Task: Support prmtop files created by chamber (openmm/openmm#3416)

org: openmm
repo: openmm
pr_number: 3416
issue_title: Support prmtop files created by chamber
issue_body: Implements #3225.
resolved_issues: title: Support prmtop files created by chamber
body: Currently, prmtop files created using the CHAMBER tool are not supported in the software, which prevents users from utilizing these files for simulations. This limitation can be inconvenient for users who rely on CHAMBER-generated prmtop files as part of their workflows.

The expected behavior is that the software should support prmtop files created by CHAMBER, allowing users to load these files, create systems, and perform simulations without encountering errors. This enhancement would improve compatibility and provide a more seamless experience for users working with CHAMBER-generated files.

## IMPORTANT INSTRUCTIONS

1. If you edit a python file, you MUST run 'make PythonInstall' inside the build directory
2. If you edit a c++ file, you MUST run 'make -j4 && make install" inside the build directory

Reference solution:
fix_patch: diff --git a/wrappers/python/openmm/app/amberprmtopfile.py b/wrappers/python/openmm/app/amberprmtopfile.py
index c8021ddb0e..5c6d280da3 100644
--- a/wrappers/python/openmm/app/amberprmtopfile.py
+++ b/wrappers/python/openmm/app/amberprmtopfile.py
@@ -6,7 +6,7 @@
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012 Stanford University and the Authors.
+Portions copyright (c) 2012-2022 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -220,10 +220,6 @@ def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*u.nanome
         System
             the newly created System
         """
-        if self._prmtop.chamber:
-            raise ValueError("CHAMBER-style topology file detected. CHAMBER "
-                             "topologies are not supported -- use the native "
-                             "CHARMM files directly.")
         methodMap = {ff.NoCutoff:'NoCutoff',
                      ff.CutoffNonPeriodic:'CutoffNonPeriodic',
                      ff.CutoffPeriodic:'CutoffPeriodic',
diff --git a/wrappers/python/openmm/app/internal/amber_file_parser.py b/wrappers/python/openmm/app/internal/amber_file_parser.py
index 677cdb77c0..77a2f4d4bf 100644
--- a/wrappers/python/openmm/app/internal/amber_file_parser.py
+++ b/wrappers/python/openmm/app/internal/amber_file_parser.py
@@ -12,7 +12,7 @@
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012-2014 Stanford University and the Authors.
+Portions copyright (c) 2012-2022 Stanford University and the Authors.
 Authors: Randall J. Radmer, John D. Chodera, Peter Eastman
 Contributors: Christoph Klein, Michael R. Shirts, Jason Swails, Kye Won Wang
 
@@ -42,7 +42,7 @@
 
 import os
 import re
-from math import ceil, cos, sin, asin, sqrt
+from math import ceil, cos, sin, asin, sqrt, pi
 import warnings
 
 try:
@@ -128,10 +128,6 @@ def __init__(self, inFilename):
                         tag, self._prmtopVersion = line.rstrip().split(None, 1)
                     elif line.startswith('%FLAG'):
                         tag, flag = line.rstrip().split(None, 1)
-                        if flag == 'CTITLE':
-                            raise TypeError('CHAMBER-style topology files are not supported here. '
-                                            'Consider using the CHARMM files directly with CharmmPsfFile '
-                                            'or ParmEd (where CHAMBER topologies are supported)')
                         self._flags.append(flag)
                         self._raw_data[flag] = []
                     elif line.startswith('%FORMAT'):
@@ -139,8 +135,12 @@ def __init__(self, inFilename):
                         index0=format.index('(')
                         index1=format.index(')')
                         format = format[index0+1:index1]
-                        m = FORMAT_RE_PATTERN.search(format)
-                        self._raw_format[self._flags[-1]] = (format, m.group(1), m.group(2), int(m.group(3)), m.group(4))
+                        try:
+                            m = FORMAT_RE_PATTERN.search(format)
+                            self._raw_format[self._flags[-1]] = (format, m.group(1), m.group(2), int(m.group(3)), m.group(4))
+                        except:
+                            # We couldn't parse the format, so just treat the whole line as a single string.
+                            self._raw_format[self._flags[-1]] = (format, 1, 'a', 80, '')
                     elif line.startswith('%COMMENT'):
                         continue
                 elif self._flags \
@@ -429,6 +429,30 @@ def getAngles(self):
                                 float(angleEquil[iType])))
         return self._angleList
 
