Skip to content

GitLab

"vscode:/vscode.git/clone" did not exist on "aac64ddaea91f6d342566c5a47cfb53c487eb769"
Commit 12fa5430 authored by peastman's avatar peastman
Browse files

Use correct parameters for nucleic acids with GBn2

parent 7f87c446
Hide whitespace changes
Inline Side-by-side
Showing with 3858 additions and 19 deletions
wrappers/python/simtk/openmm/app/data/pdbNames.xml
View file @ 12fa5430
...@@ -239,19 +239,19 @@ ...@@ -239,19 +239,19 @@
<Atom name="HN2" alt1="2H" alt2="HT2" alt3="H2"/> <Atom name="HN2" alt1="2H" alt2="HT2" alt3="H2"/>
</Residue> </Residue>
<Residue name="UNK" type="Protein"/> <Residue name="UNK" type="Protein"/>
<Residue name="A" alt1="ADE" type="Nucleic"> <Residue name="A" alt1="ADE" alt2="A3" alt3="A5" type="Nucleic">
<Atom name="H61" alt1="1H6"/> <Atom name="H61" alt1="1H6"/>
<Atom name="H62" alt1="2H6"/> <Atom name="H62" alt1="2H6"/>
</Residue> </Residue>
<Residue name="G" alt1="GUA" type="Nucleic"> <Residue name="G" alt1="GUA" alt2="G3" alt3="G5" type="Nucleic">
<Atom name="H21" alt1="1H2"/> <Atom name="H21" alt1="1H2"/>
<Atom name="H22" alt1="2H2"/> <Atom name="H22" alt1="2H2"/>
</Residue> </Residue>
<Residue name="C" alt1="CYT" type="Nucleic"> <Residue name="C" alt1="CYT" alt2="C3" alt3="C5" type="Nucleic">
<Atom name="H41" alt1="1H4"/> <Atom name="H41" alt1="1H4"/>
<Atom name="H42" alt1="2H4"/> <Atom name="H42" alt1="2H4"/>
</Residue> </Residue>
<Residue name="U" alt1="URA" type="Nucleic"/> <Residue name="U" alt1="URA" alt2="U3" alt3="U5" type="Nucleic"/>
<Residue name="DA" alt1="DAD" alt2="DA3" alt3="DA5" type="Nucleic"> <Residue name="DA" alt1="DAD" alt2="DA3" alt3="DA5" type="Nucleic">
<Atom name="H61" alt1="1H6"/> <Atom name="H61" alt1="1H6"/>
<Atom name="H62" alt1="2H6"/> <Atom name="H62" alt1="2H6"/>
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 12fa5430
...@@ -389,18 +389,20 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k ...@@ -389,18 +389,20 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions) "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
_SCREEN_PARAMETERS = { # normal, GBn, GBn2 _SCREEN_PARAMETERS = { # normal, GBn, GBn2, GBn2 nucleic
E.hydrogen : (0.85, 1.09085413633, 1.425952), E.hydrogen : (0.85, 1.09085413633, 1.425952, 1.696538),
E.carbon : (0.72, 0.48435382330, 1.058554), E.carbon : (0.72, 0.48435382330, 1.058554, 1.268902),
E.nitrogen : (0.79, 0.700147318409, 0.733599), E.nitrogen : (0.79, 0.700147318409, 0.733599, 1.4259728),
E.oxygen : (0.85, 1.06557401132, 1.061039), E.oxygen : (0.85, 1.06557401132, 1.061039, 0.1840098),
E.fluorine : (0.88, 0.5, 0.5), E.fluorine : (0.88, 0.5, 0.5, 0.5),
E.phosphorus : (0.86, 0.5, 0.5), E.phosphorus : (0.86, 0.5, 0.5, 1.5450597),
E.sulfur : (0.96, 0.602256336067, -0.703469), E.sulfur : (0.96, 0.602256336067, -0.703469, 0.05),
None : (0.8, 0.5, 0.5) # default None : (0.8, 0.5, 0.5, 0.5) # default
} }
_SCREEN_PARAMETERS[E.deuterium] = _SCREEN_PARAMETERS[E.hydrogen] _SCREEN_PARAMETERS[E.deuterium] = _SCREEN_PARAMETERS[E.hydrogen]
_NUCLEIC_ACID_RESIDUES = ['A', 'C', 'G', 'U', 'DA', 'DC', 'DG', 'DT']
def _screen_parameter(atom): def _screen_parameter(atom):
