changedAtoms))
+        self.assertEqual(1, len(patch.changedAtoms[0]))
+        self.assertEqual(1, len(patch.deletedAtoms))
+        self.assertEqual(1, len(patch.addedBonds))
+        self.assertEqual(1, len(patch.deletedBonds))
+        self.assertEqual(1, len(patch.addedExternalBonds))
+        self.assertEqual(1, len(patch.deletedExternalBonds))
+        self.assertEqual(1, len(ff._templatePatches))
+        self.assertEqual(1, len(ff._templatePatches['RES']))
+        self.assertEqual('A', patch.addedAtoms[0][0].name)
+        self.assertEqual('A type', patch.addedAtoms[0][0].type)
+        self.assertEqual('B', patch.changedAtoms[0][0].name)
+        self.assertEqual('B type', patch.changedAtoms[0][0].type)
+        self.assertEqual('C', patch.deletedAtoms[0].name)
+        self.assertEqual(0, patch.deletedAtoms[0].residue)
+        self.assertEqual('A', patch.addedBonds[0][0].name)
+        self.assertEqual(0, patch.addedBonds[0][0].residue)
+        self.assertEqual('B', patch.addedBonds[0][1].name)
+        self.assertEqual(0, patch.addedBonds[0][1].residue)
+        self.assertEqual('B', patch.deletedBonds[0][0].name)
+        self.assertEqual(0, patch.deletedBonds[0][0].residue)
+        self.assertEqual('C', patch.deletedBonds[0][1].name)
+        self.assertEqual(0, patch.deletedBonds[0][1].residue)
+        self.assertEqual('A', patch.addedExternalBonds[0].name)
+        self.assertEqual(0, patch.addedExternalBonds[0].residue)
+        self.assertEqual('C', patch.deletedExternalBonds[0].name)
+        self.assertEqual(0, patch.deletedExternalBonds[0].residue)
+        self.assertEqual('Test', ff._templatePatches['RES'][0][0])
+        self.assertEqual(0, ff._templatePatches['RES'][0][1])
+
+    def testParseMultiresiduePatch(self):
+        """Test parsing a <Patch> tag that affects two residues."""
+
+        xml = """
+<ForceField>
+ <AtomTypes>
+  <Type name="A type" class="A class" element="O" mass="15.99943"/>
+  <Type name="B type" class="B class" element="H" mass="1.007947"/>
+ </AtomTypes>
+ <Patches>
+  <Patch name="Test" residues="2">
+    <AddAtom name="1:A" type="A type"/>
+    <ChangeAtom name="2:B" type="B type"/>
+    <AddBond atomName1="1:A" atomName2="2:B"/>
+    <ApplyToResidue name="1:RESA"/>
+    <ApplyToResidue name="2:RESB"/>
+  </Patch>
+ </Patches>
+</ForceField>"""
+        ff = ForceField(StringIO(xml))
+        self.assertEqual(1, len(ff._patches))
+        patch = ff._patches['Test']
+        self.assertEqual(2, len(patch.addedAtoms))
+        self.assertEqual(1, len(patch.addedAtoms[0]))
+        self.assertEqual(0, len(patch.addedAtoms[1]))
+        self.assertEqual(2, len(patch.changedAtoms))
+        self.assertEqual(0, len(patch.changedAtoms[0]))
+        self.assertEqual(1, len(patch.changedAtoms[1]))
+        self.assertEqual(1, len(patch.addedBonds))
+        self.assertEqual(2, len(ff._templatePatches))
+        self.assertEqual(1, len(ff._templatePatches['RESA']))
+        self.assertEqual(1, len(ff._templatePatches['RESB']))
+        self.assertEqual('A', patch.addedAtoms[0][0].name)
+        self.assertEqual('A type', patch.addedAtoms[0][0].type)
+        self.assertEqual('B', patch.changedAtoms[1][0].name)
+        self.assertEqual('B type', patch.changedAtoms[1][0].type)
+        self.assertEqual('A', patch.addedBonds[0][0].name)
+        self.assertEqual(0, patch.addedBonds[0][0].residue)
+        self.assertEqual('B', patch.addedBonds[0][1].name)
+        self.assertEqual(1, patch.addedBonds[0][1].residue)
+        self.assertEqual('Test', ff._templatePatches['RESA'][0][0])
+        self.assertEqual(0, ff._templatePatches['RESA'][0][1])
+        self.assertEqual('Test', ff._templatePatches['RESB'][0][0])
+        self.assertEqual(1, ff._templatePatches['RESB'][0][1])
+
+    def testApplyPatch(self):
+        """Test applying a patch to a template."""
+
+        xml = """
+<ForceField>
+ <AtomTypes>
+  <Type name="A type" class="A class" element="O" mass="15.99943"/>
+  <Type name="B type" class="B class" element="H" mass="1.007947"/>
+  <Type name="C type" class="C class" element="H" mass="1.007947"/>
+  <Type name="D type" class="D class" element="C" mass="12.010000"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="RES">
+   <Atom name="A" type="A type"/>
+   <Atom name="B" type="B type"/>
+   <Atom name="C" type="C type"/>
+   <Bond atomName1="A" atomName2="B"/>
+   <Bond atomName1="B" atomName2="C"/>
+   <ExternalBond atomName="C"/>
+   <VirtualSite type="average2" siteName="C" atomName1="B" atomName2="C" weight1="0.6" weight2="0.4"/>
+  </Residue>
+ </Residues>
+ <Patches>
+  <Patch name="Test">
+    <AddAtom name="D" type="D type"/>
+    <ChangeAtom name="B" type="A type"/>
+    <RemoveAtom name="A"/>
+    <AddBond atomName1="B" atomName2="D"/>
+    <RemoveBond atomName1="A" atomName2="B"/>
+    <AddExternalBond atomName="D"/>
+    <RemoveExternalBond atomName="C"/>
+    <ApplyToResidue name="RES"/>
+  </Patch>
+ </Patches>
+</ForceField>"""
+        ff = ForceField(StringIO(xml))
+        self.assertEqual(1, len(ff._patches))
+        patch = ff._patches['Test']
+        template = ff._templates['RES']
+        newTemplates = patch.createPatchedTemplates([template])
+        self.assertEqual(1, len(newTemplates))
+        t = newTemplates[0]
+        self.assertEqual(3, len(t.atoms))
+        self.assertTrue(any(a.name == 'B' and a.type == 'A type' for a in t.atoms))
+        self.assertTrue(any(a.name == 'C' and a.type == 'C type' for a in t.atoms))
+        self.assertTrue(any(a.name == 'D' and a.type == 'D type' for a in t.atoms))
+        indexMap = dict([(a.name, i) for i, a in enumerate(t.atoms)])
+        self.assertEqual(2, len(t.bonds))
+        self.assertTrue((indexMap['B'], indexMap['C']) in t.bonds)
+        self.assertTrue((indexMap['B'], indexMap['D']) in t.bonds)
+        self.assertEqual(1, len(t.externalBonds))
+        self.assertTrue(indexMap['D'] in t.externalBonds)
+        self.assertEqual(1, len(t.virtualSites))
+        v = t.virtualSites[0]
+        self.assertEqual('average2', v.type)
+        self.assertEqual(0.6, v.weights[0])
+        self.assertEqual(0.4, v.weights[1])
+        self.assertEqual(indexMap['C'], v.index)
+        self.assertEqual(indexMap['B'], v.atoms[0])
+        self.assertEqual(indexMap['C'], v.atoms[1])
+
+    def testAlaAlaAla(self):
+        """Test constructing a System that involves two patches."""
+
+        xml = """
+<ForceField>
+ <AtomTypes>
+  <Type name="N" class="N" element="N" mass="14.00672"/>
+  <Type name="H" class="H" element="H" mass="1.007947"/>
+  <Type name="CT" class="CT" element="C" mass="12.01078"/>
+  <Type name="H1" class="H1" element="H" mass="1.007947"/>
+  <Type name="HC" class="HC" element="H" mass="1.007947"/>
+  <Type name="C" class="C" element="C" mass="12.01078"/>
+  <Type name="O" class="O" element="O" mass="15.99943"/>
+  <Type name="O2" class="O2" element="O" mass="15.99943"/>
+  <Type name="N3" class="N3" element="N" mass="14.00672"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="ALA">
+   <Atom name="N" type="N"/>
+   <Atom name="H" type="H"/>
+   <Atom name="CA" type="CT"/>
+   <Atom name="HA" type="H1"/>
+   <Atom name="CB" type="CT"/>
+   <Atom name="HB1" type="HC"/>
+   <Atom name="HB2" type="HC"/>
+   <Atom name="HB3" type="HC"/>
+   <Atom name="C" type="C"/>
+   <Atom name="O" type="O"/>
+   <Bond from="0" to="1"/>
+   <Bond from="0" to="2"/>
+   <Bond from="2" to="3"/>
+   <Bond from="2" to="4"/>
+   <Bond from="2" to="8"/>
+   <Bond from="4" to="5"/>
+   <Bond from="4" to="6"/>
+   <Bond from="4" to="7"/>
+   <Bond from="8" to="9"/>
+   <ExternalBond from="0"/>
+   <ExternalBond from="8"/>
+   <AllowPatch name="CTER"/>
+   <AllowPatch name="NTER"/>
+  </Residue>
+ </Residues>
+ <Patches>
+  <Patch name="CTER">
+    <AddAtom name="OXT" type="O2"/>
+    <ChangeAtom name="O" type="O2"/>
+    <AddBond atomName1="C" atomName2="OXT"/>
+    <RemoveExternalBond atomName="C"/>
+  </Patch>
+  <Patch name="NTER">
+    <RemoveAtom name="H"/>
+    <AddAtom name="H1" type="H"/>
+    <AddAtom name="H2" type="H"/>
+    <AddAtom name="H3" type="H"/>
+    <ChangeAtom name="N" type="N3"/>
+    <RemoveBond atomName1="N" atomName2="H"/>
+    <AddBond atomName1="N" atomName2="H1"/>
+    <AddBond atomName1="N" atomName2="H2"/>
+    <AddBond atomName1="N" atomName2="H3"/>
+    <RemoveExternalBond atomName="N"/>
+  </Patch>
+ </Patches>
+ <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+  <Atom type="N" charge="-0.4157" sigma="0.324999852378" epsilon="0.71128"/>
+  <Atom type="H" charge="0.2719" sigma="0.106907846177" epsilon="0.0656888"/>
+  <Atom type="CT" charge="0.0337" sigma="0.339966950842" epsilon="0.4577296"/>
+  <Atom type="H1" charge="0.0823" sigma="0.247135304412" epsilon="0.0656888"/>
+  <Atom type="HC" charge="0.0603" sigma="0.264953278775" epsilon="0.0656888"/>
+  <Atom type="C" charge="0.5973" sigma="0.339966950842" epsilon="0.359824"/>
+  <Atom type="O" charge="-0.5679" sigma="0.295992190115" epsilon="0.87864"/>
+  <Atom type="O2" charge="-0.8055" sigma="0.295992190115" epsilon="0.87864"/>
+  <Atom type="N3" charge="0.1414" sigma="0.324999852378" epsilon="0.71128"/>
+ </NonbondedForce>
+</ForceField>"""
+        ff = ForceField(StringIO(xml))
+        pdb = PDBFile(os.path.join('systems', 'ala_ala_ala.pdb'))
+        system = ff.createSystem(pdb.topology)
+        nb = system.getForce(0)
+        expectedCharges = [0.1414, 0.2719, 0.2719, 0.2719, 0.0337, 0.0823, 0.0337, 0.0603, 0.0603, 0.0603, 0.5973, -0.5679,
+                           -0.4157, 0.2719, 0.0337, 0.0823, 0.0337, 0.0603, 0.0603, 0.0603, 0.5973, -0.5679,
+                           0.5973, -0.8055, -0.8055, -0.4157, 0.2719, 0.0337, 0.0823, 0.0337, 0.0603, 0.0603, 0.0603]
+        for i in range(system.getNumParticles()):
+            self.assertEqual(expectedCharges[i], nb.getParticleParameters(i)[0].value_in_unit(elementary_charge))
+
+    def testDisulfidePatch(self):
+        pdb = PDBFile(os.path.join('systems', 'bpti.pdb'))
+        ff = ForceField('amber99sb.xml')
+        system1 = ff.createSystem(pdb.topology)
+        
+        # Override the CYX template so it will no longer match.