+    def getUreyBradleys(self):
+        """Return list of atom pairs, K, and Rmin for each Urey-Bradley term"""
+        try:
+            return self._ureyBradleyList
+        except AttributeError:
+            pass
+        self._ureyBradleyList = []
+        if 'CHARMM_UREY_BRADLEY' in self._raw_data:
+            ureyBradleyPointers = self._raw_data["CHARMM_UREY_BRADLEY"]
+            forceConstant = self._raw_data["CHARMM_UREY_BRADLEY_FORCE_CONSTANT"]
+            equilValue = self._raw_data["CHARMM_UREY_BRADLEY_EQUIL_VALUE"]
+            forceConstConversionFactor = (units.kilocalorie_per_mole/(units.angstrom*units.angstrom)).conversion_factor_to(units.kilojoule_per_mole/(units.nanometer*units.nanometer))
+            lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
+            for ii in range(0, len(ureyBradleyPointers), 3):
+                 if int(ureyBradleyPointers[ii]) < 0 or int(ureyBradleyPointers[ii+1]) < 0:
+                     raise Exception("Found negative Urey-Bradley atom pointers %s"
+                                     % ((ureyBradleyPointers[ii], ureyBradleyPointers[ii+1])))
+                 iType = int(ureyBradleyPointers[ii+2])-1
+                 self._ureyBradleyList.append((int(ureyBradleyPointers[ii])-1,
+                                    int(ureyBradleyPointers[ii+1])-1,
+                                    float(forceConstant[iType])*forceConstConversionFactor,
+                                    float(equilValue[iType])*lengthConversionFactor))
+        return self._ureyBradleyList
+
     def getDihedrals(self):
         """Return list of atom quads, K, phase and periodicity for each dihedral angle"""
         try:
@@ -459,14 +483,45 @@ def getDihedrals(self):
                                 int(0.5+float(periodicity[iType]))))
         return self._dihedralList
 
+    def getImpropers(self):
+        """Return list of atom quads, K, and phase for each improper torsion"""
+        try:
+            return self._improperList
+        except AttributeError:
+            pass
+        self._improperList = []
+        if 'CHARMM_IMPROPERS' in self._raw_data:
+            forceConstant = self._raw_data["CHARMM_IMPROPER_FORCE_CONSTANT"]
+            phase = self._raw_data["CHARMM_IMPROPER_PHASE"]
+            improperPointers = self._raw_data["CHARMM_IMPROPERS"]
+            forceConstConversionFactor = (units.kilocalorie_per_mole).conversion_factor_to(units.kilojoule_per_mole)
+            for ii in range(0,len(improperPointers),5):
+                 if int(improperPointers[ii])<0 or int(improperPointers[ii+1])<0:
+                     raise Exception("Found negative improper atom pointers %s"
+                                     % ((improperPointers[ii],
+                                        improperPointers[ii+1],
+                                        improperPointers[ii+2],
+                                        improperPointers[ii+3]),))
+                 iType = int(improperPointers[ii+4])-1
+                 self._improperList.append((int(improperPointers[ii])-1,
+                                    int(improperPointers[ii+1])-1,
+                                    abs(int(improperPointers[ii+2]))-1,
+                                    abs(int(improperPointers[ii+3]))-1,
+                                    float(forceConstant[iType])*forceConstConversionFactor,
+                                    float(phase[iType])))
+        return self._improperList
+
     def getNumMaps(self):
         """Return number of CMAPs. Return 0 if CMAP does not exist"""
         try:
             return self._numCMAP
         except AttributeError:
             pass
-        if "CMAP_COUNT" in self._raw_data.keys():
-            self._numCMAP=int(self._raw_data["CMAP_COUNT"][1])
+        flag = 'CMAP_COUNT'
+        if flag not in self._raw_data and self.chamber:
+            flag = 'CHARMM_CMAP_COUNT'
+        if flag in self._raw_data:
+            self._numCMAP = int(self._raw_data[flag][1])
             return self._numCMAP
         return 0
 