return _SCREEN_PARAMETERS.get(atom.element, _SCREEN_PARAMETERS[None]) return _SCREEN_PARAMETERS.get(atom.element, _SCREEN_PARAMETERS[None])
...@@ -873,7 +875,16 @@ class GBSAGBn2Force(GBSAGBnForce): ...@@ -873,7 +875,16 @@ class GBSAGBn2Force(GBSAGBnForce):
E.oxygen: [0.867814, 0.876635, 0.387882], E.oxygen: [0.867814, 0.876635, 0.387882],
E.sulfur: [0.867814, 0.876635, 0.387882], E.sulfur: [0.867814, 0.876635, 0.387882],
} }
_default_atom_params = [0.8, 4.85, 0.5] _atom_params_nucleic = {
E.hydrogen: [0.537050, 0.362861, 0.116704],
E.deuterium: [0.537050, 0.362861, 0.116704],
E.carbon: [0.331670, 0.196842, 0.093422],
E.nitrogen: [0.686311, 0.463189, 0.138722],
E.oxygen: [0.606344, 0.463006, 0.142262],
E.sulfur: [0.606344, 0.463006, 0.142262],
E.phosphorus: [0.418365, 0.290054, 0.1064245],
}
_default_atom_params = [1.0, 0.8, 4.851]
@classmethod @classmethod
def getStandardParameters(cls, topology): def getStandardParameters(cls, topology):
...@@ -897,14 +908,23 @@ class GBSAGBn2Force(GBSAGBnForce): ...@@ -897,14 +908,23 @@ class GBSAGBn2Force(GBSAGBnForce):
radii = numpy.empty([natoms,5], numpy.double) radii = numpy.empty([natoms,5], numpy.double)
radii[:,0] = _mbondi3_radii(topology)/10 radii[:,0] = _mbondi3_radii(topology)/10
for atom, rad in zip(topology.atoms(), radii): for atom, rad in zip(topology.atoms(), radii):
rad[1] = _screen_parameter(atom)[2] if atom.residue.name in _NUCLEIC_ACID_RESIDUES:
rad[2:] = cls._atom_params.get(atom.element, cls._default_atom_params) rad[1] = _screen_parameter(atom)[3]
rad[2:] = cls._atom_params_nucleic.get(atom.element, cls._default_atom_params)
else:
rad[1] = _screen_parameter(atom)[2]
rad[2:] = cls._atom_params.get(atom.element, cls._default_atom_params)
else: else:
radii = [[r/10, 0, 0, 0, 0] for r in _mbondi3_radii(topology)] radii = [[r/10, 0, 0, 0, 0] for r in _mbondi3_radii(topology)]
for atom, rad in zip(topology.atoms(), radii): for atom, rad in zip(topology.atoms(), radii):
rad[1] = _screen_parameter(atom)[2] if atom.residue.name in _NUCLEIC_ACID_RESIDUES:
for i, p in enumerate(cls._atom_params.get(atom.element, cls._default_atom_params)): rad[1] = _screen_parameter(atom)[3]
rad[2+i] = p for i, p in enumerate(cls._atom_params_nucleic.get(atom.element, cls._default_atom_params)):
rad[2+i] = p
else:
rad[1] = _screen_parameter(atom)[2]
for i, p in enumerate(cls._atom_params.get(atom.element, cls._default_atom_params)):
rad[2+i] = p
return radii return radii
def _addEnergyTerms(self): def _addEnergyTerms(self):
......
wrappers/python/tests/TestAmberPrmtopFile.py
View file @ 12fa5430
...@@ -384,5 +384,21 @@ class TestAmberPrmtopFile(unittest.TestCase): ...@@ -384,5 +384,21 @@ class TestAmberPrmtopFile(unittest.TestCase):
self.assertRaises(ValueError, lambda: f.addParticle([0, 0.9, 0.5])) self.assertRaises(ValueError, lambda: f.addParticle([0, 0.9, 0.5]))
self.assertRaises(ValueError, lambda: f.addParticle([0, 0.21, 0.5])) self.assertRaises(ValueError, lambda: f.addParticle([0, 0.21, 0.5]))
def testNucleicGBParametes(self):
"""Test that correct GB parameters are used for nucleic acids."""