+        
+        xml = """
+<ForceField>
+ <Residues>
+  <Residue name="CYX" override="1">
+  </Residue>
+ </Residues>
+</ForceField>"""
+        ff.loadFile(StringIO(xml))
+        try:
+            ff.createSystem(pdb.topology)
+            failed = False
+        except:
+            failed = True
+        self.assertTrue(failed)
+        
+        # Now add a patch for matching disulfides.
+        
+        xml = """
+<ForceField>
+ <Patches>
+  <Patch name="Disulfide" residues="2">
+    <RemoveAtom name="1:HG"/>
+    <RemoveAtom name="2:HG"/>
+    <ChangeAtom name="1:CA" type="83"/>
+    <ChangeAtom name="2:CA" type="83"/>
+    <ChangeAtom name="1:HA" type="84"/>
+    <ChangeAtom name="2:HA" type="84"/>
+    <ChangeAtom name="1:CB" type="85"/>
+    <ChangeAtom name="2:CB" type="85"/>
+    <ChangeAtom name="1:HB2" type="86"/>
+    <ChangeAtom name="2:HB2" type="86"/>
+    <ChangeAtom name="1:HB3" type="86"/>
+    <ChangeAtom name="2:HB3" type="86"/>
+    <ChangeAtom name="1:SG" type="87"/>
+    <ChangeAtom name="2:SG" type="87"/>
+    <AddBond atomName1="1:SG" atomName2="2:SG"/>
+    <ApplyToResidue name="1:CYS"/>
+    <ApplyToResidue name="2:CYS"/>
+  </Patch>
+ </Patches>
+</ForceField>"""
+        ff.loadFile(StringIO(xml))
+        system2 = ff.createSystem(pdb.topology)
+        self.assertEqual(XmlSerializer.serialize(system1), XmlSerializer.serialize(system2))
+
+if __name__ == '__main__':
+    unittest.main()

wrappers/python/tests/systems/bpti.pdb

+ATOM      1  N   ARG A   1       4.481  11.293   0.204                          
+ATOM      2  CA  ARG A   1       5.137  10.135   0.877                          
+ATOM      3  C   ARG A   1       5.356   9.056  -0.221                          
+ATOM      4  O   ARG A   1       4.487   8.823  -1.054                          
+ATOM      5  CB  ARG A   1       4.154   9.632   2.008                          
+ATOM      6  CG  ARG A   1       4.819   8.703   2.982                          
+ATOM      7  CD  ARG A   1       6.020   9.239   3.802                          
+ATOM      8  NE  ARG A   1       5.551  10.357   4.670                          
+ATOM      9  CZ  ARG A   1       6.185  10.965   5.621                          
+ATOM     10  NH1 ARG A   1       7.387  10.630   5.911                          
+ATOM     11  NH2 ARG A   1       5.512  11.845   6.297                          
+ATOM     12  HA  ARG A   1       6.074  10.533   1.267                          
+ATOM     13  2HB ARG A   1       3.800  10.536   2.503                          
+ATOM     14  HB3 ARG A   1       3.288   9.097   1.619                          
+ATOM     15  2HG ARG A   1       4.077   8.489   3.751                          
+ATOM     16  HG3 ARG A   1       5.138   7.850   2.383                          
+ATOM     17  2HD ARG A   1       6.551   8.496   4.398                          
+ATOM     18  HD3 ARG A   1       6.853   9.562   3.178                          
+ATOM     19  HE  ARG A   1       4.567  10.585   4.661                          
+ATOM     20 1HH1 ARG A   1       7.769  10.908   6.804                          
+ATOM     21 2HH1 ARG A   1       7.864   9.934   5.357                          
+ATOM     22 1HH2 ARG A   1       4.549  12.019   6.046                          
+ATOM     23 2HH2 ARG A   1       5.917  12.521   6.929                          
+ATOM     24  H1  ARG A   1       3.475  11.214   0.162                          
+ATOM     25  H2  ARG A   1       4.746  12.104   0.745                          
+ATOM     26  H3  ARG A   1       4.816  11.478  -0.731                          
+ATOM     27  N   PRO A   2       6.483   8.417  -0.280                          
+ATOM     28  CA  PRO A   2       6.740   7.345  -1.220                          
+ATOM     29  C   PRO A   2       5.696   6.227  -1.193                          
+ATOM     30  O   PRO A   2       5.267   5.881  -0.115                          
+ATOM     31  CB  PRO A   2       8.139   6.854  -0.953                          
+ATOM     32  CG  PRO A   2       8.744   8.003  -0.281                          
+ATOM     33  CD  PRO A   2       7.675   8.665   0.535                          
+ATOM     34  HA  PRO A   2       6.709   7.735  -2.237                          
+ATOM     35  2HB PRO A   2       8.085   6.029  -0.243                          
+ATOM     36  HB3 PRO A   2       8.553   6.512  -1.902                          
+ATOM     37  2HG PRO A   2       9.514   7.623   0.391                          
+ATOM     38  HG3 PRO A   2       9.236   8.583  -1.062                          
+ATOM     39  2HD PRO A   2       7.499   8.214   1.512                          
+ATOM     40  HD3 PRO A   2       7.854   9.740   0.545                          
+ATOM     41  N   ASP A   3       5.540   5.671  -2.406                          
+ATOM     42  CA  ASP A   3       4.355   4.870  -2.726                          
+ATOM     43  C   ASP A   3       4.328   3.566  -1.945                          
+ATOM     44  O   ASP A   3       3.258   3.076  -1.661                          
+ATOM     45  CB  ASP A   3       4.477   4.534  -4.251                          
+ATOM     46  CG  ASP A   3       3.374   3.594  -4.902                          
+ATOM     47  OD1 ASP A   3       2.182   3.935  -4.925                          
+ATOM     48  OD2 ASP A   3       3.772   2.698  -5.716                          
+ATOM     49  H   ASP A   3       6.080   6.109  -3.138                          
+ATOM     50  HA  ASP A   3       3.447   5.357  -2.373                          
+ATOM     51  2HB ASP A   3       4.514   5.458  -4.828                          
+ATOM     52  HB3 ASP A   3       5.449   4.065  -4.403                          
+ATOM     53  N   PHE A   4       5.503   3.010  -1.562                          
+ATOM     54  CA  PHE A   4       5.732   1.868  -0.668                          
+ATOM     55  C   PHE A   4       5.581   2.197   0.775                          
+ATOM     56  O   PHE A   4       5.259   1.343   1.581                          
+ATOM     57  CB  PHE A   4       7.024   1.139  -0.960                          
+ATOM     58  CG  PHE A   4       8.248   2.039  -0.997                          
+ATOM     59  CD1 PHE A   4       8.881   2.357   0.193                          
+ATOM     60  CD2 PHE A   4       8.697   2.501  -2.208                          
+ATOM     61  CE1 PHE A   4      10.030   3.230   0.154                          
+ATOM     62  CE2 PHE A   4       9.920   3.265  -2.235                          
+ATOM     63  CZ  PHE A   4      10.511   3.709  -1.056                          
+ATOM     64  H   PHE A   4       6.284   3.533  -1.931                          
+ATOM     65  HA  PHE A   4       4.960   1.129  -0.880                          
+ATOM     66  2HB PHE A   4       7.205   0.284  -0.309                          
+ATOM     67  HB3 PHE A   4       6.798   0.792  -1.968                          
+ATOM     68  HD1 PHE A   4       8.345   2.171   1.112                          
+ATOM     69  HD2 PHE A   4       8.114   2.361  -3.106                          
+ATOM     70  HE1 PHE A   4      10.504   3.653   1.027                          
+ATOM     71  HE2 PHE A   4      10.343   3.666  -3.144                          
+ATOM     72  HZ  PHE A   4      11.358   4.375  -1.122                          
+ATOM     73  N   CYS A   5       5.653   3.456   1.170                          
+ATOM     74  CA  CYS A   5       5.395   3.903   2.491                          
+ATOM     75  C   CYS A   5       3.895   4.221   2.647                          
+ATOM     76  O   CYS A   5       3.457   4.281   3.830                          
+ATOM     77  CB  CYS A   5       6.278   5.096   2.648                          
+ATOM     78  SG  CYS A   5       7.989   4.948   2.335                          
+ATOM     79  H   CYS A   5       5.843   4.156   0.467                          
+ATOM     80  HA  CYS A   5       5.686   3.121   3.193                          
+ATOM     81  2HB CYS A   5       5.930   6.055   2.266                          
+ATOM     82  HB3 CYS A   5       6.196   5.233   3.726                          
+ATOM     83  N   LEU A   6       3.043   4.407   1.573                          
+ATOM     84  CA  LEU A   6       1.634   4.834   1.750                          
+ATOM     85  C   LEU A   6       0.674   3.656   1.891                          
+ATOM     86  O   LEU A   6      -0.530   3.825   1.989                          
+ATOM     87  CB  LEU A   6       1.407   5.795   0.588                          
+ATOM     88  CG  LEU A   6       0.016   6.561   0.500                          
+ATOM     89  CD1 LEU A   6      -0.326   7.401   1.727                          
+ATOM     90  CD2 LEU A   6      -0.137   7.376  -0.792                          
+ATOM     91  H   LEU A   6       3.514   4.340   0.682                          
+ATOM     92  HA  LEU A   6       1.520   5.491   2.612                          
+ATOM     93  2HB LEU A   6       2.171   6.572   0.614                          
+ATOM     94  HB3 LEU A   6       1.553   5.267  -0.355                          
+ATOM     95  HG  LEU A   6      -0.749   5.786   0.442                          
+ATOM     96 1HD1 LEU A   6       0.528   8.029   1.982                          
+ATOM     97 2HD1 LEU A   6      -1.240   7.991   1.671                          
+ATOM     98 3HD1 LEU A   6      -0.474   6.704   2.553                          
+ATOM     99 1HD2 LEU A   6      -1.194   7.619  -0.900                          
+ATOM    100 2HD2 LEU A   6       0.445   8.278  -0.598                          
+ATOM    101 3HD2 LEU A   6       0.197   6.715  -1.591                          
+ATOM    102  N   GLU A   7       1.168   2.445   1.926                          
+ATOM    103  CA  GLU A   7       0.330   1.215   1.642                          
+ATOM    104  C   GLU A   7       0.014   0.441   2.945                          
+ATOM    105  O   GLU A   7       0.707   0.600   3.925                          
+ATOM    106  CB  GLU A   7       1.018   0.404   0.587                          
+ATOM    107  CG  GLU A   7       2.236  -0.293   1.147                          
+ATOM    108  CD  GLU A   7       3.039  -1.118   0.146                          
+ATOM    109  OE1 GLU A   7       3.059  -0.802  -1.058                          
+ATOM    110  OE2 GLU A   7       3.537  -2.227   0.572                          
+ATOM    111  H   GLU A   7       2.176   2.482   1.972                          
+ATOM    112  HA  GLU A   7      -0.665   1.402   1.238                          
+ATOM    113  2HB GLU A   7       0.365  -0.293   0.060                          
+ATOM    114  HB3 GLU A   7       1.397   1.107  -0.154                          
+ATOM    115  2HG GLU A   7       2.837   0.457   1.662                          
+ATOM    116  HG3 GLU A   7       1.907  -0.923   1.974                          
+ATOM    117  N   PRO A   8      -1.103  -0.415   3.020                          
+ATOM    118  CA  PRO A   8      -1.381  -1.343   4.103                          
+ATOM    119  C   PRO A   8      -0.271  -2.418   4.275                          