@@ -476,14 +531,19 @@ def getCMAPResolutions(self):
             return self._cmapResolution
         except AttributeError:
             pass
-        if "CMAP_RESOLUTION" in self._raw_data.keys():
-            self._cmapResolution=self._raw_data["CMAP_RESOLUTION"]
+        flag = 'CMAP_RESOLUTION'
+        if flag not in self._raw_data and self.chamber:
+            flag = 'CHARMM_CMAP_RESOLUTION'
+        if flag in self._raw_data:
+            self._cmapResolution=self._raw_data[flag]
             return self._cmapResolution
         return 0
 
     def getCMAPParameters(self, index):
         """Return list of CMAP energy values"""
-        flag="CMAP_PARAMETER_{:02d}".format(index)
+        flag = "CMAP_PARAMETER_{:02d}".format(index)
+        if flag not in self._raw_data and self.chamber:
+            flag = "CHARMM_CMAP_PARAMETER_{:02d}".format(index)
         return [float(pointer) for pointer in self._raw_data[flag]]
 
     def getCMAPDihedrals(self):
@@ -492,7 +552,10 @@ def getCMAPDihedrals(self):
             return self._cmapList
         except AttributeError:
             pass
-        cmapPointers = self._raw_data["CMAP_INDEX"]
+        flag = 'CMAP_INDEX'
+        if flag not in self._raw_data and self.chamber:
+            flag = 'CHARMM_CMAP_INDEX'
+        cmapPointers = self._raw_data[flag]
         self._cmapList=[]
         forceConstConversionFactor = (units.kilocalorie_per_mole).conversion_factor_to(units.kilojoule_per_mole)
         for ii in range(0,len(cmapPointers),6):
@@ -521,68 +584,45 @@ def get14Interactions(self):
                           +self._raw_data["DIHEDRALS_WITHOUT_HYDROGEN"]
         returnList=[]
         charges=self.getCharges()
-        try:
-            nonbondTerms = self.getNonbondTerms()
-        except NbfixPresent:
-            # We need to do the unit conversions here, since getNonbondTerms
-            # never finished and it has unit conversions in there
-            length_conv = units.angstrom.conversion_factor_to(units.nanometers)
-            ene_conv = units.kilocalories_per_mole.conversion_factor_to(
-                                units.kilojoules_per_mole)
+        length_conv = units.angstrom.conversion_factor_to(units.nanometers)
+        ene_conv = units.kilocalories_per_mole.conversion_factor_to(
+                            units.kilojoules_per_mole)
+        if self.chamber:
+            parm_acoef = [float(x) for x in self._raw_data['LENNARD_JONES_14_ACOEF']]
+            parm_bcoef = [float(x) for x in self._raw_data['LENNARD_JONES_14_BCOEF']]
+        else:
             parm_acoef = [float(x) for x in self._raw_data['LENNARD_JONES_ACOEF']]
             parm_bcoef = [float(x) for x in self._raw_data['LENNARD_JONES_BCOEF']]
-            nbidx = [int(x) for x in self._raw_data['NONBONDED_PARM_INDEX']]
-            numTypes = self.getNumTypes()
-            atomTypeIndexes=self._getAtomTypeIndexes()
-            for ii in range(0, len(dihedralPointers), 5):
-                if int(dihedralPointers[ii+2])>0 and int(dihedralPointers[ii+3])>0:
-                    iAtom = int(dihedralPointers[ii])//3
-                    lAtom = int(dihedralPointers[ii+3])//3
-                    iidx = int(dihedralPointers[ii+4]) - 1
-                    chargeProd = charges[iAtom]*charges[lAtom]
-                    typ1 = atomTypeIndexes[iAtom] - 1
-                    typ2 = atomTypeIndexes[lAtom] - 1
-                    idx = nbidx[numTypes*typ1+typ2] - 1
-                    if idx < 0: continue
-                    a = parm_acoef[idx]
-                    b = parm_bcoef[idx]
-                    try:
-                        epsilon = b * b / (4 * a) * ene_conv
-                        rMin = (2 * a / b) ** (1/6.0) * length_conv
-                    except ZeroDivisionError:
-                        rMin = 1
-                        epsilon = 0
-                    try:
-                        iScee = float(self._raw_data['SCEE_SCALE_FACTOR'][iidx])
-                    except KeyError:
-                        iScee = 1.2
-                    try:
-                        iScnb = float(self._raw_data['SCNB_SCALE_FACTOR'][iidx])
-                    except KeyError:
-                        iScnb = 2.0
-                    returnList.append((iAtom, lAtom, chargeProd, rMin, epsilon, iScee, iScnb))
-        else:
-            # This block gets hit if NbfixPresent is _not_ caught
-            for ii in range(0,len(dihedralPointers),5):
-                if int(dihedralPointers[ii+2])>0 and int(dihedralPointers[ii+3])>0:
-                    iAtom = int(dihedralPointers[ii])//3
-                    lAtom = int(dihedralPointers[ii+3])//3
-                    iidx = int(dihedralPointers[ii+4]) - 1
-                    chargeProd = charges[iAtom]*charges[lAtom]
-                    (rVdwI, epsilonI) = nonbondTerms[iAtom]
-                    (rVdwL, epsilonL) = nonbondTerms[lAtom]
-                    rMin = (rVdwI+rVdwL)
-                    epsilon = sqrt(epsilonI*epsilonL)
-                    try:
-                        iScee = float(self._raw_data["SCEE_SCALE_FACTOR"][iidx])
-                    except KeyError:
-                        iScee = 1.2
-                    try:
-                        iScnb = float(self._raw_data["SCNB_SCALE_FACTOR"][iidx])
-                    except KeyError:
-                        iScnb = 2.0
-
-                    returnList.append((iAtom, lAtom, chargeProd, rMin, epsilon, iScee, iScnb))
+        nbidx = [int(x) for x in self._raw_data['NONBONDED_PARM_INDEX']]
+        numTypes = self.getNumTypes()
+        atomTypeIndexes=self._getAtomTypeIndexes()
+        for ii in range(0, len(dihedralPointers), 5):
+            if int(dihedralPointers[ii+2])>0 and int(dihedralPointers[ii+3])>0:
+                iAtom = int(dihedralPointers[ii])//3
+                lAtom = int(dihedralPointers[ii+3])//3
+                iidx = int(dihedralPointers[ii+4]) - 1
+                chargeProd = charges[iAtom]*charges[lAtom]
+                typ1 = atomTypeIndexes[iAtom] - 1
+                typ2 = atomTypeIndexes[lAtom] - 1
+                idx = nbidx[numTypes*typ1+typ2] - 1
+                if idx < 0: continue
+                a = parm_acoef[idx]
+                b = parm_bcoef[idx]
+                try:
+                    epsilon = b * b / (4 * a) * ene_conv
+                    rMin = (2 * a / b) ** (1/6.0) * length_conv
+                except ZeroDivisionError:
+                    rMin = 1
+                    epsilon = 0
+                try:
+                    iScee = float(self._raw_data['SCEE_SCALE_FACTOR'][iidx])
+                except KeyError:
+                    iScee = 1.0 if self.chamber else 1.2
+                try:
+                    iScnb = float(self._raw_data['SCNB_SCALE_FACTOR'][iidx])
+                except KeyError:
+                    iScnb = 1.0 if self.chamber else 2.0
+                returnList.append((iAtom, lAtom, chargeProd, rMin, epsilon, iScee, iScnb))
         return returnList
 