prmtop = AmberPrmtopFile('systems/DNA_mbondi3.prmtop')
inpcrd = AmberInpcrdFile('systems/DNA_mbondi3.inpcrd')
sanderEnergy = [-19223.87993545, -19527.40433175, -19788.1070698]
for solvent, expectedEnergy in zip([OBC2, GBn, GBn2], sanderEnergy):
system = prmtop.createSystem(implicitSolvent=solvent, gbsaModel=None)
for f in system.getForces():
if isinstance(f, CustomGBForce) or isinstance(f, GBSAOBCForce):
f.setForceGroup(1)
integrator = VerletIntegrator(0.001)
context = Context(system, integrator, Platform.getPlatformByName('Reference'))
context.setPositions(inpcrd.positions)
energy = context.getState(getEnergy=True, groups={1}).getPotentialEnergy().value_in_unit(kilojoules_per_mole)
self.assertAlmostEqual(energy, expectedEnergy, delta=5e-4*abs(energy))
if __name__ == '__main__': if __name__ == '__main__':
unittest.main() unittest.main()
wrappers/python/tests/systems/DNA_mbondi3.inpcrd 0 → 100644
View file @ 12fa5430
default_name
628
-1.0164436 9.7204202 -1.3496514 -1.5620000 8.9700000 -1.1030000
-2.3800000 8.3410000 -2.1080000 -1.7179782 7.9601325 -2.8856681
-3.0821711 9.0510193 -2.5449544 -3.1520000 7.1860000 -1.5010000
-4.0109994 7.0112223 -2.1488220 -2.4040000 5.9370000 -1.5420000
-2.4650000 5.3370000 -0.2560000 -3.3042020 4.6425056 -0.2170330
-1.2970000 4.4760000 -0.1030000 0.0080000 4.8710000 0.0720000
0.2697674 5.9181807 0.1079058 0.8370000 3.8690000 0.1800000
0.0320000 2.7420000 0.0700000 0.3670000 1.3650000 0.1110000
1.4810000 0.8470000 0.2580000 -0.7570000 0.5590000 -0.0400000
-0.6224177 -0.4317938 -0.0253663 -2.0390000 1.0200000 -0.2090000
-2.9910000 0.0830000 -0.3390000 -2.8621932 -0.9187515 -0.3370285
-3.9355033 0.4149725 -0.4724460 -2.3650000 2.3010000 -0.2490000
-1.2880000 3.1010000 -0.1050000 -3.5320000 7.3410000 -0.0280000
-3.5123763 8.3641638 0.3473002 -2.5000000 6.5010000 0.7270000
-1.7984795 7.1599851 1.2385736 -3.0074918 5.8728140 1.4590750
-4.8180000 6.7680000 0.1780000 -5.8420000 7.9490000 1.9600000
-6.6600000 9.0120000 1.3350000 -5.0280000 8.3570000 3.1270000
-6.7800000 6.7170000 2.3660000 -7.0690000 5.7060000 1.3810000
-6.3331501 5.7993265 0.5823041 -8.0811551 5.8464212 1.0016260
-6.9570000 4.3290000 2.0030000 -7.5464700 3.6571448 1.3791130
-5.6030000 3.7970000 1.9340000 -5.2520000 3.3030000 3.2170000
-5.4904599 2.2410471 3.2760949 -3.7870000 3.3370000 3.3330000
-3.1070000 4.5160000 3.4680000 -3.6473914 5.4507935 3.4911987
-1.7720000 4.5350000 3.5730000 -1.2564625 5.4892729 3.6810955
-1.0930000 3.2840000 3.5380000 0.2390000 3.2410000 3.6390000
0.6830222 2.3343046 3.6098747 0.7696948 4.0943254 3.7404903
-1.7470000 2.1280000 3.4070000 -3.0960000 2.1240000 3.3020000
-3.7380000 1.0700000 3.1790000 -7.3140000 4.2390000 3.4870000
-7.9144987 5.0655961 3.8667881 -5.9660000 4.2150000 4.2080000
-5.8013377 5.1717774 4.7035427 -5.9646181 3.4169155 4.9504011
-7.9760000 3.0020000 3.7260000 -9.3240000 3.6410000 5.5670000
-10.6180000 4.0540000 4.9780000 -8.8450000 4.4470000 6.7120000
-9.3940000 2.0990000 5.9870000 -9.0950000 1.0920000 5.0010000
-8.5645733 1.5750459 4.1803818 -10.0221846 0.6359194 4.6539843
-8.2090000 0.0210000 5.6050000 -8.3371874 -0.8716110 4.9926986
-6.7920000 0.3430000 5.4890000 -6.1840000 0.1430000 6.7560000
-5.7825725 -0.8688055 6.8126118 -4.9970000 0.9900000 6.8270000
-4.9620000 2.3590000 6.9540000 -5.8738631 2.9347696 7.0122840
-3.7490000 2.8380000 6.9900000 -2.9320000 1.7200000 6.8820000
-1.5190000 1.6120000 6.8620000 -0.6760000 2.5140000 6.9410000
-1.1070000 0.2890000 6.7370000 -0.1234970 0.1097499 6.7127162
