added test for scaled 1-4 LJ

wrappers/python/tests/TestForceField.py

@@ -539,9 +539,12 @@ class AmoebaTestForceField(unittest.TestCase):
     def test_LennardJones_generator(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')
+        psf = CharmmPsfFile('systems/methanol_ions.psf')
+        pdb = PDBFile('systems/methanol_ions.pdb')
+        params = CharmmParameterSet('systems/top_all36_cgenff.rtf',
+                                    'systems/par_all36_cgenff.prm',
+                                    'systems/toppar_water_ions.str'
+                                    )
 
         # Box dimensions (found from bounding box)
         psf.setBox(12.009*angstroms,   12.338*angstroms,   11.510*angstroms)
@@ -562,10 +565,27 @@ class AmoebaTestForceField(unittest.TestCase):
         xml = """
 <ForceField>
  <AtomTypes>
+  <Type name="CG331" class="CG331" element="C" mass="12.011"/>
+  <Type name="OG311" class="OG311" element="O" mass="15.9994"/>
+  <Type name="HGP1" class="HGP1" element="H" mass="1.008"/>
+  <Type name="HGA3" class="HGA3" element="H" mass="1.008"/>
   <Type name="SOD" class="SOD" element="Na" mass="22.98977"/>
   <Type name="CLA" class="CLA" element="Cl" mass="35.45"/>
  </AtomTypes>
  <Residues>
+  <Residue name="MEOH">
+   <Atom name="CB" type="CG331" charge="0.0"/>
+   <Atom name="OG" type="OG311" charge="0.0"/>
+   <Atom name="HG1" type="HGP1" charge="0.0"/>
+   <Atom name="HB1" type="HGA3" charge="0.0"/>
+   <Atom name="HB2" type="HGA3" charge="0.0"/>
+   <Atom name="HB3" type="HGA3" charge="0.0"/>
+   <Bond atomName1="CB" atomName2="OG"/>
+   <Bond atomName1="OG" atomName2="HG1"/>
+   <Bond atomName1="CB" atomName2="HB1"/>
+   <Bond atomName1="CB" atomName2="HB2"/>
+   <Bond atomName1="CB" atomName2="HB3"/>
+  </Residue>
   <Residue name="CLA">
    <Atom name="CLA" type="CLA" charge="0.0"/>
   </Residue>
@@ -573,18 +593,42 @@ class AmoebaTestForceField(unittest.TestCase):
    <Atom name="SOD" type="SOD" charge="0.0"/>
   </Residue>
  </Residues>
+ <HarmonicBondForce>
+  <Bond type1="CG331" type2="OG311" length="0.142" k="358150.4"/>
+  <Bond type1="CG331" type2="HGA3" length="0.1111" k="269449.6"/>
+  <Bond type1="OG311" type2="HGP1" length="0.096" k="456056.0"/>
+ </HarmonicBondForce>
+ <HarmonicAngleForce>
+  <Angle type1="HGA3" type2="CG331" type3="HGA3" angle="1.89193690916" k="297.064"/>
+  <Angle type1="CG331" type2="OG311" type3="HGP1" angle="1.85004900711" k="481.16"/>
+  <Angle type1="OG311" type2="CG331" type3="HGA3" angle="1.9004890225" k="384.0912"/>
+ </HarmonicAngleForce>
+ <!-- Urey-Bradley terms -->
+ <AmoebaUreyBradleyForce>
+  <UreyBradley type1="HGA3" type2="CG331" type3="HGA3" d="0.1802" k="2259.36"/>
+ </AmoebaUreyBradleyForce>
+ <PeriodicTorsionForce>
+  <Proper type1="HGA3" type2="CG331" type3="OG311" type4="HGP1" periodicity1="3" phase1="0.0" k1="0.75312"/>
+ </PeriodicTorsionForce>
  <NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
   <UseAttributeFromResidue name="charge"/>
+  <Atom type="CG331" sigma="1.0" epsilon="0.0"/>
+  <Atom type="OG311" sigma="1.0" epsilon="0.0"/>
+  <Atom type="HGP1" sigma="1.0" epsilon="0.0"/>
+  <Atom type="HGA3" sigma="1.0" epsilon="0.0"/>
   <Atom type="SOD" sigma="1.0" epsilon="0.0"/>
   <Atom type="CLA" sigma="1.0" epsilon="0.0"/>
  </NonbondedForce>
  <LennardJonesForce lj14scale="1.0">
+  <Atom type="CG331" sigma="0.365268474438" epsilon="0.326352"/>
+  <Atom type="OG311" sigma="0.314487247504" epsilon="0.8037464"/>
+  <Atom type="HGP1" sigma="0.0400013524445" epsilon="0.192464"/>
+  <Atom type="HGA3" sigma="0.238760856462" epsilon="0.100416"/>
   <Atom type="CLA" sigma="0.404468018036" epsilon="0.6276"/>
   <Atom type="SOD" sigma="0.251367073323" epsilon="0.1962296"/>
   <NBFixPair type1="CLA" type2="SOD" emin="0.350933" rmin="0.3731"/>
  </LennardJonesForce>
 </ForceField> """
-
         ff = ForceField(StringIO(xml))
         system2 = ff.createSystem(pdb.topology, nonbondedMethod=PME,
                                   nonbondedCutoff=5*angstroms)

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
+