     def getExcludedAtoms(self):
@@ -750,6 +790,15 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
         for (iAtom, jAtom, k, rMin) in prmtop.getBondsNoH():
             force.addBond(iAtom, jAtom, rMin, 2*k)
     system.addForce(force)
+    
+    # Add Urey-Bradley terms.
+    if len(prmtop.getUreyBradleys()) > 0:
+        if verbose: print("Adding Urey-Bradley terms...")
+        force = mm.HarmonicBondForce()
+        force.setName('UreyBradleyForce')
+        for (iAtom, jAtom, k, rMin) in prmtop.getUreyBradleys():
+            force.addBond(iAtom, jAtom, rMin, 2*k)
+        system.addForce(force)
 
     # Add harmonic angles.
     if verbose: print("Adding angles...")
@@ -796,6 +845,17 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
         force.addTorsion(iAtom, jAtom, kAtom, lAtom, periodicity, phase, forceConstant)
     system.addForce(force)
 
+    # Add impropers.
+    if len(prmtop.getImpropers()) > 0:
+        if verbose: print("Adding impropers...")
+        force = mm.CustomTorsionForce(f'k*min(dtheta, 2*{pi}-dtheta)^2; dtheta = abs(theta-theta0)')
+        force.addPerTorsionParameter('k')
+        force.addPerTorsionParameter('theta0')
+        force.setName('ImproperTorsionForce')
+        for (iAtom, jAtom, kAtom, lAtom, forceConstant, phase) in prmtop.getImpropers():
+            force.addTorsion(iAtom, jAtom, kAtom, lAtom, (forceConstant, phase))
+        system.addForce(force)
+
     # Add CMAP info.
     ## Get mapSize and Resolutions
     numMap = prmtop.getNumMaps()