-1.9490000 -0.7920000 6.6430000 -1.3590000 -1.9920000 6.5270000
-0.3674884 -2.1808308 6.4902842 -1.9723579 -2.7905925 6.4486228
-3.2680000 -0.7050000 6.6600000 -3.6890000 0.5710000 6.7800000
-8.4060000 -0.2410000 7.0990000 -9.3552262 0.1077726 7.5057261
-7.2560000 0.5040000 7.7780000 -7.6426972 1.3919120 8.2781767
-6.7826230 -0.1485106 8.5116513 -8.2500000 -1.6340000 7.3450000
-9.6070000 -2.1800000 9.2120000 -10.8980000 -2.6490000 8.6600000
-9.6900000 -1.2400000 10.3520000 -8.7080000 -3.4390000 9.6190000
-7.8820000 -4.0610000 8.6160000 -7.7790523 -3.3607937 7.7870170
-8.3458037 -4.9914356 8.2884694 -6.5110000 -4.3620000 9.1870000
-6.0834186 -5.1516884 8.5692090 -5.5900000 -3.2430000 9.0380000
-4.9540000 -3.0190000 10.2870000 -4.0159596 -3.5729975 10.3225840
-4.5290000 -1.6130000 10.3360000 -5.4320000 -0.5960000 10.4780000
-6.4857431 -0.8189733 10.5574249 -5.0340000 0.6810000 10.5210000
-5.7773556 1.4699821 10.6351496 -3.6370000 0.9380000 10.4140000
-3.1800000 2.1930000 10.4520000 -2.1827618 2.3321121 10.3728525
-3.8219922 2.9656474 10.5567060 -2.7460000 -0.0470000 10.2750000
-3.1640000 -1.3330000 10.2330000 -2.3670000 -2.2750000 10.1060000
-6.4670000 -4.6780000 10.6830000 -7.4205169 -4.9791591 11.1168290
-5.9960000 -3.3800000 11.3390000 -6.8317655 -2.9103316 11.8576587
-5.2031228 -3.6004128 12.0537476 -5.4860000 -5.6830000 10.9120000
-6.4270000 -6.7010000 12.8340000 -7.2460000 -7.8220000 12.3190000
-6.9920000 -5.9560000 13.9810000 -4.9650000 -7.2320000 13.2060000
-3.9610000 -7.2940000 12.1750000 -4.2932710 -6.6675165 11.3472232
-3.8302188 -8.3281013 11.8562031 -2.6420000 -6.7650000 12.7020000
-1.8616519 -7.1849960 12.0673666 -2.5150000 -5.3230000 12.5310000
-2.0790000 -4.7640000 13.7610000 -0.9912566 -4.6939661 13.7639629
-2.5150000 -3.3710000 13.8040000 -3.7980000 -2.9090000 13.9740000
-4.6238576 -3.5945880 14.0937095 -3.8770000 -1.6060000 13.9690000
-2.5680000 -1.1810000 13.7860000 -2.0290000 0.1270000 13.6980000
-2.6220000 1.2110000 13.7670000 -0.6510000 0.1040000 13.5110000
-0.1778738 0.9819332 13.4376278 0.1120000 -1.0350000 13.4200000
1.4290000 -0.8510000 13.2380000 1.9130654 0.0310652 13.1500112
1.9946079 -1.6842686 13.1615015 -0.3780000 -2.2610000 13.5020000
-1.7150000 -2.2610000 13.6830000 -2.3860000 -6.9830000 14.1940000
-2.9923453 -7.7621770 14.6558738 -2.7070000 -5.6350000 14.8430000
-3.6473613 -5.7088956 15.3892227 -1.9074376 -5.3634206 15.5322349
-1.0030000 -7.2590000 14.3870000 -0.8220000 -8.6540000 16.2960000
-0.8010000 -10.0440000 15.7900000 -1.6890000 -8.4020000 17.4690000
0.6710000 -8.1770000 16.6200000 1.4720000 -7.6200000 15.5600000
0.8007167 -7.3327300 14.7507073 2.1977505 -8.3608756 15.2246045
2.2070000 -6.3920000 16.0570000 3.0611861 -6.2524930 15.3944268
1.4220000 -5.1740000 15.9020000 1.4630000 -4.4580000 17.1260000
2.2811380 -3.7382382 17.0996860 0.2610000 -3.6150000 17.2010000
-0.9780000 -4.1530000 17.4180000 -1.0888032 -5.2204626 17.5390214
-2.0660000 -3.3760000 17.4840000 -3.0402391 -3.8330400 17.6574154
-1.8830000 -1.9730000 17.3210000 -2.9320000 -1.1480000 17.3780000
-2.7594942 -0.1601674 17.2574630 -3.8597395 -1.5142917 17.5368435
-0.6780000 -1.4380000 17.1090000 0.4130000 -2.2360000 17.0440000
1.5480000 -1.7760000 16.8500000 2.5890000 -6.3980000 17.5370000
2.5993699 -7.3826345 18.0044250 1.5320000 -5.5240000 18.2130000
0.8511530 -6.1537671 18.7856604 2.0197362 -4.8150087 18.8819879
3.8580000 -5.7700000 17.6880000 4.6210000 -6.9150000 19.6170000
5.4090000 -8.0590000 19.1040000 3.7910000 -7.1820000 20.8130000