+ATOM    120  O   PRO A   8       0.415  -2.841   3.323                          
+ATOM    121  CB  PRO A   8      -2.700  -1.908   3.748                          
+ATOM    122  CG  PRO A   8      -2.888  -1.727   2.224                          
+ATOM    123  CD  PRO A   8      -2.022  -0.525   1.858                          
+ATOM    124  HA  PRO A   8      -1.505  -0.796   5.038                          
+ATOM    125  2HB PRO A   8      -2.657  -2.963   4.017                          
+ATOM    126  HB3 PRO A   8      -3.448  -1.313   4.271                          
+ATOM    127  2HG PRO A   8      -2.508  -2.611   1.712                          
+ATOM    128  HG3 PRO A   8      -3.958  -1.528   2.153                          
+ATOM    129  2HD PRO A   8      -1.521  -0.824   0.937                          
+ATOM    130  HD3 PRO A   8      -2.534   0.437   1.879                          
+ATOM    131  N   PRO A   9      -0.040  -2.911   5.500                          
+ATOM    132  CA  PRO A   9       0.785  -4.139   5.864                          
+ATOM    133  C   PRO A   9       0.103  -5.504   5.481                          
+ATOM    134  O   PRO A   9      -0.988  -5.534   5.004                          
+ATOM    135  CB  PRO A   9       1.124  -3.990   7.336                          
+ATOM    136  CG  PRO A   9      -0.128  -3.245   7.915                          
+ATOM    137  CD  PRO A   9      -0.450  -2.295   6.736                          
+ATOM    138  HA  PRO A   9       1.766  -4.173   5.391                          
+ATOM    139  2HB PRO A   9       1.311  -5.011   7.668                          
+ATOM    140  HB3 PRO A   9       2.012  -3.394   7.546                          
+ATOM    141  2HG PRO A   9      -1.024  -3.849   8.058                          
+ATOM    142  HG3 PRO A   9       0.057  -2.585   8.763                          
+ATOM    143  2HD PRO A   9      -1.519  -2.082   6.697                          
+ATOM    144  HD3 PRO A   9       0.121  -1.374   6.854                          
+ATOM    145  N   TYR A  10       0.784  -6.614   5.626                          
+ATOM    146  CA  TYR A  10       0.338  -7.965   5.239                          
+ATOM    147  C   TYR A  10       1.070  -9.115   5.979                          
+ATOM    148  O   TYR A  10       2.288  -9.343   5.819                          
+ATOM    149  CB  TYR A  10       0.711  -8.120   3.779                          
+ATOM    150  CG  TYR A  10       0.399  -9.379   2.974                          
+ATOM    151  CD1 TYR A  10      -0.906  -9.617   2.468                          
+ATOM    152  CD2 TYR A  10       1.441 -10.305   2.744                          
+ATOM    153  CE1 TYR A  10      -1.171 -10.795   1.817                          
+ATOM    154  CE2 TYR A  10       1.171 -11.534   2.135                          
+ATOM    155  CZ  TYR A  10      -0.144 -11.787   1.672                          
+ATOM    156  OH  TYR A  10      -0.509 -12.988   1.248                          
+ATOM    157  H   TYR A  10       1.712  -6.457   5.993                          
+ATOM    158  HA  TYR A  10      -0.731  -8.039   5.436                          
+ATOM    159  2HB TYR A  10       0.295  -7.247   3.276                          
+ATOM    160  HB3 TYR A  10       1.796  -8.015   3.750                          
+ATOM    161  HD1 TYR A  10      -1.717  -8.917   2.600                          
+ATOM    162  HD2 TYR A  10       2.401 -10.213   3.231                          
+ATOM    163  HE1 TYR A  10      -2.192 -10.947   1.499                          
+ATOM    164  HE2 TYR A  10       1.867 -12.359   2.086                          
+ATOM    165  HH  TYR A  10       0.246 -13.495   0.940                          
+ATOM    166  N   THR A  11       0.448  -9.759   6.976                          
+ATOM    167  CA  THR A  11       1.073 -10.832   7.801                          
+ATOM    168  C   THR A  11       1.509 -12.075   6.926                          
+ATOM    169  O   THR A  11       2.482 -12.721   7.340                          
+ATOM    170  CB  THR A  11       0.108 -11.338   8.905                          
+ATOM    171  OG1 THR A  11      -0.132 -10.234   9.629                          
+ATOM    172  CG2 THR A  11       0.644 -12.429   9.866                          
+ATOM    173  H   THR A  11      -0.517  -9.559   7.195                          
+ATOM    174  HA  THR A  11       1.906 -10.449   8.391                          
+ATOM    175  HB  THR A  11      -0.838 -11.730   8.532                          
+ATOM    176  HG1 THR A  11       0.614 -10.069  10.210                          
+ATOM    177 1HG2 THR A  11      -0.268 -12.872  10.265                          
+ATOM    178 2HG2 THR A  11       1.179 -13.130   9.225                          
+ATOM    179 3HG2 THR A  11       1.335 -12.016  10.601                          
+ATOM    180  N   GLY A  12       0.896 -12.411   5.764                          
+ATOM    181  CA  GLY A  12       1.165 -13.584   4.948                          
+ATOM    182  C   GLY A  12       0.753 -15.016   5.427                          
+ATOM    183  O   GLY A  12       0.506 -15.143   6.609                          
+ATOM    184  H   GLY A  12       0.073 -11.936   5.422                          
+ATOM    185  2HA GLY A  12       0.646 -13.419   4.004                          
+ATOM    186  HA3 GLY A  12       2.228 -13.572   4.710                          
+ATOM    187  N   PRO A  13       0.761 -16.086   4.597                          
+ATOM    188  CA  PRO A  13       0.230 -17.400   5.025                          
+ATOM    189  C   PRO A  13       0.929 -18.198   6.082                          
+ATOM    190  O   PRO A  13       0.387 -19.195   6.636                          
+ATOM    191  CB  PRO A  13       0.121 -18.179   3.750                          
+ATOM    192  CG  PRO A  13      -0.021 -17.112   2.638                          
+ATOM    193  CD  PRO A  13       0.964 -15.994   3.146                          
+ATOM    194  HA  PRO A  13      -0.781 -17.292   5.417                          
+ATOM    195  2HB PRO A  13       0.962 -18.839   3.538                          
+ATOM    196  HB3 PRO A  13      -0.776 -18.798   3.784                          
+ATOM    197  2HG PRO A  13       0.393 -17.595   1.753                          
+ATOM    198  HG3 PRO A  13      -1.042 -16.752   2.510                          
+ATOM    199  2HD PRO A  13       2.003 -16.178   2.874                          
+ATOM    200  HD3 PRO A  13       0.539 -15.063   2.770                          
+ATOM    201  N   CYS A  14       2.190 -17.769   6.354                          
+ATOM    202  CA  CYS A  14       3.079 -18.621   7.107                          
+ATOM    203  C   CYS A  14       2.758 -18.607   8.657                          
+ATOM    204  O   CYS A  14       2.081 -17.691   9.077                          
+ATOM    205  CB  CYS A  14       4.547 -18.426   6.685                          
+ATOM    206  SG  CYS A  14       4.794 -18.857   4.907                          
+ATOM    207  H   CYS A  14       2.596 -16.879   6.102                          
+ATOM    208  HA  CYS A  14       2.904 -19.637   6.753                          
+ATOM    209  2HB CYS A  14       4.881 -17.391   6.752                          
+ATOM    210  HB3 CYS A  14       5.095 -19.084   7.361                          
+ATOM    211  N   LYS A  15       3.040 -19.689   9.488                          
+ATOM    212  CA  LYS A  15       2.582 -19.937  10.866                          
+ATOM    213  C   LYS A  15       3.168 -19.140  12.066                          
+ATOM    214  O   LYS A  15       2.488 -19.101  13.088                          
+ATOM    215  CB  LYS A  15       2.487 -21.458  11.142                          
+ATOM    216  CG  LYS A  15       3.842 -22.211  11.339                          
+ATOM    217  CD  LYS A  15       3.681 -23.752  11.416                          
+ATOM    218  CE  LYS A  15       5.070 -24.360  11.277                          
+ATOM    219  NZ  LYS A  15       4.972 -25.819  11.056                          
+ATOM    220  H   LYS A  15       3.526 -20.427   8.998                          
+ATOM    221  HA  LYS A  15       1.581 -19.519  10.755                          
+ATOM    222  2HB LYS A  15       1.813 -21.575  11.991                          
+ATOM    223  HB3 LYS A  15       2.038 -21.894  10.250                          
+ATOM    224  2HG LYS A  15       4.476 -21.920  10.502                          
+ATOM    225  HG3 LYS A  15       4.265 -21.803  12.257                          
+ATOM    226  2HD LYS A  15       3.258 -23.842  12.417                          
+ATOM    227  HD3 LYS A  15       3.027 -24.160  10.645                          
+ATOM    228  2HE LYS A  15       5.572 -23.854  10.452                          
+ATOM    229  HE3 LYS A  15       5.650 -24.058  12.149                          
+ATOM    230  1HZ LYS A  15       5.891 -26.196  10.873                          
+ATOM    231  2HZ LYS A  15       4.525 -26.294  11.827                          
+ATOM    232  3HZ LYS A  15       4.457 -26.071  10.224                          
+ATOM    233  N   ALA A  16       4.183 -18.308  11.893                          
+ATOM    234  CA  ALA A  16       4.792 -17.419  12.911                          
+ATOM    235  C   ALA A  16       4.012 -16.102  13.171                          
+ATOM    236  O   ALA A  16       3.077 -15.829  12.483                          
+ATOM    237  CB  ALA A  16       6.245 -17.369  12.505                          
+ATOM    238  H   ALA A  16       4.660 -18.353  11.004                          
+ATOM    239  HA  ALA A  16       4.710 -17.902  13.884                          
+ATOM    240  1HB ALA A  16       6.370 -16.590  11.752                          
+ATOM    241  2HB ALA A  16       6.905 -17.116  13.335                          
+ATOM    242  3HB ALA A  16       6.666 -18.338  12.238                          
+ATOM    243  N   ARG A  17       4.434 -15.382  14.265                          
+ATOM    244  CA  ARG A  17       3.794 -14.113  14.750                          
+ATOM    245  C   ARG A  17       4.885 -13.022  14.910                          
+ATOM    246  O   ARG A  17       4.694 -12.039  15.591                          
+ATOM    247  CB  ARG A  17       3.032 -14.451  16.064                          
+ATOM    248  CG  ARG A  17       2.110 -15.629  16.028                          
+ATOM    249  CD  ARG A  17       0.974 -15.737  14.993                          
+ATOM    250  NE  ARG A  17      -0.087 -14.742  15.265                          
+ATOM    251  CZ  ARG A  17      -0.609 -14.001  14.338                          
+ATOM    252  NH1 ARG A  17      -0.400 -14.031  13.046                          
+ATOM    253  NH2 ARG A  17      -1.470 -13.060  14.730                          
+ATOM    254  H   ARG A  17       5.184 -15.819  14.783                          
+ATOM    255  HA  ARG A  17       3.075 -13.764  14.008                          
