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Commit 8c85cdce authored by ChayaSt's avatar ChayaSt
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added test for scaled 1-4 LJ

parent 30cd2c16
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Showing with 37405 additions and 4 deletions
wrappers/python/tests/TestForceField.py
View file @ 8c85cdce
...@@ -539,9 +539,12 @@ class AmoebaTestForceField(unittest.TestCase): ...@@ -539,9 +539,12 @@ class AmoebaTestForceField(unittest.TestCase):
def test_LennardJones_generator(self): def test_LennardJones_generator(self):
""" Test the LennardJones generator""" """ Test the LennardJones generator"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning) warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/ions.psf') psf = CharmmPsfFile('systems/methanol_ions.psf')
pdb = PDBFile('systems/ions.pdb') pdb = PDBFile('systems/methanol_ions.pdb')
params = CharmmParameterSet('systems/toppar_water_ions.str') params = CharmmParameterSet('systems/top_all36_cgenff.rtf',
'systems/par_all36_cgenff.prm',
'systems/toppar_water_ions.str'
)
# Box dimensions (found from bounding box) # Box dimensions (found from bounding box)
psf.setBox(12.009*angstroms, 12.338*angstroms, 11.510*angstroms) psf.setBox(12.009*angstroms, 12.338*angstroms, 11.510*angstroms)
...@@ -562,10 +565,27 @@ class AmoebaTestForceField(unittest.TestCase): ...@@ -562,10 +565,27 @@ class AmoebaTestForceField(unittest.TestCase):
xml = """ xml = """
<ForceField> <ForceField>
<AtomTypes> <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="SOD" class="SOD" element="Na" mass="22.98977"/>
<Type name="CLA" class="CLA" element="Cl" mass="35.45"/> <Type name="CLA" class="CLA" element="Cl" mass="35.45"/>
</AtomTypes> </AtomTypes>
<Residues> <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"> <Residue name="CLA">
<Atom name="CLA" type="CLA" charge="0.0"/> <Atom name="CLA" type="CLA" charge="0.0"/>
</Residue> </Residue>
...@@ -573,18 +593,42 @@ class AmoebaTestForceField(unittest.TestCase): ...@@ -573,18 +593,42 @@ class AmoebaTestForceField(unittest.TestCase):
<Atom name="SOD" type="SOD" charge="0.0"/> <Atom name="SOD" type="SOD" charge="0.0"/>
</Residue> </Residue>
</Residues> </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"> <NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge"/> <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="SOD" sigma="1.0" epsilon="0.0"/>
<Atom type="CLA" sigma="1.0" epsilon="0.0"/> <Atom type="CLA" sigma="1.0" epsilon="0.0"/>
</NonbondedForce> </NonbondedForce>
<LennardJonesForce lj14scale="1.0"> <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="CLA" sigma="0.404468018036" epsilon="0.6276"/>
<Atom type="SOD" sigma="0.251367073323" epsilon="0.1962296"/> <Atom type="SOD" sigma="0.251367073323" epsilon="0.1962296"/>
<NBFixPair type1="CLA" type2="SOD" emin="0.350933" rmin="0.3731"/> <NBFixPair type1="CLA" type2="SOD" emin="0.350933" rmin="0.3731"/>
</LennardJonesForce> </LennardJonesForce>
</ForceField> """ </ForceField> """
ff = ForceField(StringIO(xml)) ff = ForceField(StringIO(xml))
system2 = ff.createSystem(pdb.topology, nonbondedMethod=PME, system2 = ff.createSystem(pdb.topology, nonbondedMethod=PME,
nonbondedCutoff=5*angstroms) nonbondedCutoff=5*angstroms)
......
wrappers/python/tests/systems/methanol_ions.pdb 0 → 100644
View file @ 8c85cdce
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 0 → 100644
View file @ 8c85cdce
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
wrappers/python/tests/systems/par_all36_cgenff.prm 0 → 100644
View file @ 8c85cdce
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wrappers/python/tests/systems/top_all36_cgenff.rtf 0 → 100644
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