5.5940000 -5.6790000 19.9030000 5.9170000 -4.7790000 18.8250000
5.1809968 -4.9285318 18.0350383 6.9256405 -4.9864668 18.4676451
5.8450000 -3.3440000 19.3080000 6.4564338 -2.7549869 18.6243980
4.5080000 -2.7820000 19.1780000 4.1670000 -2.1520000 20.4040000
4.4375573 -1.0970298 20.3600010 2.7120000 -2.1310000 20.5130000
1.8830000 -3.2010000 20.7570000 2.2840469 -4.1946171 20.8922346
0.6210000 -2.8710000 20.7980000 0.6140000 -1.5010000 20.5690000
-0.4670000 -0.5860000 20.4980000 -1.6770000 -0.8100000 20.6290000
-0.0260000 0.7090000 20.2470000 -0.7173199 1.4284061 20.1796934
1.2870000 1.0770000 20.0840000 1.5110000 2.3790000 19.8470000
0.8186781 3.1098080 19.7650829 2.4739352 2.6548260 19.7174750
2.3040000 0.2340000 20.1480000 1.8980000 -1.0300000 20.3910000
6.2000000 -3.1180000 20.7780000 6.7736449 -3.9206164 21.2415054
4.8500000 -2.9820000 21.4850000 4.6547319 -3.8793468 22.0721443
4.8703687 -2.1142902 22.1443672 6.8980000 -1.8840000 20.8980000
8.3670000 -2.0770000 22.7490000 9.6710000 -2.5060000 22.1970000
7.9130000 -2.7820000 23.9680000 8.3900000 -0.5000000 23.0190000
8.0600000 0.3980000 21.9420000 7.5434235 -0.1781573 21.1743468
8.9726988 0.8463811 21.5495258 7.1420000 1.4950000 22.4440000
7.2430386 2.3275711 21.7477846 5.7370000 1.1220000 22.3650000
5.1240000 1.4240000 23.6090000 4.6917269 2.4237842 23.5681236
3.9560000 0.5470000 23.7670000 4.0940000 -0.7890000 24.0240000
5.0794757 -1.2212915 24.1154420 3.0220000 -1.5800000 24.1660000
3.1627782 -2.6415980 24.3692030 1.7390000 -0.9760000 24.0400000
0.6340000 -1.7140000 24.1720000 -0.2565303 -1.2473729 24.0754826
0.7023947 -2.7036568 24.3617446 1.5930000 0.3270000 23.7890000
2.6850000 1.1140000 23.6480000 2.5900000 2.3290000 23.4170000
7.3330000 1.9060000 23.9040000 8.2932558 1.6262424 24.3372936
6.2080000 1.1960000 24.6570000 6.6227941 0.3737560 25.2400608
5.7151797 1.9021944 25.3252199 7.1360000 3.3110000 24.0160000
8.5470000 3.7460000 25.8690000 9.8540000 4.1220000 25.2830000
8.5980000 2.9150000 27.0930000 7.6860000 5.0640000 26.1500000
6.8830000 5.6130000 25.0880000 6.7619185 4.8408654 24.3282320
7.3758321 6.4943355 24.6775552 5.5190000 6.0070000 25.6200000
5.1177105 6.7474854 24.9280842 4.5650000 4.9070000 25.5710000
3.9180000 4.8210000 26.8320000 2.9974109 5.4042001 26.8098070
3.4530000 3.4480000 27.0080000 4.2240000 2.3370000 27.2550000
5.2979937 2.4143869 27.3383714 3.5230000 1.2420000 27.3660000
2.2090000 1.6530000 27.1820000 1.0020000 0.9090000 27.1920000
0.8480000 -0.3060000 27.3710000 -0.1030000 1.7200000 26.9620000
-1.0029788 1.2842958 26.9479047 -0.0540000 3.0760000 26.7510000
-1.2320000 3.6860000 26.5460000 -2.1441441 3.2531200 26.5193843
-1.2016531 4.6820544 26.3815140 1.0640000 3.7830000 26.7400000
2.1500000 3.0130000 26.9600000 5.4800000 6.4640000 27.0790000
6.4410063 6.7756753 27.4881750 4.9670000 5.2480000 27.8520000
5.7862036 4.8045434 28.4179956 4.1787377 5.5587771 28.5376824
4.5290000 7.5150000 27.2070000 5.2520000 8.9120000 28.9800000
6.0370000 9.9990000 28.3550000 5.8370000 8.3030000 30.1960000
3.7730000 9.4330000 29.3000000 2.7690000 9.3620000 28.2690000
3.1209393 8.6665679 27.5070204 2.6077636 10.3548903 27.8491520
1.4670000 8.8490000 28.8480000 0.6756813 9.1798251 28.1753420
1.3830000 7.3950000 28.8230000 0.9620000 6.9490000 30.1030000
-0.1231724 6.8471821 30.1145435 1.4420000 5.5720000 30.2870000
2.7660000 5.2970000 30.4930000 3.4857415 6.1016302 30.5236981
3.1920000 4.0380000 30.6590000 4.2527815 3.8488328 30.8234950
2.2160000 3.0030000 30.6120000 2.5810000 1.7280000 30.7720000