+ATOM    256  2HB ARG A  17       3.773 -14.712  16.819                          
+ATOM    257  HB3 ARG A  17       2.505 -13.607  16.510                          
+ATOM    258  2HG ARG A  17       2.638 -16.548  15.773                          
+ATOM    259  HG3 ARG A  17       1.644 -15.713  17.010                          
+ATOM    260  2HD ARG A  17       1.282 -15.703  13.948                          
+ATOM    261  HD3 ARG A  17       0.632 -16.762  15.140                          
+ATOM    262  HE  ARG A  17      -0.440 -14.534  16.189                          
+ATOM    263 1HH1 ARG A  17       0.204 -14.718  12.617                          
+ATOM    264 2HH1 ARG A  17      -0.922 -13.340  12.528                          
+ATOM    265 1HH2 ARG A  17      -1.774 -13.060  15.693                          
+ATOM    266 2HH2 ARG A  17      -1.935 -12.511  14.020                          
+ATOM    267  N   ILE A  18       6.007 -13.111  14.253                          
+ATOM    268  CA  ILE A  18       7.191 -12.307  14.496                          
+ATOM    269  C   ILE A  18       6.939 -10.792  14.150                          
+ATOM    270  O   ILE A  18       6.517 -10.435  13.050                          
+ATOM    271  CB  ILE A  18       8.320 -12.892  13.575                          
+ATOM    272  CG1 ILE A  18       8.597 -14.396  13.719                          
+ATOM    273  CG2 ILE A  18       9.761 -12.226  13.877                          
+ATOM    274  CD1 ILE A  18       9.360 -15.080  12.562                          
+ATOM    275  H   ILE A  18       5.960 -13.877  13.597                          
+ATOM    276  HA  ILE A  18       7.447 -12.347  15.555                          
+ATOM    277  HB  ILE A  18       8.151 -12.525  12.563                          
+ATOM    278 2HG1 ILE A  18       9.068 -14.693  14.656                          
+ATOM    279 HG13 ILE A  18       7.615 -14.870  13.695                          
+ATOM    280 1HG2 ILE A  18       9.725 -11.186  13.551                          
+ATOM    281 2HG2 ILE A  18       9.934 -12.186  14.953                          
+ATOM    282 3HG2 ILE A  18      10.590 -12.686  13.340                          
+ATOM    283 1HD1 ILE A  18       9.299 -16.161  12.690                          
+ATOM    284 2HD1 ILE A  18       8.711 -15.061  11.686                          
+ATOM    285 3HD1 ILE A  18      10.313 -14.694  12.202                          
+ATOM    286  N   ILE A  19       7.306  -9.925  15.155                          
+ATOM    287  CA  ILE A  19       7.143  -8.504  14.984                          
+ATOM    288  C   ILE A  19       8.120  -8.017  13.910                          
+ATOM    289  O   ILE A  19       9.341  -8.009  14.103                          
+ATOM    290  CB  ILE A  19       7.343  -7.858  16.368                          
+ATOM    291  CG1 ILE A  19       6.338  -8.250  17.406                          
+ATOM    292  CG2 ILE A  19       7.524  -6.343  16.256                          
+ATOM    293  CD1 ILE A  19       4.922  -7.651  17.391                          
+ATOM    294  H   ILE A  19       7.787 -10.221  15.992                          
+ATOM    295  HA  ILE A  19       6.128  -8.366  14.613                          
+ATOM    296  HB  ILE A  19       8.343  -8.126  16.706                          
+ATOM    297 2HG1 ILE A  19       6.183  -9.329  17.377                          
+ATOM    298 HG13 ILE A  19       6.680  -8.112  18.432                          
+ATOM    299 1HG2 ILE A  19       7.722  -5.928  17.244                          
+ATOM    300 2HG2 ILE A  19       8.325  -6.086  15.563                          
+ATOM    301 3HG2 ILE A  19       6.592  -5.894  15.911                          
+ATOM    302 1HD1 ILE A  19       4.265  -8.098  18.137                          
+ATOM    303 2HD1 ILE A  19       5.067  -6.573  17.459                          
+ATOM    304 3HD1 ILE A  19       4.405  -7.799  16.444                          
+ATOM    305  N   ARG A  20       7.484  -7.559  12.847                          
+ATOM    306  CA  ARG A  20       8.006  -6.620  11.818                          
+ATOM    307  C   ARG A  20       7.381  -5.195  12.051                          
+ATOM    308  O   ARG A  20       6.469  -4.925  12.841                          
+ATOM    309  CB  ARG A  20       7.768  -7.155  10.394                          
+ATOM    310  CG  ARG A  20       8.471  -8.394   9.998                          
+ATOM    311  CD  ARG A  20       9.928  -8.192  10.186                          
+ATOM    312  NE  ARG A  20      10.648  -9.365   9.593                          
+ATOM    313  CZ  ARG A  20      11.302  -9.440   8.479                          
+ATOM    314  NH1 ARG A  20      11.310  -8.543   7.656                          
+ATOM    315  NH2 ARG A  20      12.074 -10.411   8.398                          
+ATOM    316  H   ARG A  20       6.488  -7.631  12.997                          
+ATOM    317  HA  ARG A  20       9.080  -6.560  11.990                          
+ATOM    318  2HB ARG A  20       6.695  -7.300  10.265                          
+ATOM    319  HB3 ARG A  20       8.047  -6.370   9.692                          
+ATOM    320  2HG ARG A  20       8.135  -9.295  10.511                          
+ATOM    321  HG3 ARG A  20       8.230  -8.607   8.957                          
+ATOM    322  2HD ARG A  20      10.179  -7.264   9.672                          
+ATOM    323  HD3 ARG A  20      10.270  -8.122  11.218                          
+ATOM    324  HE  ARG A  20      10.583 -10.257  10.062                          
+ATOM    325 1HH1 ARG A  20      11.948  -8.654   6.881                          
+ATOM    326 2HH1 ARG A  20      10.434  -8.064   7.501                          
+ATOM    327 1HH2 ARG A  20      12.664 -10.491   7.582                          
+ATOM    328 2HH2 ARG A  20      12.076 -11.064   9.168                          
+ATOM    329  N   TYR A  21       8.057  -4.274  11.316                          
+ATOM    330  CA  TYR A  21       7.877  -2.855  11.290                          
+ATOM    331  C   TYR A  21       7.370  -2.405   9.910                          
+ATOM    332  O   TYR A  21       7.715  -3.011   8.928                          
+ATOM    333  CB  TYR A  21       9.189  -2.077  11.595                          
+ATOM    334  CG  TYR A  21       9.588  -2.396  13.044                          
+ATOM    335  CD1 TYR A  21      10.289  -3.582  13.268                          
+ATOM    336  CD2 TYR A  21       9.131  -1.658  14.140                          
+ATOM    337  CE1 TYR A  21      10.703  -3.986  14.591                          
+ATOM    338  CE2 TYR A  21       9.479  -2.044  15.471                          
+ATOM    339  CZ  TYR A  21      10.212  -3.279  15.719                          
+ATOM    340  OH  TYR A  21      10.433  -3.726  16.978                          
+ATOM    341  H   TYR A  21       8.824  -4.517  10.706                          
+ATOM    342  HA  TYR A  21       7.137  -2.522  12.018                          
+ATOM    343  2HB TYR A  21       9.930  -2.319  10.833                          
+ATOM    344  HB3 TYR A  21       9.054  -0.996  11.570                          
+ATOM    345  HD1 TYR A  21      10.711  -4.133  12.441                          
+ATOM    346  HD2 TYR A  21       8.452  -0.822  14.065                          
+ATOM    347  HE1 TYR A  21      11.369  -4.836  14.619                          
+ATOM    348  HE2 TYR A  21       9.419  -1.347  16.293                          
+ATOM    349  HH  TYR A  21      10.182  -3.094  17.655                          
+ATOM    350  N   PHE A  22       6.477  -1.373   9.838                          
+ATOM    351  CA  PHE A  22       5.979  -0.736   8.661                          
+ATOM    352  C   PHE A  22       5.656   0.773   8.907                          
+ATOM    353  O   PHE A  22       5.717   1.236  10.042                          
+ATOM    354  CB  PHE A  22       4.736  -1.449   8.149                          
+ATOM    355  CG  PHE A  22       3.435  -1.094   8.844                          
+ATOM    356  CD1 PHE A  22       2.423  -0.309   8.345                          
+ATOM    357  CD2 PHE A  22       3.242  -1.546  10.167                          
+ATOM    358  CE1 PHE A  22       1.219  -0.036   9.014                          
+ATOM    359  CE2 PHE A  22       2.066  -1.269  10.895                          
+ATOM    360  CZ  PHE A  22       1.071  -0.451  10.318                          
+ATOM    361  H   PHE A  22       6.145  -0.982  10.708                          
+ATOM    362  HA  PHE A  22       6.686  -0.643   7.838                          
+ATOM    363  2HB PHE A  22       4.466  -1.293   7.104                          
+ATOM    364  HB3 PHE A  22       4.966  -2.509   8.251                          
+ATOM    365  HD1 PHE A  22       2.560   0.133   7.368                          
+ATOM    366  HD2 PHE A  22       3.985  -2.177  10.632                          
+ATOM    367  HE1 PHE A  22       0.420   0.549   8.580                          
+ATOM    368  HE2 PHE A  22       1.933  -1.708  11.873                          
+ATOM    369  HZ  PHE A  22       0.142  -0.244  10.829                          
+ATOM    370  N   TYR A  23       5.442   1.527   7.791                          
+ATOM    371  CA  TYR A  23       4.972   2.928   7.941                          
+ATOM    372  C   TYR A  23       3.452   3.055   7.889                          
+ATOM    373  O   TYR A  23       2.869   2.997   6.803                          
+ATOM    374  CB  TYR A  23       5.729   3.807   6.860                          
+ATOM    375  CG  TYR A  23       5.726   5.334   7.253                          
+ATOM    376  CD1 TYR A  23       4.739   6.105   6.715                          
+ATOM    377  CD2 TYR A  23       6.682   5.875   8.052                          
+ATOM    378  CE1 TYR A  23       4.763   7.476   6.969                          
+ATOM    379  CE2 TYR A  23       6.656   7.212   8.473                          
+ATOM    380  CZ  TYR A  23       5.633   8.031   7.885                          
+ATOM    381  OH  TYR A  23       5.600   9.331   8.298                          
+ATOM    382  H   TYR A  23       5.566   1.202   6.843                          
+ATOM    383  HA  TYR A  23       5.207   3.388   8.900                          
+ATOM    384  2HB TYR A  23       6.777   3.513   6.820                          
+ATOM    385  HB3 TYR A  23       5.193   3.709   5.916                          
+ATOM    386  HD1 TYR A  23       4.053   5.744   5.963                          
+ATOM    387  HD2 TYR A  23       7.506   5.271   8.403                          
+ATOM    388  HE1 TYR A  23       4.097   8.209   6.539                          
+ATOM    389  HE2 TYR A  23       7.450   7.527   9.133                          
+ATOM    390  HH  TYR A  23       6.417   9.577   8.737                          
+ATOM    391  N   ASN A  24       2.828   3.289   9.070                          
+ATOM    392  CA  ASN A  24       1.390   3.611   9.146                          
+ATOM    393  C   ASN A  24       1.145   5.035   8.696                          
+ATOM    394  O   ASN A  24       1.263   5.995   9.458                          
+ATOM    395  CB  ASN A  24       0.811   3.319  10.533                          
+ATOM    396  CG  ASN A  24      -0.680   3.743  10.614                          
+ATOM    397  OD1 ASN A  24      -1.355   3.814   9.536                          
+ATOM    398  ND2 ASN A  24      -1.133   4.049  11.793                          
+ATOM    399  H   ASN A  24       3.459   3.346   9.856                          
+ATOM    400  HA  ASN A  24       0.808   3.014   8.444                          
+ATOM    401  2HB ASN A  24       0.868   2.247  10.721                          
+ATOM    402  HB3 ASN A  24       1.391   3.841  11.295                          
+ATOM    403 1HD2 ASN A  24      -2.114   4.252  11.924                          
+ATOM    404 2HD2 ASN A  24      -0.547   3.660  12.517                          
+ATOM    405  N   ALA A  25       0.760   5.106   7.429                          
+ATOM    406  CA  ALA A  25       0.700   6.390   6.695                          
+ATOM    407  C   ALA A  25      -0.451   7.206   7.424                          
+ATOM    408  O   ALA A  25      -0.343   8.402   7.648                          
+ATOM    409  CB  ALA A  25       0.392   6.017   5.190                          
+ATOM    410  H   ALA A  25       0.742   4.243   6.906                          
+ATOM    411  HA  ALA A  25       1.662   6.901   6.665                          
+ATOM    412  1HB ALA A  25      -0.470   5.364   5.051                          
+ATOM    413  2HB ALA A  25       0.280   6.895   4.554                          
+ATOM    414  3HB ALA A  25       1.279   5.475   4.861                          
+ATOM    415  N   LYS A  26      -1.536   6.511   7.843                          
+ATOM    416  CA  LYS A  26      -2.664   7.139   8.539                          
+ATOM    417  C   LYS A  26      -2.289   7.873   9.837                          
+ATOM    418  O   LYS A  26      -2.947   8.845  10.153                          
+ATOM    419  CB  LYS A  26      -3.810   6.050   8.872                          
+ATOM    420  CG  LYS A  26      -5.180   6.725   8.689                          
+ATOM    421  CD  LYS A  26      -6.349   5.849   9.045                          
+ATOM    422  CE  LYS A  26      -7.693   6.571   8.721                          
+ATOM    423  NZ  LYS A  26      -8.784   5.744   9.268                          
+ATOM    424  H   LYS A  26      -1.759   5.707   7.274                          
+ATOM    425  HA  LYS A  26      -3.066   7.791   7.764                          
+ATOM    426  2HB LYS A  26      -3.735   5.225   8.163                          
+ATOM    427  HB3 LYS A  26      -3.800   5.581   9.856                          
+ATOM    428  2HG LYS A  26      -5.150   7.634   9.289                          
+ATOM    429  HG3 LYS A  26      -5.213   6.939   7.620                          
+ATOM    430  2HD LYS A  26      -6.165   4.906   8.530                          
+ATOM    431  HD3 LYS A  26      -6.306   5.644  10.114                          
+ATOM    432  2HE LYS A  26      -7.623   7.585   9.116                          
+ATOM    433  HE3 LYS A  26      -7.645   6.687   7.638                          
+ATOM    434  1HZ LYS A  26      -9.668   6.158   9.013                          
+ATOM    435  2HZ LYS A  26      -8.755   4.780   8.968                          
+ATOM    436  3HZ LYS A  26      -8.785   5.714  10.278                          
+ATOM    437  N   ALA A  27      -1.203   7.405  10.559                          
+ATOM    438  CA  ALA A  27      -0.686   8.124  11.724                          
+ATOM    439  C   ALA A  27       0.677   8.788  11.413                          
+ATOM    440  O   ALA A  27       1.226   9.450  12.333                          
+ATOM    441  CB  ALA A  27      -0.726   7.280  12.952                          
+ATOM    442  H   ALA A  27      -0.731   6.562  10.262                          
+ATOM    443  HA  ALA A  27      -1.415   8.910  11.919                          
+ATOM    444  1HB ALA A  27      -0.595   7.987  13.772                          
+ATOM    445  2HB ALA A  27      -1.711   6.845  13.123                          
+ATOM    446  3HB ALA A  27       0.072   6.546  12.845                          
+ATOM    447  N   GLY A  28       1.248   8.681  10.218                          
+ATOM    448  CA  GLY A  28       2.403   9.458   9.885                          
+ATOM    449  C   GLY A  28       3.641   9.062  10.729                          
+ATOM    450  O   GLY A  28       4.407   9.936  11.218                          
+ATOM    451  H   GLY A  28       0.863   8.117   9.474                          
+ATOM    452  2HA GLY A  28       2.698   9.222   8.862                          
+ATOM    453  HA3 GLY A  28       2.226  10.500  10.151                          
+ATOM    454  N   LEU A  29       3.714   7.754  11.018                          
+ATOM    455  CA  LEU A  29       4.794   7.134  11.896                          
+ATOM    456  C   LEU A  29       5.105   5.684  11.533                          
+ATOM    457  O   LEU A  29       4.175   5.026  11.037                          
+ATOM    458  CB  LEU A  29       4.314   7.073  13.362                          
+ATOM    459  CG  LEU A  29       5.444   7.414  14.411                          
+ATOM    460  CD1 LEU A  29       5.713   8.941  14.534                          
+ATOM    461  CD2 LEU A  29       4.977   6.812  15.750                          
+ATOM    462  H   LEU A  29       2.939   7.177  10.723                          
+ATOM    463  HA  LEU A  29       5.695   7.744  11.845                          
+ATOM    464  2HB LEU A  29       3.644   7.928  13.446                          
+ATOM    465  HB3 LEU A  29       3.885   6.105  13.623                          
+ATOM    466  HG  LEU A  29       6.330   6.899  14.038                          
+ATOM    467 1HD1 LEU A  29       4.838   9.512  14.846                          
+ATOM    468 2HD1 LEU A  29       6.418   9.013  15.362                          
+ATOM    469 3HD1 LEU A  29       6.104   9.386  13.619                          
+ATOM    470 1HD2 LEU A  29       5.715   6.953  16.540                          
+ATOM    471 2HD2 LEU A  29       4.049   7.273  16.089                          
+ATOM    472 3HD2 LEU A  29       4.812   5.749  15.573                          
+ATOM    473  N   CYS A  30       6.299   5.155  11.773                          
+ATOM    474  CA  CYS A  30       6.628   3.768  11.766                          
+ATOM    475  C   CYS A  30       6.129   3.109  13.108                          
+ATOM    476  O   CYS A  30       6.237   3.592  14.230                          
+ATOM    477  CB  CYS A  30       8.205   3.616  11.774                          
+ATOM    478  SG  CYS A  30       9.044   4.016  10.229                          
+ATOM    479  H   CYS A  30       7.040   5.799  12.011                          
+ATOM    480  HA  CYS A  30       6.178   3.346  10.867                          
+ATOM    481  2HB CYS A  30       8.551   4.267  12.577                          
+ATOM    482  HB3 CYS A  30       8.458   2.574  11.970                          
+ATOM    483  N   GLN A  31       5.647   1.840  12.924                          
+ATOM    484  CA  GLN A  31       4.809   1.106  13.924                          
+ATOM    485  C   GLN A  31       4.962  -0.411  13.649                          
+ATOM    486  O   GLN A  31       5.518  -0.779  12.632                          
+ATOM    487  CB  GLN A  31       3.334   1.617  13.977                          
+ATOM    488  CG  GLN A  31       3.039   3.023  14.324                          
+ATOM    489  CD  GLN A  31       1.528   3.328  14.415                          
+ATOM    490  OE1 GLN A  31       0.713   2.677  13.797                          
+ATOM    491  NE2 GLN A  31       1.181   4.459  15.046                          
+ATOM    492  H   GLN A  31       5.671   1.475  11.982                          
+ATOM    493  HA  GLN A  31       5.211   1.188  14.934                          
+ATOM    494  2HB GLN A  31       2.906   1.543  12.978                          
+ATOM    495  HB3 GLN A  31       2.752   0.961  14.624                          
+ATOM    496  2HG GLN A  31       3.509   3.268  15.276                          
+ATOM    497  HG3 GLN A  31       3.562   3.586  13.550                          
+ATOM    498 1HE2 GLN A  31       0.247   4.834  15.130                          
+ATOM    499 2HE2 GLN A  31       1.961   4.885  15.525                          
+ATOM    500  N   THR A  32       4.466  -1.218  14.575                          
+ATOM    501  CA  THR A  32       4.558  -2.660  14.660                          
+ATOM    502  C   THR A  32       3.360  -3.332  13.955                          
+ATOM    503  O   THR A  32       2.204  -2.870  14.037                          
+ATOM    504  CB  THR A  32       4.760  -3.213  16.144                          
+ATOM    505  OG1 THR A  32       3.848  -2.618  17.043                          
+ATOM    506  CG2 THR A  32       6.172  -2.908  16.645                          
+ATOM    507  H   THR A  32       4.011  -0.903  15.420                          
+ATOM    508  HA  THR A  32       5.457  -2.945  14.113                          
+ATOM    509  HB  THR A  32       4.559  -4.284  16.182                          
+ATOM    510  HG1 THR A  32       3.372  -3.323  17.488                          
+ATOM    511 1HG2 THR A  32       6.365  -1.851  16.827                          
+ATOM    512 2HG2 THR A  32       6.244  -3.338  17.644                          
+ATOM    513 3HG2 THR A  32       6.923  -3.285  15.951                          
+ATOM    514  N   PHE A  33       3.704  -4.519  13.398                          
+ATOM    515  CA  PHE A  33       2.741  -5.558  13.036                          
+ATOM    516  C   PHE A  33       3.316  -6.967  13.044                          
+ATOM    517  O   PHE A  33       4.513  -7.185  12.939                          
+ATOM    518  CB  PHE A  33       2.029  -5.210  11.699                          
+ATOM    519  CG  PHE A  33       2.826  -5.715  10.519                          
+ATOM    520  CD1 PHE A  33       2.321  -6.793   9.740                          
+ATOM    521  CD2 PHE A  33       4.015  -5.088  10.095                          
+ATOM    522  CE1 PHE A  33       3.093  -7.286   8.608                          
+ATOM    523  CE2 PHE A  33       4.645  -5.509   8.900                          
+ATOM    524  CZ  PHE A  33       4.206  -6.608   8.178                          
+ATOM    525  H   PHE A  33       4.662  -4.695  13.131                          
+ATOM    526  HA  PHE A  33       1.985  -5.629  13.818                          
+ATOM    527  2HB PHE A  33       1.082  -5.729  11.847                          
+ATOM    528  HB3 PHE A  33       1.749  -4.165  11.565                          
+ATOM    529  HD1 PHE A  33       1.524  -7.355  10.205                          
+ATOM    530  HD2 PHE A  33       4.280  -4.231  10.697                          
+ATOM    531  HE1 PHE A  33       2.721  -8.132   8.050                          
+ATOM    532  HE2 PHE A  33       5.503  -4.950   8.558                          
+ATOM    533  HZ  PHE A  33       4.799  -6.963   7.348                          
+ATOM    534  N   VAL A  34       2.452  -7.989  13.168                          
+ATOM    535  CA  VAL A  34       2.912  -9.385  13.166                          
+ATOM    536  C   VAL A  34       2.894 -10.062  11.815                          
+ATOM    537  O   VAL A  34       2.043  -9.804  10.991                          
+ATOM    538  CB  VAL A  34       2.134 -10.252  14.125                          
+ATOM    539  CG1 VAL A  34       2.112  -9.683  15.584                          
+ATOM    540  CG2 VAL A  34       0.588 -10.294  13.716                          
+ATOM    541  H   VAL A  34       1.525  -7.851  13.546                          
+ATOM    542  HA  VAL A  34       3.951  -9.341  13.493                          
+ATOM    543  HB  VAL A  34       2.590 -11.242  14.160                          
+ATOM    544 1HG1 VAL A  34       3.133  -9.744  15.961                          
+ATOM    545 2HG1 VAL A  34       1.983  -8.603  15.514                          
+ATOM    546 3HG1 VAL A  34       1.473 -10.263  16.248                          
+ATOM    547 1HG2 VAL A  34       0.190  -9.281  13.644                          
+ATOM    548 2HG2 VAL A  34       0.469 -10.701  12.712                          
+ATOM    549 3HG2 VAL A  34       0.106 -10.985  14.407                          
+ATOM    550  N   TYR A  35       3.814 -10.982  11.645                          
+ATOM    551  CA  TYR A  35       4.160 -11.476  10.334                          
+ATOM    552  C   TYR A  35       4.542 -12.988  10.394                          
+ATOM    553  O   TYR A  35       5.414 -13.426  11.118                          
+ATOM    554  CB  TYR A  35       5.203 -10.543   9.874                          
+ATOM    555  CG  TYR A  35       6.004 -10.946   8.613                          
+ATOM    556  CD1 TYR A  35       5.348 -10.903   7.365                          
+ATOM    557  CD2 TYR A  35       7.332 -11.351   8.673                          
+ATOM    558  CE1 TYR A  35       6.062 -11.323   6.208                          
+ATOM    559  CE2 TYR A  35       8.123 -11.576   7.524                          
+ATOM    560  CZ  TYR A  35       7.464 -11.535   6.278                          
+ATOM    561  OH  TYR A  35       8.148 -11.824   5.176                          
+ATOM    562  H   TYR A  35       4.601 -10.930  12.276                          
+ATOM    563  HA  TYR A  35       3.297 -11.395   9.673                          
+ATOM    564  2HB TYR A  35       4.731  -9.574   9.714                          
+ATOM    565  HB3 TYR A  35       5.981 -10.439  10.630                          
+ATOM    566  HD1 TYR A  35       4.319 -10.579   7.297                          
+ATOM    567  HD2 TYR A  35       7.900 -11.256   9.587                          
+ATOM    568  HE1 TYR A  35       5.595 -11.384   5.236                          
+ATOM    569  HE2 TYR A  35       9.187 -11.761   7.543                          
+ATOM    570  HH  TYR A  35       9.094 -11.880   5.329                          
+ATOM    571  N   GLY A  36       4.106 -13.725   9.407                          
+ATOM    572  CA  GLY A  36       4.181 -15.187   9.310                          
+ATOM    573  C   GLY A  36       5.541 -15.769   8.895                          
+ATOM    574  O   GLY A  36       5.752 -16.993   9.080                          
+ATOM    575  H   GLY A  36       3.488 -13.296   8.733                          
+ATOM    576  2HA GLY A  36       4.030 -15.572  10.318                          
+ATOM    577  HA3 GLY A  36       3.287 -15.514   8.779                          
+ATOM    578  N   GLY A  37       6.518 -14.952   8.545                          
+ATOM    579  CA  GLY A  37       7.863 -15.378   8.107                          
+ATOM    580  C   GLY A  37       7.965 -15.804   6.669                          
+ATOM    581  O   GLY A  37       8.796 -16.604   6.374                          
+ATOM    582  H   GLY A  37       6.260 -13.985   8.684                          
+ATOM    583  2HA GLY A  37       8.656 -14.644   8.247                          
+ATOM    584  HA3 GLY A  37       8.115 -16.335   8.566                          
+ATOM    585  N   CYS A  38       7.161 -15.319   5.791                          
+ATOM    586  CA  CYS A  38       7.170 -15.482   4.311                          
+ATOM    587  C   CYS A  38       6.413 -14.398   3.594                          
+ATOM    588  O   CYS A  38       5.578 -13.722   4.185                          
+ATOM    589  CB  CYS A  38       6.754 -16.815   3.824                          
+ATOM    590  SG  CYS A  38       4.937 -17.145   3.840                          
+ATOM    591  H   CYS A  38       6.538 -14.628   6.184                          
+ATOM    592  HA  CYS A  38       8.215 -15.445   4.001                          
+ATOM    593  2HB CYS A  38       7.174 -16.971   2.830                          
+ATOM    594  HB3 CYS A  38       7.211 -17.580   4.452                          
+ATOM    595  N   ARG A  39       6.772 -14.282   2.293                          
+ATOM    596  CA  ARG A  39       6.097 -13.526   1.228                          
+ATOM    597  C   ARG A  39       5.858 -12.029   1.522                          
+ATOM    598  O   ARG A  39       4.698 -11.587   1.496                          
+ATOM    599  CB  ARG A  39       4.867 -14.303   0.628                          
+ATOM    600  CG  ARG A  39       5.207 -15.756   0.229                          
+ATOM    601  CD  ARG A  39       4.004 -16.561  -0.314                          
+ATOM    602  NE  ARG A  39       4.562 -17.905  -0.627                          
+ATOM    603  CZ  ARG A  39       3.936 -19.017  -0.980                          
+ATOM    604  NH1 ARG A  39       2.638 -19.088  -1.273                          
+ATOM    605  NH2 ARG A  39       4.621 -20.147  -0.945                          
+ATOM    606  H   ARG A  39       7.524 -14.812   1.875                          
+ATOM    607  HA  ARG A  39       6.866 -13.477   0.457                          
+ATOM    608  2HB ARG A  39       4.111 -14.544   1.375                          
+ATOM    609  HB3 ARG A  39       4.241 -13.755  -0.076                          
+ATOM    610  2HG ARG A  39       6.053 -15.727  -0.458                          
+ATOM    611  HG3 ARG A  39       5.573 -16.373   1.050                          
+ATOM    612  2HD ARG A  39       3.292 -16.747   0.490                          
+ATOM    613  HD3 ARG A  39       3.615 -16.098  -1.221                          
+ATOM    614  HE  ARG A  39       5.566 -18.012  -0.659                          
+ATOM    615 1HH1 ARG A  39       2.080 -18.250  -1.185                          
+ATOM    616 2HH1 ARG A  39       2.079 -19.870  -1.582                          
+ATOM    617 1HH2 ARG A  39       5.594 -20.041  -0.696                          
+ATOM    618 2HH2 ARG A  39       4.182 -21.041  -0.781                          
+ATOM    619  N   ALA A  40       6.854 -11.319   1.959                          
+ATOM    620  CA  ALA A  40       6.717  -9.865   2.308                          
+ATOM    621  C   ALA A  40       5.884  -9.145   1.334                          
+ATOM    622  O   ALA A  40       6.154  -9.243   0.108                          
+ATOM    623  CB  ALA A  40       8.136  -9.265   2.420                          
+ATOM    624  H   ALA A  40       7.762 -11.748   2.068                          
+ATOM    625  HA  ALA A  40       6.337  -9.868   3.330                          
+ATOM    626  1HB ALA A  40       8.817  -9.431   1.585                          
+ATOM    627  2HB ALA A  40       8.098  -8.262   2.847                          
+ATOM    628  3HB ALA A  40       8.665  -9.799   3.209                          
+ATOM    629  N   LYS A  41       5.081  -8.146   1.750                          
+ATOM    630  CA  LYS A  41       4.813  -6.980   0.893                          
+ATOM    631  C   LYS A  41       5.903  -5.937   1.023                          
+ATOM    632  O   LYS A  41       6.776  -5.994   1.909                          
+ATOM    633  CB  LYS A  41       3.350  -6.565   1.046                          
+ATOM    634  CG  LYS A  41       2.435  -7.643   0.544                          
+ATOM    635  CD  LYS A  41       1.060  -7.188   0.196                          
+ATOM    636  CE  LYS A  41       0.165  -8.134  -0.614                          
+ATOM    637  NZ  LYS A  41      -0.895  -7.367  -1.214                          
+ATOM    638  H   LYS A  41       4.946  -8.044   2.746                          
+ATOM    639  HA  LYS A  41       4.756  -7.366  -0.124                          
+ATOM    640  2HB LYS A  41       3.106  -6.504   2.106                          
+ATOM    641  HB3 LYS A  41       3.236  -5.633   0.491                          
+ATOM    642  2HG LYS A  41       2.831  -7.969  -0.418                          
+ATOM    643  HG3 LYS A  41       2.471  -8.562   1.130                          
+ATOM    644  2HD LYS A  41       0.561  -6.954   1.136                          
+ATOM    645  HD3 LYS A  41       1.045  -6.187  -0.235                          
+ATOM    646  2HE LYS A  41       0.715  -8.613  -1.424                          
+ATOM    647  HE3 LYS A  41      -0.192  -8.938   0.030                          
+ATOM    648  1HZ LYS A  41      -1.548  -6.955  -0.563                          
+ATOM    649  2HZ LYS A  41      -0.547  -6.734  -1.919                          
+ATOM    650  3HZ LYS A  41      -1.437  -7.994  -1.792                          
+ATOM    651  N   ARG A  42       5.880  -4.879   0.157                          
+ATOM    652  CA  ARG A  42       6.897  -3.891   0.135                          
+ATOM    653  C   ARG A  42       7.090  -3.129   1.442                          
+ATOM    654  O   ARG A  42       8.237  -2.801   1.847                          
+ATOM    655  CB  ARG A  42       6.572  -2.752  -0.892                          
+ATOM    656  CG  ARG A  42       6.433  -3.218  -2.267                          
+ATOM    657  CD  ARG A  42       6.403  -2.043  -3.308                          
+ATOM    658  NE  ARG A  42       5.289  -1.052  -3.048                          
+ATOM    659  CZ  ARG A  42       4.668  -0.234  -3.928                          
+ATOM    660  NH1 ARG A  42       4.993  -0.206  -5.192                          
+ATOM    661  NH2 ARG A  42       3.718   0.513  -3.507                          
+ATOM    662  H   ARG A  42       5.203  -4.900  -0.593                          
+ATOM    663  HA  ARG A  42       7.833  -4.353  -0.179                          
+ATOM    664  2HB ARG A  42       5.650  -2.257  -0.587                          
+ATOM    665  HB3 ARG A  42       7.335  -1.977  -0.828                          
+ATOM    666  2HG ARG A  42       7.265  -3.863  -2.550                          
+ATOM    667  HG3 ARG A  42       5.523  -3.793  -2.434                          
+ATOM    668  2HD ARG A  42       7.384  -1.576  -3.395                          
+ATOM    669  HD3 ARG A  42       6.162  -2.367  -4.321                          
+ATOM    670  HE  ARG A  42       4.750  -1.203  -2.207                          
+ATOM    671 1HH1 ARG A  42       4.811   0.637  -5.717                          
+ATOM    672 2HH1 ARG A  42       5.740  -0.845  -5.423                          
+ATOM    673 1HH2 ARG A  42       3.275   0.317  -2.620                          
+ATOM    674 2HH2 ARG A  42       3.204   1.143  -4.106                          
+ATOM    675  N   ASN A  43       5.973  -2.758   2.160                          
+ATOM    676  CA  ASN A  43       5.975  -2.121   3.481                          
+ATOM    677  C   ASN A  43       6.208  -3.110   4.663                          
+ATOM    678  O   ASN A  43       5.292  -3.470   5.397                          
+ATOM    679  CB  ASN A  43       4.754  -1.247   3.721                          
+ATOM    680  CG  ASN A  43       4.921  -0.094   4.704                          
+ATOM    681  OD1 ASN A  43       5.872   0.050   5.351                          
+ATOM    682  ND2 ASN A  43       3.863   0.719   4.723                          
+ATOM    683  H   ASN A  43       5.079  -2.804   1.692                          
+ATOM    684  HA  ASN A  43       6.848  -1.475   3.384                          
+ATOM    685  2HB ASN A  43       4.375  -0.760   2.822                          
+ATOM    686  HB3 ASN A  43       3.973  -1.902   4.107                          
+ATOM    687 1HD2 ASN A  43       3.076   0.604   4.100                          
+ATOM    688 2HD2 ASN A  43       3.782   1.482   5.380                          
+ATOM    689  N   ASN A  44       7.442  -3.651   4.757                          
+ATOM    690  CA  ASN A  44       7.760  -4.726   5.781                          
+ATOM    691  C   ASN A  44       9.267  -4.609   5.992                          
+ATOM    692  O   ASN A  44       9.984  -4.694   5.047                          
+ATOM    693  CB  ASN A  44       7.427  -6.179   5.245                          
+ATOM    694  CG  ASN A  44       7.725  -7.283   6.219                          
+ATOM    695  OD1 ASN A  44       8.653  -7.241   7.033                          
+ATOM    696  ND2 ASN A  44       7.057  -8.391   6.034                          
+ATOM    697  H   ASN A  44       8.172  -3.465   4.085                          
+ATOM    698  HA  ASN A  44       7.221  -4.689   6.728                          
+ATOM    699  2HB ASN A  44       6.369  -6.170   4.983                          
+ATOM    700  HB3 ASN A  44       7.979  -6.327   4.316                          
+ATOM    701 1HD2 ASN A  44       7.209  -9.098   6.739                          
+ATOM    702 2HD2 ASN A  44       6.285  -8.431   5.383                          
+ATOM    703  N   PHE A  45       9.665  -4.190   7.168                          
+ATOM    704  CA  PHE A  45      10.990  -3.890   7.611                          
+ATOM    705  C   PHE A  45      11.339  -4.643   8.918                          
+ATOM    706  O   PHE A  45      10.511  -4.965   9.791                          
+ATOM    707  CB  PHE A  45      11.184  -2.337   7.715                          
+ATOM    708  CG  PHE A  45      10.654  -1.448   6.615                          
+ATOM    709  CD1 PHE A  45       9.429  -0.733   6.916                          
+ATOM    710  CD2 PHE A  45      11.263  -1.279   5.372                          
+ATOM    711  CE1 PHE A  45       8.888   0.180   5.973                          
+ATOM    712  CE2 PHE A  45      10.652  -0.483   4.424                          
+ATOM    713  CZ  PHE A  45       9.478   0.282   4.699                          
+ATOM    714  H   PHE A  45       8.932  -4.150   7.862                          
+ATOM    715  HA  PHE A  45      11.579  -4.294   6.788                          
+ATOM    716  2HB PHE A  45      10.703  -2.065   8.654                          
+ATOM    717  HB3 PHE A  45      12.241  -2.211   7.953                          
+ATOM    718  HD1 PHE A  45       8.935  -0.819   7.872                          
+ATOM    719  HD2 PHE A  45      12.151  -1.858   5.166                          
+ATOM    720  HE1 PHE A  45       8.066   0.817   6.265                          
+ATOM    721  HE2 PHE A  45      11.056  -0.566   3.426                          
+ATOM    722  HZ  PHE A  45       9.044   0.854   3.892                          
+ATOM    723  N   LYS A  46      12.628  -4.866   9.013                          
+ATOM    724  CA  LYS A  46      13.280  -5.405  10.215                          
+ATOM    725  C   LYS A  46      13.335  -4.493  11.399                          
+ATOM    726  O   LYS A  46      13.449  -4.951  12.547                          
+ATOM    727  CB  LYS A  46      14.730  -5.783   9.887                          
+ATOM    728  CG  LYS A  46      15.689  -4.616   9.542                          
+ATOM    729  CD  LYS A  46      17.095  -4.998   9.051                          
+ATOM    730  CE  LYS A  46      17.022  -5.652   7.759                          
+ATOM    731  NZ  LYS A  46      18.359  -5.783   7.094                          
+ATOM    732  H   LYS A  46      13.134  -4.664   8.163                          
+ATOM    733  HA  LYS A  46      12.825  -6.346  10.525                          
+ATOM    734  2HB LYS A  46      15.174  -6.393  10.674                          
+ATOM    735  HB3 LYS A  46      14.632  -6.503   9.074                          
+ATOM    736  2HG LYS A  46      15.232  -3.816   8.960                          
+ATOM    737  HG3 LYS A  46      16.032  -4.230  10.501                          
+ATOM    738  2HD LYS A  46      17.759  -4.134   9.073                          
+ATOM    739  HD3 LYS A  46      17.515  -5.773   9.691                          
+ATOM    740  2HE LYS A  46      16.450  -6.575   7.857                          
+ATOM    741  HE3 LYS A  46      16.469  -4.994   7.089                          
+ATOM    742  1HZ LYS A  46      18.289  -6.042   6.120                          
+ATOM    743  2HZ LYS A  46      18.959  -4.979   7.205                          
+ATOM    744  3HZ LYS A  46      18.922  -6.541   7.454                          
+ATOM    745  N   SER A  47      13.134  -3.218  11.175                          
+ATOM    746  CA  SER A  47      13.349  -2.293  12.285                          
+ATOM    747  C   SER A  47      12.694  -0.923  11.947                          
+ATOM    748  O   SER A  47      12.532  -0.518  10.757                          
+ATOM    749  CB  SER A  47      14.866  -2.123  12.645                          
+ATOM    750  OG  SER A  47      15.642  -1.718  11.559                          
+ATOM    751  H   SER A  47      13.233  -2.909  10.219                          
+ATOM    752  HA  SER A  47      12.882  -2.674  13.193                          
+ATOM    753  2HB SER A  47      14.933  -1.428  13.482                          
+ATOM    754  HB3 SER A  47      15.294  -3.094  12.895                          
+ATOM    755  HG  SER A  47      16.556  -1.903  11.785                          
+ATOM    756  N   ALA A  48      12.375  -0.176  12.984                          
+ATOM    757  CA  ALA A  48      11.836   1.205  12.902                          
+ATOM    758  C   ALA A  48      13.040   2.166  12.619                          
+ATOM    759  O   ALA A  48      12.846   3.238  12.092                          
+ATOM    760  CB  ALA A  48      11.053   1.480  14.189                          
+ATOM    761  H   ALA A  48      12.322  -0.637  13.881                          
+ATOM    762  HA  ALA A  48      11.138   1.234  12.066                          
+ATOM    763  1HB ALA A  48      10.159   0.856  14.158                          
+ATOM    764  2HB ALA A  48      11.798   1.116  14.896                          
+ATOM    765  3HB ALA A  48      10.853   2.539  14.347                          
+ATOM    766  N   GLU A  49      14.269   1.696  12.738                          
+ATOM    767  CA  GLU A  49      15.549   2.323  12.263                          
+ATOM    768  C   GLU A  49      15.719   2.179  10.791                          
+ATOM    769  O   GLU A  49      15.858   3.202  10.072                          
+ATOM    770  CB  GLU A  49      16.632   1.725  13.112                          
+ATOM    771  CG  GLU A  49      18.128   1.981  12.727                          
+ATOM    772  CD  GLU A  49      19.158   1.239  13.644                          
+ATOM    773  OE1 GLU A  49      20.058   0.577  13.143                          
+ATOM    774  OE2 GLU A  49      18.948   1.246  14.886                          
+ATOM    775  H   GLU A  49      14.400   0.821  13.225                          
+ATOM    776  HA  GLU A  49      15.454   3.387  12.483                          
+ATOM    777  2HB GLU A  49      16.366   2.199  14.056                          
+ATOM    778  HB3 GLU A  49      16.450   0.653  13.037                          
+ATOM    779  2HG GLU A  49      18.136   1.596  11.708                          
+ATOM    780  HG3 GLU A  49      18.356   3.047  12.715                          
+ATOM    781  N   ASP A  50      15.449   1.003  10.228                          
+ATOM    782  CA  ASP A  50      15.332   0.878   8.725                          
+ATOM    783  C   ASP A  50      14.041   1.488   8.071                          
+ATOM    784  O   ASP A  50      14.120   2.223   7.069                          
+ATOM    785  CB  ASP A  50      15.633  -0.573   8.282                          
+ATOM    786  CG  ASP A  50      15.895  -0.626   6.774                          
+ATOM    787  OD1 ASP A  50      16.848   0.049   6.344                          
+ATOM    788  OD2 ASP A  50      15.221  -1.371   5.994                          
+ATOM    789  H   ASP A  50      15.155   0.218  10.791                          
+ATOM    790  HA  ASP A  50      16.161   1.422   8.272                          
+ATOM    791  2HB ASP A  50      16.524  -0.852   8.844                          
+ATOM    792  HB3 ASP A  50      14.821  -1.269   8.494                          
+ATOM    793  N   CYS A  51      12.845   1.354   8.656                          
+ATOM    794  CA  CYS A  51      11.618   2.060   8.308                          
+ATOM    795  C   CYS A  51      11.758   3.594   8.285                          
+ATOM    796  O   CYS A  51      11.353   4.228   7.311                          
+ATOM    797  CB  CYS A  51      10.506   1.644   9.228                          
+ATOM    798  SG  CYS A  51       8.832   2.388   9.059                          
+ATOM    799  H   CYS A  51      12.798   0.918   9.566                          
+ATOM    800  HA  CYS A  51      11.237   1.680   7.360                          
+ATOM    801  2HB CYS A  51      10.393   0.561   9.184                          
+ATOM    802  HB3 CYS A  51      10.791   1.961  10.232                          
+ATOM    803  N   MET A  52      12.378   4.204   9.299                          
+ATOM    804  CA  MET A  52      12.708   5.603   9.261                          
+ATOM    805  C   MET A  52      13.856   6.049   8.296                          
+ATOM    806  O   MET A  52      13.895   7.083   7.678                          
+ATOM    807  CB  MET A  52      12.970   6.087  10.726                          
+ATOM    808  CG  MET A  52      11.722   6.125  11.691                          
+ATOM    809  SD  MET A  52      12.141   6.646  13.366                          
+ATOM    810  CE  MET A  52      13.123   5.328  14.092                          
+ATOM    811  H   MET A  52      12.758   3.665  10.064                          
+ATOM    812  HA  MET A  52      11.855   6.179   8.904                          
+ATOM    813  2HB MET A  52      13.736   5.442  11.157                          
+ATOM    814  HB3 MET A  52      13.368   7.101  10.752                          
+ATOM    815  2HG MET A  52      10.975   6.787  11.253                          
+ATOM    816  HG3 MET A  52      11.234   5.156  11.792                          
+ATOM    817  1HE MET A  52      12.556   4.411  14.253                          
+ATOM    818  2HE MET A  52      14.012   5.183  13.478                          
+ATOM    819  3HE MET A  52      13.450   5.730  15.051                          
+ATOM    820  N   ARG A  53      14.821   5.165   8.029                          
+ATOM    821  CA  ARG A  53      15.884   5.306   7.040                          
+ATOM    822  C   ARG A  53      15.300   5.136   5.579                          
+ATOM    823  O   ARG A  53      15.792   5.696   4.634                          
+ATOM    824  CB  ARG A  53      17.046   4.333   7.370                          
+ATOM    825  CG  ARG A  53      18.257   4.651   6.467                          
+ATOM    826  CD  ARG A  53      19.511   3.977   6.716                          
+ATOM    827  NE  ARG A  53      19.279   2.554   6.875                          
+ATOM    828  CZ  ARG A  53      19.602   1.776   7.898                          
+ATOM    829  NH1 ARG A  53      20.396   2.076   8.869                          
+ATOM    830  NH2 ARG A  53      19.123   0.539   7.954                          
+ATOM    831  H   ARG A  53      14.949   4.313   8.556                          
+ATOM    832  HA  ARG A  53      16.289   6.317   7.093                          
+ATOM    833  2HB ARG A  53      17.345   4.503   8.404                          
+ATOM    834  HB3 ARG A  53      16.712   3.301   7.265                          
+ATOM    835  2HG ARG A  53      17.986   4.585   5.413                          
+ATOM    836  HG3 ARG A  53      18.426   5.725   6.542                          
+ATOM    837  2HD ARG A  53      20.226   4.008   5.894                          
+ATOM    838  HD3 ARG A  53      19.785   4.278   7.727                          
+ATOM    839  HE  ARG A  53      18.788   2.067   6.138                          
+ATOM    840 1HH1 ARG A  53      20.621   1.358   9.543                          
+ATOM    841 2HH1 ARG A  53      21.040   2.852   8.807                          
+ATOM    842 1HH2 ARG A  53      18.381   0.314   7.306                          
+ATOM    843 2HH2 ARG A  53      19.382  -0.106   8.687                          
+ATOM    844  N   THR A  54      14.153   4.454   5.497                          
+ATOM    845  CA  THR A  54      13.448   4.173   4.196                          
+ATOM    846  C   THR A  54      12.283   5.120   3.871                          
+ATOM    847  O   THR A  54      12.211   5.569   2.723                          
+ATOM    848  CB  THR A  54      13.092   2.651   4.096                          
+ATOM    849  OG1 THR A  54      14.248   1.842   4.091                          
+ATOM    850  CG2 THR A  54      12.397   2.301   2.778                          
+ATOM    851  H   THR A  54      13.893   4.034   6.378                          
+ATOM    852  HA  THR A  54      14.193   4.293   3.409                          
+ATOM    853  HB  THR A  54      12.469   2.218   4.879                          
+ATOM    854  HG1 THR A  54      14.440   1.874   5.031                          
+ATOM    855 1HG2 THR A  54      12.609   1.260   2.532                          
+ATOM    856 2HG2 THR A  54      11.329   2.516   2.740                          
+ATOM    857 3HG2 THR A  54      12.858   2.856   1.961                          
+ATOM    858  N   CYS A  55      11.414   5.465   4.884                          
+ATOM    859  CA  CYS A  55      10.100   6.043   4.700                          
+ATOM    860  C   CYS A  55       9.920   7.406   5.386                          
+ATOM    861  O   CYS A  55       8.855   7.913   5.661                          
+ATOM    862  CB  CYS A  55       9.033   4.974   5.073                          
+ATOM    863  SG  CYS A  55       8.585   3.686   3.823                          
+ATOM    864  H   CYS A  55      11.490   4.844   5.677                          
+ATOM    865  HA  CYS A  55      10.087   6.261   3.632                          
+ATOM    866  2HB CYS A  55       9.447   4.531   5.979                          
+ATOM    867  HB3 CYS A  55       8.111   5.482   5.354                          
+ATOM    868  N   GLY A  56      11.088   8.105   5.711                          
+ATOM    869  CA  GLY A  56      11.076   9.290   6.702                          
+ATOM    870  C   GLY A  56      10.557  10.564   5.980                          
+ATOM    871  O   GLY A  56      10.245  11.546   6.679                          
+ATOM    872  H   GLY A  56      12.000   7.772   5.435                          
+ATOM    873  2HA GLY A  56      10.290   9.053   7.420                          
+ATOM    874  HA3 GLY A  56      12.083   9.460   7.083                          
+ATOM    875  N   GLY A  57      10.609  10.624   4.640                          
+ATOM    876  CA  GLY A  57      10.474  11.834   3.826                          
+ATOM    877  C   GLY A  57       9.017  12.157   3.304                          
+ATOM    878  O   GLY A  57       8.350  11.205   2.818                          
+ATOM    879  H   GLY A  57      10.889   9.765   4.190                          
+ATOM    880  2HA GLY A  57      10.807  12.611   4.514                          
+ATOM    881  HA3 GLY A  57      11.067  11.892   2.913                          
+ATOM    882  N   ALA A  58       8.698  13.452   3.182                          
+ATOM    883  CA  ALA A  58       7.286  13.898   2.917                          
+ATOM    884  C   ALA A  58       6.836  13.499   1.596                          
+ATOM    885  O   ALA A  58       5.636  13.446   1.333                          
+ATOM    886  CB  ALA A  58       7.261  15.464   2.893                          
+ATOM    887  OXT ALA A  58       7.692  13.378   0.682                          
+ATOM    888  H   ALA A  58       9.320  14.138   3.585                          
+ATOM    889  HA  ALA A  58       6.658  13.407   3.660                          
+ATOM    890  1HB ALA A  58       7.720  15.835   3.810                          
+ATOM    891  2HB ALA A  58       7.761  15.829   1.996                          
+ATOM    892  3HB ALA A  58       6.238  15.811   3.037                          
+ENDMDL

wrappers/python/tests/systems/ions.pdb

+CRYST1   12.009   12.338   11.510  90.00  90.00  90.00 P 1
+ATOM      1  SOD SOD I   1      -5.844   1.432   3.239  1.00  0.00      ION NA
+ATOM      2  CLA CLA I   2      -5.605  -3.153   1.213  1.00  0.00      ION CL
+END
\ No newline at end of file

wrappers/python/tests/systems/ions.psf

+PSF
+
+       4 !NTITLE
+ REMARKS original generated structure x-plor psf file
+ REMARKS topology ../../../../../Charmm36_FF/toppar/top_all36_cgenff.rtf 
+ REMARKS topology ../../../../../Charmm36_FF/toppar/toppar_water_ions.str 
+ REMARKS segment ION { first NONE; last NONE; auto angles dihedrals }
+
+       2 !NATOM
+       1 ION  1    SOD  SOD  SOD    1.000000       22.9898           0
+       2 ION  2    CLA  CLA  CLA   -1.000000       35.4500           0
+
+       0 !NBOND: bonds
+
+
+       0 !NTHETA: angles
+
+
+       0 !NPHI: dihedrals
+
+
+       0 !NIMPHI: impropers
+
+
+       0 !NDON: donors
+
+
+       0 !NACC: acceptors
+
+
+       0 !NNB
+
+       0       0
+
+       1       0 !NGRP
+       0       0       0
+

wrappers/python/tests/systems/methanol_ions.pdb

+CRYST1   12.009   12.338   11.510  90.00  90.00  90.00 P 1           1
+ATOM      1  CB  MEOHM   1      -0.748  -0.015   0.024  1.00  0.00      METH C
+ATOM      2  OG  MEOHM   1       0.558   0.420  -0.278  1.00  0.00      METH O
+ATOM      3  HG1 MEOHM   1       0.716   1.404   0.137  1.00  0.00      METH H
+ATOM      4  HB1 MEOHM   1      -1.293  -0.202  -0.901  1.00  0.00      METH H
+ATOM      5  HB2 MEOHM   1      -1.263   0.754   0.600  1.00  0.00      METH H
+ATOM      6  HB3 MEOHM   1      -0.699  -0.934   0.609  1.00  0.00      METH H
+ATOM      7  SOD SOD I   2      -5.844   1.432   3.239  1.00  0.00      ION NA
+ATOM      8  CLA CLA I   3      -5.605  -3.153   1.213  1.00  0.00      ION CL
+CONECT 1    2    4     5     6
+CONECT 2    3
+END
+END
\ No newline at end of file

wrappers/python/tests/systems/methanol_ions.psf

+PSF EXT
+
+       4 !NTITLE
+ REMARKS original generated structure x-plor psf file
+ REMARKS topology ../../../../../Charmm36_FF/toppar/top_all36_cgenff.rtf 
+ REMARKS topology ../../../../../Charmm36_FF/toppar/toppar_water_ions.str 
+ REMARKS segment ION { first NONE; last NONE; auto angles dihedrals }
+
+       8 !NATOM
+         1 METH     1        MEOH     CB       CG331   -0.040000       12.0110           0
+         2 METH     1        MEOH     OG       OG311   -0.650000       15.9994           0
+         3 METH     1        MEOH     HG1      HGP1     0.420000        1.0080           0
+         4 METH     1        MEOH     HB1      HGA3     0.090000        1.0080           0
+         5 METH     1        MEOH     HB2      HGA3     0.090000        1.0080           0
+         6 METH     1        MEOH     HB3      HGA3     0.090000        1.0080           0
+         7 ION      2        SOD      SOD      SOD      1.000000       22.9898           0
+         8 ION      3        CLA      CLA      CLA     -1.000000       35.4500           0
+
+       5 !NBOND: bonds
+         1         2         1         4         1         5         1         6
+         2         3
+
+       7 !NTHETA: angles
+         1         2         3         2         1         6         2         1         5
+         2         1         4         4         1         6         4         1         5
+         5         1         6
+
+       3 !NPHI: dihedrals
+         3         2         1         4         3         2         1         5
+         3         2         1         6
+
+       0 !NIMPHI: impropers
+
+
+       0 !NDON: donors
+
+
+       0 !NACC: acceptors
+
+
+       0 !NNB
+
+         0         0         0         0         0         0         0         0
+
+
+       1       0 !NGRP
+         0         0         0
+