1.8578611 1.0240444 30.7317855 3.5506330 1.4916312 30.9270582
0.9210000 3.2600000 30.4120000 0.5050000 4.5370000 30.2460000
-0.6890000 4.8170000 30.0580000 1.2020000 9.2070000 30.3110000
1.7838797 10.0466269 30.6911862 1.5620000 7.9430000 31.0910000
2.4986836 8.0999176 31.6258832 0.7697469 7.7180450 31.8050242
-0.1900000 9.4600000 30.4770000 -0.4556964 9.6945525 31.3691822
-6.4046301 -6.2620556 31.6392957 -6.4310000 -5.3370000 31.3840000
-6.7870000 -4.3500000 32.3710000 -6.0483911 -4.3968665 33.1712256
-7.7783825 -4.5438430 32.7804955 -6.7650000 -2.9660000 31.7530000
-7.3975401 -2.3355782 32.3779495 -5.4480000 -2.3470000 31.8250000
-5.1280000 -1.8260000 30.5440000 -5.4351049 -0.7816994 30.4872226
-3.6740000 -1.7650000 30.4310000 -2.8080000 -2.8230000 30.2900000
-3.1734657 -3.8386036 30.2528125 -1.5580000 -2.4540000 30.2140000
-1.6000000 -1.0690000 30.3110000 -0.5530000 -0.1140000 30.2910000
0.6650000 -0.3070000 30.1800000 -1.0390000 1.1830000 30.4170000
-0.3737792 1.9296378 30.4135087 -2.3640000 1.5180000 30.5460000
-2.6350000 2.8280000 30.6570000 -1.9694813 3.5876610 30.6670586
-3.6074380 3.0802891 30.7609936 -3.3510000 0.6370000 30.5650000
-2.9000000 -0.6290000 30.4450000 -7.1250000 -2.8950000 30.2680000
-7.6694959 -3.7581354 29.8850889 -5.7790000 -2.7810000 29.5490000
-5.5513966 -3.7236220 29.0512445 -5.8284150 -1.9824782 28.8087160
-7.8660000 -1.7040000 30.0310000 -9.3240000 -2.1260000 28.2090000
-10.6130000 -2.5460000 28.8020000 -8.8430000 -2.9290000 27.0630000
-9.4020000 -0.5850000 27.7880000 -9.1060000 0.4240000 28.7740000
-8.5706365 -0.0564898 29.5929112 -10.0348150 0.8751581 29.1230840
-8.2270000 1.4990000 28.1670000 -8.3583910 2.3908738 28.7796964
-6.8090000 1.1850000 28.2790000 -6.2050000 1.3880000 27.0100000
-5.8081139 2.4016434 26.9542540 -5.0060000 0.5410000 26.9360000
-5.0970000 -0.8170000 26.8100000 -6.0666455 -1.2902634 26.7629970
-3.9980000 -1.5800000 26.7430000 -4.1004771 -2.6604591 26.6419710
-2.7370000 -0.9210000 26.8080000 -1.6060000 -1.6290000 26.7450000
-0.7326617 -1.1240981 26.7945471 -1.6390933 -2.6340780 26.6510615
-2.6380000 0.4040000 26.9310000 -3.7570000 1.1620000 26.9970000
-3.7050000 2.3960000 27.1100000 -8.4300000 1.7600000 26.6740000
-9.3784890 1.4060128 26.2700688 -7.2780000 1.0210000 25.9920000
-7.6613283 0.1308192 25.4932648 -6.8102685 1.6757780 25.2567495
-8.2820000 3.1540000 26.4270000 -9.7050000 3.3580000 24.5430000
-11.0250000 3.7430000 25.0920000 -9.7240000 2.4120000 23.4050000
-8.8900000 4.6730000 24.1340000 -8.1080000 5.3500000 25.1370000
-7.9608289 4.6592305 25.9672278 -8.6322331 6.2487977 25.4617199
-6.7580000 5.7390000 24.5670000 -6.3837983 6.5565858 25.1831379
-5.7670000 4.6830000 24.7210000 -5.1140000 4.4980000 23.4730000
-4.2145000 5.1125618 23.4367688 -4.6010000 3.1320000 23.4290000
-5.3320000 1.9760000 23.2920000 -6.4079448 2.0065211 23.2036078
-4.5920000 0.9010000 23.2860000 -3.2940000 1.3740000 23.4270000
-2.0620000 0.6750000 23.4870000 -1.8640000 -0.5450000 23.4250000
-0.9860000 1.5440000 23.6350000 -0.0708497 1.1443558 23.6877542
-1.0840000 2.9110000 23.7150000 0.0720000 3.5790000 23.8580000
0.9987517 3.1829196 23.9239683 0.0065039 4.5845579 23.9262976
-2.2260000 3.5750000 23.6600000 -3.2840000 2.7500000 23.5170000
-6.7330000 6.0540000 23.0710000 -7.7034398 6.2905730 22.6346761
-6.1760000 4.7880000 22.4190000 -6.9780766 4.2626514 21.9005589
-5.3984151 5.0585384 21.7046675 -5.8200000 7.1200000 22.8410000
-6.5880000 8.3140000 20.9420000 -7.4130000 9.4280000 21.4610000
-7.1500000 7.5700000 19.7920000 -5.1290000 8.8540000 20.5710000
-4.1250000 8.9180000 21.6030000 -4.4542527 8.2863168 22.4280267
-3.9995586 9.9517758 21.9249823 -2.8040000 8.3970000 21.0730000
-2.0261643 8.8192075 21.7092482 -2.6690000 6.9560000 21.2390000
-2.2300000 6.4040000 20.0060000 -1.1419076 6.3396911 20.0016951
-2.6610000 5.0000000 19.9570000 -3.9730000 4.6590000 19.7810000
-4.7198686 5.4317572 19.6740728 -4.3550000 3.3770000 19.7380000
-5.4082947 3.1362196 19.5941408 -3.3430000 2.3850000 19.8830000
-3.6630000 1.0890000 19.8470000 -2.9158713 0.4177925 19.9536764
-4.6235298 0.8051847 19.7168737 -2.0580000 2.7070000 20.0550000
-1.6880000 4.0080000 20.0970000 -0.5050000 4.3460000 20.2540000
-2.5490000 8.6220000 19.5820000 -3.1595701 9.4001005 19.1238924
-2.8630000 7.2770000 18.9280000 -3.8035793 7.3487368 18.3818648
-2.0619912 7.0121975 18.2378082 -1.1670000 8.9070000 19.3900000
-1.3270000 10.2600000 17.4510000 -1.3960000 11.6520000 17.9520000
-2.1790000 9.9480000 16.2820000 0.1920000 9.8820000 17.1250000
1.0310000 9.3820000 18.1850000 0.3822746 9.0546490 18.9974633
1.7075788 10.1699368 18.5159038 1.8440000 8.2030000 17.6910000
2.7072575 8.1218541 18.3515309 1.1400000 6.9370000 17.8530000
1.2250000 6.2190000 16.6310000 2.0883952 5.5541782 16.6566894
0.0880000 5.3060000 16.5630000 -1.2300000 5.6370000 16.3530000
-1.5299006 6.6655161 16.2165587 -2.0220000 4.5990000 16.3440000
-1.1780000 3.5180000 16.5610000 -1.4630000 2.1320000 16.6530000
-2.5580000 1.5630000 16.5580000 -0.3120000 1.3850000 16.8790000
-0.4115714 0.3932031 16.9591432 0.9530000 1.9050000 17.0010000
1.9370000 1.0200000 17.2190000 1.8440403 0.0187528 17.3136722
2.8687953 1.3967970 17.3184105 1.2330000 3.1950000 16.9160000
0.1290000 3.9390000 16.6980000 2.2210000 8.2280000 16.2090000
2.1656707 9.2091943 15.7375180 1.2210000 7.2830000 15.5390000
0.4986711 7.8643970 14.9660099 1.7523925 6.6048962 14.8712444
3.5270000 7.6840000 16.0570000 4.5110000 8.7230000 14.1670000
5.2900000 9.8700000 14.6850000 3.6850000 8.9880000 12.9680000
5.4920000 7.4920000 13.8810000 5.8160000 6.5920000 14.9580000
5.0770025 6.7354381 15.7462945 6.8221052 6.8044844 15.3195290
5.7540000 5.1580000 14.4720000 6.3656414 4.5704633 15.1566859
4.4200000 4.5880000 14.5940000 4.0880000 3.9590000 13.3650000
4.3637534 2.9053904 13.4093395 2.6230000 3.9300000 13.2490000
1.9020000 5.0660000 13.0020000 2.4086235 6.0129378 12.8878010
0.5680000 5.0270000 12.8980000 0.0198099 5.9482250 12.7006871
-0.0670000 3.7630000 13.0540000 -1.3960000 3.6630000 12.9600000
-1.8074137 2.7480327 13.0769365 -1.9566545 4.4831257 12.7778962
0.6270000 2.6480000 13.2960000 1.9750000 2.7020000 13.3980000
2.6550000 1.6890000 13.6210000 6.1160000 4.9380000 13.0030000
6.6874275 5.7450600 12.5444987 4.7710000 4.7970000 12.2900000
4.5732851 5.6953120 11.7051550 4.7992372 3.9317695 11.6276715
6.8230000 3.7070000 12.8830000 8.1500000 4.2140000 10.9870000
9.4270000 4.7270000 11.5310000 7.6440000 4.8880000 9.7700000
8.2750000 2.6420000 10.7170000 8.0100000 1.7250000 11.7960000
7.4605582 2.2661289 12.5663203 8.9521082 1.3379241 12.1842074
7.1640000 0.5700000 11.2990000 7.3229233 -0.2540577 11.9945369
5.7370000 0.8510000 11.3860000 5.1380000 0.5080000 10.1450000
4.7724936 -0.5180357 10.1868935 3.9220000 1.3020000 9.9950000
3.8390000 2.6500000 9.7370000 4.7298530 3.2496542 9.6221183
2.6090000 3.0800000 9.6570000 1.8320000 1.9490000 9.8740000
0.4240000 1.7930000 9.9060000 -0.4510000 2.6540000 9.7430000
0.0590000 0.4750000 10.1590000 -0.9176253 0.2641648 10.2008347
0.9380000 -0.5610000 10.3560000 0.3910000 -1.7640000 10.5880000
-0.5932476 -1.9836089 10.6439368 1.0321992 -2.5289225 10.7424606
2.2540000 -0.4300000 10.3280000 2.6300000 0.8430000 10.0850000
7.3730000 0.1720000 9.8380000 8.3097832 0.5141013 9.3981106
6.1980000 0.8060000 9.0920000 6.5534915 1.6542594 8.5070376
5.7492721 0.0687479 8.4262653 7.2670000 -1.2430000 9.7270000
8.6450000 -1.9180000 7.9200000 9.9510000 -2.2850000 8.5120000
8.6970000 -1.0900000 6.6940000 7.7920000 -3.2420000 7.6370000
6.9870000 -3.7930000 8.6970000 6.8585988 -3.0194037 9.4540746
7.4825909 -4.6708743 9.1115202 5.6280000 -4.1950000 8.1600000
5.2277154 -4.9362316 8.8516988 4.6680000 -3.1010000 8.2020000
4.0260000 -3.0210000 6.9380000 3.1080633 -3.6084757 6.9570758
3.5520000 -1.6420000 6.7540000 4.4190000 -0.6130000 6.5140000
5.4801650 -0.8052026 6.4558028 3.9760000 0.6400000 6.3480000
4.6909680 1.4404290 6.1576466 2.5710000 0.8560000 6.4320000
2.0700000 2.0840000 6.2750000 1.0682966 2.1944877 6.3419573
2.6843303 2.8654469 6.0960014 1.7150000 -0.1420000 6.6670000
2.1780000 -1.4030000 6.8320000 1.4150000 -2.3560000 7.0510000
5.5990000 -4.6560000 6.7020000 6.5636024 -4.9632869 6.2980003
5.0830000 -3.4450000 5.9240000 5.9024866 -2.9979318 5.3612647
4.3001069 -3.7618456 5.2349518 4.6540000 -5.7130000 6.5720000
5.6340000 -6.8770000 4.7560000 6.4910000 -7.9140000 5.3750000
6.1740000 -6.2270000 3.5420000 4.1920000 -7.4930000 4.4390000
3.1890000 -7.4910000 5.4730000 3.4975514 -6.7766054 6.2362408
3.0942573 -8.4936374 5.8899445 1.8530000 -7.0620000 4.9000000
1.0869842 -7.4459106 5.5737446 1.6750000 -5.6160000 4.9310000
1.2220000 -5.1940000 3.6530000 0.1324592 -5.1644836 3.6416460
1.6070000 -3.7980000 3.4750000 2.8740000 -3.3080000 3.2600000
3.7238309 -3.9723273 3.2065340 2.9070000 -2.0090000 3.1390000
1.5830000 -1.6150000 3.2820000 0.9980000 -0.3240000 3.2450000
1.5530000 0.7680000 3.0710000 -0.3790000 -0.3790000 3.4350000
-0.8832334 0.4844898 3.4234868 -1.1010000 -1.5300000 3.6370000
-2.4240000 -1.3760000 3.8030000 -2.9391247 -0.5072448 3.8063723
-2.9598550 -2.2174786 3.9607151 -0.5680000 -2.7390000 3.6730000
0.7690000 -2.7090000 3.4910000 1.6070000 -7.4320000 3.4360000
2.2411112 -8.2304127 3.0505925 1.8820000 -6.1430000 2.6600000
2.8253191 -6.2364448 2.1219328 1.0746984 -5.9670158 1.9490894
0.2360000 -7.7740000 3.2730000 0.1070000 -9.3520000 1.5080000
0.1350000 -10.6870000 2.1460000 0.9670000 -9.1840000 0.3150000
-1.4010000 -8.9630000 1.1420000 -2.2230000 -8.3340000 2.1440000
-1.5634084 -7.9465600 2.9204852 -2.9229570 -9.0637396 2.5509900
-3.0000000 -7.1870000 1.5330000 -3.8598665 -7.0147340 2.1803433
-2.2590000 -5.9330000 1.5690000 -2.3230000 -5.3400000 0.2810000
-3.1663490 -4.6507105 0.2392668 -1.1520000 -4.4660000 0.1230000
0.1050000 -4.9780000 -0.0430000 0.2532187 -6.0476423 -0.0602193
1.1660000 -4.1730000 -0.1860000 2.1558360 -4.6096997 -0.3187345
0.9330000 -2.7680000 -0.1580000 1.9520000 -1.9160000 -0.2970000
1.7446019 -0.9278532 -0.2714544 2.8921980 -2.2629310 -0.4225705
-0.2910000 -2.2580000 0.0030000 -1.3530000 -3.0840000 0.1460000
-2.5040000 -2.6480000 0.2980000 -3.3790000 -7.3490000 0.0600000
-3.3542540 -8.3737211 -0.3107197 -2.3520000 -6.5080000 -0.6980000
-1.6479131 -7.1657806 -1.2075935 -2.8626471 -5.8846952 -1.4320509
-4.6690000 -6.7840000 -0.1480000 -4.9947625 -6.8385221 -1.0493905
wrappers/python/tests/systems/DNA_mbondi3.prmtop 0 → 100644
View file @ 12fa5430
This source diff could not be displayed because it is too large. You can view the blob instead.
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment