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Unverified Commit 0993868a authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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NBFIX is applied correctly to 1-4 interactions (#3324)

parent 892839b8
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Showing with 6043 additions and 2 deletions
wrappers/python/openmm/app/charmmpsffile.py
View file @ 0993868a
......@@ -1387,6 +1387,11 @@ class CharmmPsfFile(object):
atom1 = self.atom_list[ia1]
atom4 = self.atom_list[ia4]
charge_prod = (atom1.charge * atom4.charge) * params.e14fac
try:
rij, wdij, rij14, wdij14 = atom1.type.nbfix[atom4.type.name]
epsilon = wdij14*ene_conv
sigma = rij14*length_conv*sigma_scale
except KeyError:
epsilon = sqrt(abs(atom1.type.epsilon_14 * atom4.type.epsilon_14)) * ene_conv
sigma = (atom1.type.rmin_14 + atom4.type.rmin_14) * (length_conv * sigma_scale)
force.addException(ia1, ia4, charge_prod, sigma, epsilon)
......
wrappers/python/tests/TestCharmmFiles.py
View file @ 0993868a
......@@ -150,6 +150,30 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15559.71602, delta=0.05)
def test_NBFIX14(self):
"""Tests CHARMM systems with NBFIX modifications to 1-4 interactions"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/chl1.psf')
crd = CharmmCrdFile('systems/chl1.crd')
params = CharmmParameterSet('systems/par_all36_lipid.prm', 'systems/par_all36_cgenff.prm', 'systems/toppar_all36_lipid_cholesterol.str')
# Turn off charges so we only test the Lennard-Jones energies
for a in psf.atom_list:
a.charge = 0.0
# Compute the Lennard-Jones energy
system = psf.createSystem(params, nonbondedMethod=CutoffNonPeriodic, nonbondedCutoff=12*angstroms)
for i, f in enumerate(system.getForces()):
if isinstance(f, NonbondedForce) or isinstance(f, CustomNonbondedForce):
f.setForceGroup(1)
else:
f.setForceGroup(0)
context = Context(system, VerletIntegrator(2*femtoseconds), Platform.getPlatformByName('Reference'))
context.setPositions(crd.positions)
state = context.getState(getEnergy=True, groups={1})
energy = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(energy, 3.1166, delta=1e-4)
def test_NBThole(self):
"""Tests CHARMM system with NBTHole"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
......
wrappers/python/tests/systems/chl1.crd 0 → 100644
View file @ 0993868a
* GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON APR, 20. 2017. JOB
* GET A DIFFERENT CONFORMATION FOR LIPIDS PENETRATING PROTEIN / CHOL
* DATE: 9/22/21 15:13: 3 CREATED BY USER: jlee
*
74 EXT
1 1 CHL1 C3 2.0758430000 1.4287490000 -0.0024380000 CHL1 1 0.0000000000
2 1 CHL1 H3 1.7789920000 1.9075100000 -0.9655430000 CHL1 1 0.0000000000
3 1 CHL1 O3 3.4901020000 1.4114150000 0.0741910000 CHL1 1 0.0000000000
4 1 CHL1 H3' 3.6956580000 0.9624930000 0.8967140000 CHL1 1 0.0000000000
5 1 CHL1 C4 1.5114820000 2.2413810000 1.1750860000 CHL1 1 0.0000000000
6 1 CHL1 H4A 1.9148670000 3.2768030000 1.0908510000 CHL1 1 0.0000000000
7 1 CHL1 H4B 1.9116520000 1.8253500000 2.1234900000 CHL1 1 0.0000000000
8 1 CHL1 C5 -0.0042430000 2.2232410000 1.2047520000 CHL1 1 0.0000000000
9 1 CHL1 C6 -0.7185500000 3.3605640000 1.1867230000 CHL1 1 0.0000000000
10 1 CHL1 H6 -0.1961740000 4.3287470000 1.1811170000 CHL1 1 0.0000000000
11 1 CHL1 C7 -2.2182720000 3.4093590000 1.2529030000 CHL1 1 0.0000000000
12 1 CHL1 H7A -2.6174250000 3.6976270000 0.2559360000 CHL1 1 0.0000000000
13 1 CHL1 H7B -2.5510300000 4.1816550000 1.9801080000 CHL1 1 0.0000000000
14 1 CHL1 C8 -2.8493790000 2.0493740000 1.6586470000 CHL1 1 0.0000000000
15 1 CHL1 H8 -2.6976970000 1.9177710000 2.7522240000 CHL1 1 0.0000000000
16 1 CHL1 C14 -4.3402020000 2.0530670000 1.3479140000 CHL1 1 0.0000000000
17 1 CHL1 H14 -4.4174730000 2.1586370000 0.2344860000 CHL1 1 0.0000000000
18 1 CHL1 C15 -5.1864690000 3.2052640000 1.9147900000 CHL1 1 0.0000000000
19 1 CHL1 H15A -5.0243010000 4.1528850000 1.3633690000 CHL1 1 0.0000000000
20 1 CHL1 H15B -4.9339520000 3.3605530000 2.9859010000 CHL1 1 0.0000000000
21 1 CHL1 C16 -6.6269070000 2.6905440000 1.7787000000 CHL1 1 0.0000000000
22 1 CHL1 H16A -7.1958500000 3.2680330000 1.0215770000 CHL1 1 0.0000000000
23 1 CHL1 H16B -7.1376360000 2.7834600000 2.7609420000 CHL1 1 0.0000000000
24 1 CHL1 C17 -6.5372270000 1.1878570000 1.3493380000 CHL1 1 0.0000000000
25 1 CHL1 H17 -6.6019490000 1.1763380000 0.2350740000 CHL1 1 0.0000000000
26 1 CHL1 C13 -5.0880620000 0.7643510000 1.6898470000 CHL1 1 0.0000000000
27 1 CHL1 C18 -5.0064860000 0.4701080000 3.2112890000 CHL1 1 0.0000000000
28 1 CHL1 H18A -5.4771980000 1.2760610000 3.8078890000 CHL1 1 0.0000000000
29 1 CHL1 H18B -3.9571470000 0.3656950000 3.5470390000 CHL1 1 0.0000000000
30 1 CHL1 H18C -5.5253140000 -0.4812360000 3.4456420000 CHL1 1 0.0000000000
31 1 CHL1 C12 -4.4501040000 -0.3574190000 0.8429720000 CHL1 1 0.0000000000
32 1 CHL1 H12A -4.6174580000 -0.1329160000 -0.2328530000 CHL1 1 0.0000000000
33 1 CHL1 H12B -4.9071470000 -1.3405780000 1.0619880000 CHL1 1 0.0000000000
34 1 CHL1 C11 -2.9326770000 -0.4609040000 1.1008090000 CHL1 1 0.0000000000
35 1 CHL1 H11A -2.5100440000 -1.2251340000 0.4155920000 CHL1 1 0.0000000000
36 1 CHL1 H11B -2.8003630000 -0.8324760000 2.1373400000 CHL1 1 0.0000000000
37 1 CHL1 C9 -2.1768110000 0.8895300000 0.9143010000 CHL1 1 0.0000000000
38 1 CHL1 H9 -2.2977970000 1.1402610000 -0.1695780000 CHL1 1 0.0000000000
39 1 CHL1 C10 -0.6446230000 0.8183080000 1.1682710000 CHL1 1 0.0000000000
40 1 CHL1 C19 -0.3877040000 0.1475000000 2.5441910000 CHL1 1 0.0000000000
41 1 CHL1 H19A -0.9335740000 0.6777980000 3.3513270000 CHL1 1 0.0000000000
42 1 CHL1 H19B 0.6897940000 0.1400840000 2.8025550000 CHL1 1 0.0000000000
43 1 CHL1 H19C -0.7162580000 -0.9108240000 2.5315180000 CHL1 1 0.0000000000
44 1 CHL1 C1 0.0140190000 -0.0227780000 0.0327100000 CHL1 1 0.0000000000
45 1 CHL1 H1A -0.3316670000 0.3767310000 -0.9472730000 CHL1 1 0.0000000000
46 1 CHL1 H1B -0.3334130000 -1.0747520000 0.1067690000 CHL1 1 0.0000000000
47 1 CHL1 C2 1.5521950000 -0.0100270000 0.0330650000 CHL1 1 0.0000000000
48 1 CHL1 H2A 1.9243040000 -0.5230830000 0.9458070000 CHL1 1 0.0000000000
49 1 CHL1 H2B 1.9346080000 -0.5653680000 -0.8513700000 CHL1 1 0.0000000000
50 1 CHL1 C20 -7.7246780000 0.3593490000 1.8737490000 CHL1 1 0.0000000000
51 1 CHL1 H20 -7.7090080000 0.3716970000 2.9880740000 CHL1 1 0.0000000000
52 1 CHL1 C21 -7.6153060000 -1.1076400000 1.4054310000 CHL1 1 0.0000000000
53 1 CHL1 H21A -6.7567890000 -1.6098270000 1.8911100000 CHL1 1 0.0000000000
54 1 CHL1 H21B -7.4954750000 -1.1568730000 0.3031920000 CHL1 1 0.0000000000
55 1 CHL1 H21C -8.5172290000 -1.6860490000 1.6875930000 CHL1 1 0.0000000000
56 1 CHL1 C22 -9.0849100000 0.9697470000 1.4326760000 CHL1 1 0.0000000000
57 1 CHL1 H22A -9.1561990000 0.9304830000 0.3238230000 CHL1 1 0.0000000000
58 1 CHL1 H22B -9.1287420000 2.0387760000 1.7346150000 CHL1 1 0.0000000000
59 1 CHL1 C23 -10.3258450000 0.2922230000 2.0422060000 CHL1 1 0.0000000000
60 1 CHL1 H23A -10.2114010000 0.2526360000 3.1483210000 CHL1 1 0.0000000000
61 1 CHL1 H23B -10.4034320000 -0.7498490000 1.6668930000 CHL1 1 0.0000000000
62 1 CHL1 C24 -11.6240990000 1.0427750000 1.7005560000 CHL1 1 0.0000000000
63 1 CHL1 H24A -11.7579260000 1.0650290000 0.5968610000 CHL1 1 0.0000000000
64 1 CHL1 H24B -11.5215770000 2.0951660000 2.0485660000 CHL1 1 0.0000000000
65 1 CHL1 C25 -12.8929290000 0.4444570000 2.3453720000 CHL1 1 0.0000000000
66 1 CHL1 H25 -12.7160890000 0.3730380000 3.4453480000 CHL1 1 0.0000000000
67 1 CHL1 C26 -14.0995530000 1.3709480000 2.1214960000 CHL1 1 0.0000000000
68 1 CHL1 H26A -14.3073370000 1.4755350000 1.0355250000 CHL1 1 0.0000000000
69 1 CHL1 H26B -13.8988040000 2.3788300000 2.5421330000 CHL1 1 0.0000000000
70 1 CHL1 H26C -15.0033380000 0.9555930000 2.6153310000 CHL1 1 0.0000000000
71 1 CHL1 C27 -13.2063260000 -0.9657240000 1.8173800000 CHL1 1 0.0000000000
72 1 CHL1 H27A -12.3832270000 -1.6705450000 2.0552520000 CHL1 1 0.0000000000
73 1 CHL1 H27B -13.3457700000 -0.9412980000 0.7159300000 CHL1 1 0.0000000000
74 1 CHL1 H27C -14.1385570000 -1.3514600000 2.2815630000 CHL1 1 0.0000000000
wrappers/python/tests/systems/chl1.psf 0 → 100644
View file @ 0993868a
PSF EXT CMAP CHEQ XPLOR
3 !NTITLE
* GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON APR, 20. 2017. JOB
* GET A DIFFERENT CONFORMATION FOR LIPIDS PENETRATING PROTEIN / CHOL
* DATE: 9/22/21 15:13: 3 CREATED BY USER: jlee
74 !NATOM
1 CHL1 1 CHL1 C3 CRL1 0.140000 12.0110 0 0.00000 -0.301140E-02
2 CHL1 1 CHL1 H3 HGA1 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
3 CHL1 1 CHL1 O3 OHL -0.660000 15.9994 0 0.00000 -0.301140E-02
4 CHL1 1 CHL1 H3' HOL 0.430000 1.00800 0 0.00000 -0.301140E-02
5 CHL1 1 CHL1 C4 CRL2 -0.180000 12.0110 0 0.00000 -0.301140E-02
6 CHL1 1 CHL1 H4A HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
7 CHL1 1 CHL1 H4B HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
8 CHL1 1 CHL1 C5 CEL1 0.00000 12.0110 0 0.00000 -0.301140E-02
9 CHL1 1 CHL1 C6 CEL1 -0.150000 12.0110 0 0.00000 -0.301140E-02
10 CHL1 1 CHL1 H6 HEL1 0.150000 1.00800 0 0.00000 -0.301140E-02
11 CHL1 1 CHL1 C7 CRL2 -0.180000 12.0110 0 0.00000 -0.301140E-02
12 CHL1 1 CHL1 H7A HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
13 CHL1 1 CHL1 H7B HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
14 CHL1 1 CHL1 C8 CRL1 -0.900000E-01 12.0110 0 0.00000 -0.301140E-02
15 CHL1 1 CHL1 H8 HGA1 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
16 CHL1 1 CHL1 C14 CRL1 -0.900000E-01 12.0110 0 0.00000 -0.301140E-02
17 CHL1 1 CHL1 H14 HGA1 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
18 CHL1 1 CHL1 C15 CRL2 -0.180000 12.0110 0 0.00000 -0.301140E-02
19 CHL1 1 CHL1 H15A HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
20 CHL1 1 CHL1 H15B HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
21 CHL1 1 CHL1 C16 CRL2 -0.180000 12.0110 0 0.00000 -0.301140E-02
22 CHL1 1 CHL1 H16A HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
23 CHL1 1 CHL1 H16B HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
24 CHL1 1 CHL1 C17 CRL1 -0.900000E-01 12.0110 0 0.00000 -0.301140E-02
25 CHL1 1 CHL1 H17 HGA1 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
26 CHL1 1 CHL1 C13 CRL1 0.00000 12.0110 0 0.00000 -0.301140E-02
27 CHL1 1 CHL1 C18 CTL3 -0.270000 12.0110 0 0.00000 -0.301140E-02
28 CHL1 1 CHL1 H18A HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
29 CHL1 1 CHL1 H18B HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
30 CHL1 1 CHL1 H18C HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
31 CHL1 1 CHL1 C12 CRL2 -0.180000 12.0110 0 0.00000 -0.301140E-02
32 CHL1 1 CHL1 H12A HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
33 CHL1 1 CHL1 H12B HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
34 CHL1 1 CHL1 C11 CRL2 -0.180000 12.0110 0 0.00000 -0.301140E-02
35 CHL1 1 CHL1 H11A HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
36 CHL1 1 CHL1 H11B HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
37 CHL1 1 CHL1 C9 CRL1 -0.900000E-01 12.0110 0 0.00000 -0.301140E-02
38 CHL1 1 CHL1 H9 HGA1 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
39 CHL1 1 CHL1 C10 CRL1 0.00000 12.0110 0 0.00000 -0.301140E-02
40 CHL1 1 CHL1 C19 CTL3 -0.270000 12.0110 0 0.00000 -0.301140E-02
41 CHL1 1 CHL1 H19A HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
42 CHL1 1 CHL1 H19B HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
43 CHL1 1 CHL1 H19C HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
44 CHL1 1 CHL1 C1 CRL2 -0.180000 12.0110 0 0.00000 -0.301140E-02
45 CHL1 1 CHL1 H1A HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
46 CHL1 1 CHL1 H1B HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
47 CHL1 1 CHL1 C2 CRL2 -0.180000 12.0110 0 0.00000 -0.301140E-02
48 CHL1 1 CHL1 H2A HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
49 CHL1 1 CHL1 H2B HGA2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
50 CHL1 1 CHL1 C20 CTL1 -0.900000E-01 12.0110 0 0.00000 -0.301140E-02
51 CHL1 1 CHL1 H20 HAL1 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
52 CHL1 1 CHL1 C21 CTL3 -0.270000 12.0110 0 0.00000 -0.301140E-02
53 CHL1 1 CHL1 H21A HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
54 CHL1 1 CHL1 H21B HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
55 CHL1 1 CHL1 H21C HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
56 CHL1 1 CHL1 C22 CTL2 -0.180000 12.0110 0 0.00000 -0.301140E-02
57 CHL1 1 CHL1 H22A HAL2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
58 CHL1 1 CHL1 H22B HAL2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
59 CHL1 1 CHL1 C23 CTL2 -0.180000 12.0110 0 0.00000 -0.301140E-02
60 CHL1 1 CHL1 H23A HAL2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
61 CHL1 1 CHL1 H23B HAL2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
62 CHL1 1 CHL1 C24 CTL2 -0.180000 12.0110 0 0.00000 -0.301140E-02
63 CHL1 1 CHL1 H24A HAL2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
64 CHL1 1 CHL1 H24B HAL2 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
65 CHL1 1 CHL1 C25 CTL1 -0.900000E-01 12.0110 0 0.00000 -0.301140E-02
66 CHL1 1 CHL1 H25 HAL1 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
67 CHL1 1 CHL1 C26 CTL3 -0.270000 12.0110 0 0.00000 -0.301140E-02
68 CHL1 1 CHL1 H26A HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
69 CHL1 1 CHL1 H26B HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
70 CHL1 1 CHL1 H26C HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
71 CHL1 1 CHL1 C27 CTL3 -0.270000 12.0110 0 0.00000 -0.301140E-02
72 CHL1 1 CHL1 H27A HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
73 CHL1 1 CHL1 H27B HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
74 CHL1 1 CHL1 H27C HAL3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
77 !NBOND: bonds
1 3 1 2 3 4 1 47
47 48 47 49 47 44 44 45
44 46 1 5 5 6 5 7
5 8 8 39 39 44 39 40
40 41 40 42 40 43 8 9
9 10 9 11 11 12 11 13
11 14 14 15 14 37 37 38
37 39 14 16 16 17 16 26
26 31 31 32 31 33 31 34
34 35 34 36 34 37 26 27
27 28 27 29 27 30 16 18
18 19 18 20 18 21 21 22
21 23 21 24 24 25 24 26
24 50 50 51 50 52 52 53
52 54 52 55 50 56 56 57
56 58 56 59 59 60 59 61
59 62 62 63 62 64 62 65
65 66 65 67 67 68 67 69
67 70 65 71 71 72 71 73
71 74
157 !NTHETA: angles
2 1 3 2 1 5 2 1 47
3 1 5 3 1 47 5 1 47
1 3 4 1 5 6 1 5 7
1 5 8 6 5 7 6 5 8
7 5 8 5 8 9 5 8 39
9 8 39 8 9 10 8 9 11
10 9 11 9 11 12 9 11 13
9 11 14 12 11 13 12 11 14
13 11 14 11 14 15 11 14 16
11 14 37 15 14 16 15 14 37
16 14 37 14 16 17 14 16 18
14 16 26 17 16 18 17 16 26
18 16 26 16 18 19 16 18 20
16 18 21 19 18 20 19 18 21
20 18 21 18 21 22 18 21 23
18 21 24 22 21 23 22 21 24
23 21 24 21 24 25 21 24 26
21 24 50 25 24 26 25 24 50
26 24 50 16 26 24 16 26 27
16 26 31 24 26 27 24 26 31
27 26 31 26 27 28 26 27 29
26 27 30 28 27 29 28 27 30
29 27 30 26 31 32 26 31 33
26 31 34 32 31 33 32 31 34
33 31 34 31 34 35 31 34 36
31 34 37 35 34 36 35 34 37
36 34 37 14 37 34 14 37 38
14 37 39 34 37 38 34 37 39
38 37 39 8 39 37 8 39 40
8 39 44 37 39 40 37 39 44
40 39 44 39 40 41 39 40 42
39 40 43 41 40 42 41 40 43
42 40 43 39 44 45 39 44 46
39 44 47 45 44 46 45 44 47
46 44 47 1 47 44 1 47 48
1 47 49 44 47 48 44 47 49
48 47 49 24 50 51 24 50 52
24 50 56 51 50 52 51 50 56
52 50 56 50 52 53 50 52 54
50 52 55 53 52 54 53 52 55
54 52 55 50 56 57 50 56 58
50 56 59 57 56 58 57 56 59
58 56 59 56 59 60 56 59 61
56 59 62 60 59 61 60 59 62
61 59 62 59 62 63 59 62 64
59 62 65 63 62 64 63 62 65
64 62 65 62 65 66 62 65 67
62 65 71 66 65 67 66 65 71
67 65 71 65 67 68 65 67 69
65 67 70 68 67 69 68 67 70
69 67 70 65 71 72 65 71 73
65 71 74 72 71 73 72 71 74
73 71 74
259 !NPHI: dihedrals
1 5 8 9 1 5 8 39
1 47 44 39 1 47 44 45
1 47 44 46 2 1 3 4
2 1 5 6 2 1 5 7
2 1 5 8 2 1 47 44
2 1 47 48 2 1 47 49
3 1 5 6 3 1 5 7
3 1 5 8 3 1 47 44
3 1 47 48 3 1 47 49
4 3 1 5 4 3 1 47
5 1 47 44 5 1 47 48
5 1 47 49 5 8 9 10
5 8 9 11 5 8 39 37
5 8 39 40 5 8 39 44
6 5 1 47 6 5 8 9
6 5 8 39 7 5 1 47
7 5 8 9 7 5 8 39
8 5 1 47 8 9 11 12
8 9 11 13 8 9 11 14
8 39 37 14 8 39 37 34
8 39 37 38 8 39 40 41
8 39 40 42 8 39 40 43
8 39 44 45 8 39 44 46
8 39 44 47 9 8 39 37
9 8 39 40 9 8 39 44
9 11 14 15 9 11 14 16
9 11 14 37 10 9 8 39
10 9 11 12 10 9 11 13
10 9 11 14 11 9 8 39
11 14 16 17 11 14 16 18
11 14 16 26 11 14 37 34
11 14 37 38 11 14 37 39
12 11 14 15 12 11 14 16
12 11 14 37 13 11 14 15
13 11 14 16 13 11 14 37
14 16 18 19 14 16 18 20
14 16 18 21 14 16 26 24
14 16 26 27 14 16 26 31
14 37 34 31 14 37 34 35
14 37 34 36 14 37 39 40
14 37 39 44 15 14 16 17
15 14 16 18 15 14 16 26
15 14 37 34 15 14 37 38
15 14 37 39 16 14 37 34
16 14 37 38 16 14 37 39
16 18 21 22 16 18 21 23
16 18 21 24 16 26 24 21
16 26 24 25 16 26 24 50
16 26 27 28 16 26 27 29
16 26 27 30 16 26 31 32
16 26 31 33 16 26 31 34
17 16 14 37 17 16 18 19
17 16 18 20 17 16 18 21
17 16 26 24 17 16 26 27
17 16 26 31 18 16 14 37
18 16 26 24 18 16 26 27
18 16 26 31 18 21 24 25
18 21 24 26 18 21 24 50
19 18 16 26 19 18 21 22
19 18 21 23 19 18 21 24
20 18 16 26 20 18 21 22
20 18 21 23 20 18 21 24
21 18 16 26 21 24 26 27
21 24 26 31 21 24 50 51
21 24 50 52 21 24 50 56
22 21 24 25 22 21 24 26
22 21 24 50 23 21 24 25
23 21 24 26 23 21 24 50
24 26 27 28 24 26 27 29
24 26 27 30 24 26 31 32
24 26 31 33 24 26 31 34
24 50 52 53 24 50 52 54
24 50 52 55 24 50 56 57
24 50 56 58 24 50 56 59
25 24 26 27 25 24 26 31
25 24 50 51 25 24 50 52
25 24 50 56 26 16 14 37
26 24 50 51 26 24 50 52
26 24 50 56 26 31 34 35
26 31 34 36 26 31 34 37
27 26 24 50 27 26 31 32
27 26 31 33 27 26 31 34
28 27 26 31 29 27 26 31
30 27 26 31 31 26 24 50
31 34 37 38 31 34 37 39
32 31 34 35 32 31 34 36
32 31 34 37 33 31 34 35
33 31 34 36 33 31 34 37
34 37 39 40 34 37 39 44
35 34 37 38 35 34 37 39
36 34 37 38 36 34 37 39
37 39 40 41 37 39 40 42
37 39 40 43 37 39 44 45
37 39 44 46 37 39 44 47
38 37 39 40 38 37 39 44
39 44 47 48 39 44 47 49
40 39 44 45 40 39 44 46
40 39 44 47 41 40 39 44
42 40 39 44 43 40 39 44
45 44 47 48 45 44 47 49
46 44 47 48 46 44 47 49
50 56 59 60 50 56 59 61
50 56 59 62 51 50 52 53
51 50 52 54 51 50 52 55
51 50 56 57 51 50 56 58
51 50 56 59 52 50 56 57
52 50 56 58 52 50 56 59
53 52 50 56 54 52 50 56
55 52 50 56 56 59 62 63
56 59 62 64 56 59 62 65
57 56 59 60 57 56 59 61
57 56 59 62 58 56 59 60
58 56 59 61 58 56 59 62
59 62 65 66 59 62 65 67
59 62 65 71 60 59 62 63
60 59 62 64 60 59 62 65
61 59 62 63 61 59 62 64
61 59 62 65 62 65 67 68
62 65 67 69 62 65 67 70
62 65 71 72 62 65 71 73
62 65 71 74 63 62 65 66
63 62 65 67 63 62 65 71
64 62 65 66 64 62 65 67
64 62 65 71 66 65 67 68
66 65 67 69 66 65 67 70
66 65 71 72 66 65 71 73
66 65 71 74 67 65 71 72
67 65 71 73 67 65 71 74
68 67 65 71 69 67 65 71
70 67 65 71
0 !NIMPHI: impropers
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0
26 0 !NGRP NST2
0 1 0 4 1 0 7 1 0
10 1 0 13 1 0 15 1 0
17 1 0 20 1 0 23 1 0
25 0 0 26 1 0 30 1 0
33 1 0 36 1 0 38 0 0
39 1 0 43 1 0 46 1 0
49 1 0 51 1 0 55 1 0
58 1 0 61 1 0 64 1 0
66 1 0 70 1 0
1 !MOLNT
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1
0 0 !NUMLP NUMLPH
0 !NCRTERM: cross-terms
wrappers/python/tests/systems/par_all36_lipid.prm 0 → 100644
View file @ 0993868a
* \\\\\\\ CHARMM36 All-Hydrogen Lipid Parameter File ///////
* All comments and questions should be submitted to the
* parameter forum at the CHARMM website: www.charmm.org
*
!references
!
!Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph
!W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor
!Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of
!the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six
!Lipid Types" J. Phys. Chem. B 2010, 114, 7830-7843
!
! PUFA Modifications
!Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im. "Improving
!the CHARMM Force Field for Polyunsaturated Fatty Acid Chains" J. Phys. Chem. B.
!2012 ASAP http://dx.doi.org/10.1021/jp304056p
ATOMS
MASS -1 HL 1.00800 ! polar H (equivalent to protein H)
MASS -1 HCL 1.00800 ! charged H for PE (equivalent to protein HC)
MASS -1 HOL 1.00800 ! Nucleic acid phosphate hydroxyl proton
MASS -1 HAL1 1.00800 ! alphatic proton
MASS -1 HAL2 1.00800 ! alphatic proton
MASS -1 HAL3 1.00800 ! alphatic proton
MASS -1 HEL1 1.00800 ! for alkene; RHC=CR
MASS -1 HEL2 1.00800 ! for alkene; H2C=CR
MASS -1 HBL 1.00800 ! POPS SER backbone H
MASS -1 CL 12.01100 ! carbonyl C (acetic acid/methyl acetate)
MASS -1 CTL1 12.01100 ! sp3 carbon with 1 H (-CH1-)
MASS -1 CTL2 12.01100 ! carbon of methylene group (-CH2-)
MASS -1 CTL3 12.01100 ! carbon of methyl group (-CH3)
MASS -1 CTL5 12.01100 ! carbon of methyl group (-CH3) for tetramethylammonium
MASS -1 CEL1 12.01100 ! for alkene; RHC=CR
MASS -1 CEL2 12.01100 ! for alkene; H2C=CR
MASS -1 CCL 12.01100 ! for POPS
MASS -1 NTL 14.00700 ! ammonium nitrogen
MASS -1 NH3L 14.00700 ! nitrogen phosphatidylethanolamine
MASS -1 OBL 15.99940 ! acetic acid carboxyl oxygen (e. to protein OB)
MASS -1 OCL 15.99940 ! acetate oxygen
MASS -1 OSL 15.99940 ! ester oxygen
MASS -1 O2L 15.99940 ! Nucleic acid =O in phosphate or sulfate
MASS -1 OHL 15.99940 ! Nucleic acid phosphate hydroxyl oxygen
MASS -1 OSLP 15.99940 ! Phosphate oxygen, to avoid conflict with methylacetate type O
MASS -1 PL 30.97400 ! phosphorus
MASS -1 SL 32.06000 ! Sulfate sulfur
MASS -1 CRL1 12.01100 ! sp3 carbon with 1 H on a ring (-CH1-) for sterols
MASS -1 CRL2 12.01100 ! carbon of methylene group on a ring (-CH2-) for sterols
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
CTL3 CL 200.0 1.522 ! methyl acetate
CTL2 CL 200.0 1.522 ! methyl acetate
CTL1 CL 200.0 1.522 ! methyl acetate
CTL1 CCL 200.0 1.522 ! for POPS
OBL CL 750.0 1.220 ! methyl acetate
OCL CL 525.0 1.260 ! acetate, protein
OCL CCL 525.0 1.260 ! for POPS
OSL CL 150.0 1.334 ! methyl acetate
OSLP CL 150.0 1.334 ! methyl acetate
OHL CL 230.0 1.40 ! methyl acetate
HOL OHL 545.0 0.960 ! acetic acid
CTL1 HAL1 309.00 1.111 ! alkanes, 3/92
CTL1 HBL 330.00 1.080 ! for POPS
CTL2 HAL2 309.00 1.111 ! alkanes, 4/98
CTL3 HAL3 322.00 1.111 ! alkanes, 4/98
CTL3 OSL 340.0 1.43 ! phosphate
CTL2 OSL 340.0 1.43 ! phosphate
CTL1 OSL 340.0 1.43 ! phosphate
CTL3 OSLP 340.0 1.43 !
CTL2 OSLP 340.0 1.43 !
CTL1 OSLP 340.0 1.43 !
OSL PL 270.0 1.60 ! phosphate
OSLP PL 270.0 1.60 !
O2L PL 580.0 1.48 ! phosphate
OHL PL 237.0 1.59 ! phosphate
NH3L HCL 410.0 1.04 ! ethanolamine
NH3L CTL1 200.0 1.48 ! for POPS
NH3L CTL2 261.0 1.51 ! ethanolamine
NTL CTL2 215.00 1.51 ! tetramethylammonium
NTL CTL5 215.00 1.51 ! tetramethylammonium
CTL5 HL 300.00 1.08 ! tetramethylammonium
CTL2 HL 300.00 1.08 ! tetramethylammonium
CTL1 CTL1 222.500 1.500 ! alkanes, 3/92
CTL1 CTL2 222.500 1.538 ! alkanes, 3/92
CTL1 CTL3 222.500 1.538 ! alkanes, 3/92
CTL2 CTL2 222.500 1.530 ! alkanes, 3/92
CTL2 CTL3 222.500 1.528 ! alkanes, 3/92
CTL3 CTL3 222.500 1.530 ! alkanes, 3/92
OHL CTL1 428.0 1.420 ! glycerol
OHL CTL2 428.0 1.420 ! glycerol
OHL CTL3 428.0 1.420 ! glycerol
SL O2L 540.0 1.448 ! methylsulfate
SL OSL 250.0 1.575 ! methylsulfate
CEL2 CEL2 510.000 1.330 ! ethene yin,adm jr., 12/95
HEL2 CEL2 365.000 1.100 ! propene; from ethene, yin,adm jr., 12/95
CEL1 CTL3 383.000 1.504 ! butene, yin,adm jr., 12/95
CEL1 CEL2 500.000 1.342 ! propene, yin,adm jr., 12/95
HEL1 CEL1 360.500 1.100 ! propene, yin,adm jr., 12/95
CEL1 CTL2 365.000 1.502 ! butene; from propene, yin,adm jr., 12/95
CEL1 CEL1 440.000 1.340 ! butene, yin,adm jr., 12/95
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
!
OBL CL CTL3 70.0 125.0 20.0 2.442 ! methyl acetate
OBL CL CTL2 70.0 125.0 20.0 2.442 ! methyl acetate
OBL CL CTL1 70.0 125.0 20.0 2.442 ! methyl acetate
OSL CL OBL 90.0 125.9 160.0 2.2576 ! acetic acid
CL OSL CTL1 40.0 109.6 30.0 2.2651 ! methyl acetate
CL OSL CTL2 40.0 109.6 30.0 2.2651 ! methyl acetate
CL OSL CTL3 40.0 109.6 30.0 2.2651 ! methyl acetate
HAL2 CTL2 CL 33.00 109.50 30.00 2.163 ! methyl acetate
HAL3 CTL3 CL 33.00 109.50 30.00 2.163 ! methyl acetate
CTL2 CTL2 CL 52.0 108.00 ! alkane
CTL2 CTL1 CCL 52.0 108.00 ! for POPS
CTL3 CTL2 CL 52.0 108.00 ! alkane
OSL CL CTL3 55.0 109.0 20.00 2.3260 ! methyl acetate
OSL CL CTL2 55.0 109.0 20.00 2.3260 ! methyl acetate
OSL CL CTL1 55.0 109.0 20.00 2.3260 ! methyl acetate
OHL CL OBL 50.0 123.0 210.0 2.2620 ! acetic acid
OCL CL CTL2 40.0 118.0 50.0 2.3880 ! acetate
OCL CL CTL3 40.0 118.0 50.0 2.3880 ! acetate
OCL CL OCL 100.0 124.0 70.0 2.2250 ! acetate
OCL CCL OCL 100.0 124.0 70.0 2.2250 ! for POPS
OCL CCL CTL1 40.0 118.0 50.0 2.3880 ! for POPS
OHL CL CTL3 55.0 110.50 ! acetic acid
OHL CL CTL2 55.0 110.50 ! acetic acid
HOL OHL CL 55.0 115.0 ! acetic acid
OSL CTL1 CTL1 75.700 110.10 ! acetic acid, PIP
OSL CTL1 CTL2 75.700 110.10 ! acetic acid
OSL CTL1 CTL3 75.700 110.10 ! acetic acid
OSL CTL2 CTL1 75.700 110.10 ! acetic acid
OSL CTL2 CTL2 75.700 110.10 ! acetic acid
OSL CTL2 CTL3 75.700 110.10 ! acetic acid
OSLP CTL1 CTL1 75.700 110.10 ! acetic acid, PIP
OSLP CTL1 CTL2 75.700 110.10 ! acetic acid
OSLP CTL1 CTL3 75.700 110.10 ! acetic acid
OSLP CTL2 CTL1 75.700 110.10 ! acetic acid
OSLP CTL2 CTL2 75.700 110.10 ! acetic acid
OSLP CTL2 CTL3 75.700 110.10 ! acetic acid
HAL2 CTL2 HAL2 35.500 109.00 5.40 1.80200 ! alkane, 3/92
HAL3 CTL3 HAL3 35.500 108.40 5.40 1.80200 ! alkane, 3/92
HAL1 CTL1 OSL 60.0 109.5 ! phosphate
HAL2 CTL2 OSL 60.0 109.5 ! phosphate
HAL3 CTL3 OSL 60.0 109.5 ! phosphate
HAL1 CTL1 OSLP 60.0 109.5 ! phosphate
HAL2 CTL2 OSLP 60.0 109.5 ! phosphate
HAL3 CTL3 OSLP 60.0 109.5 ! phosphate
CTL1 OSL PL 20.0 120.0 35.0 2.33 ! phosphate, PIP
CTL2 OSL PL 20.0 120.0 35.0 2.33 ! phosphate
CTL3 OSL PL 20.0 120.0 35.0 2.33 ! phosphate
CTL1 OSLP PL 20.0 120.0 35.0 2.33 ! phosphate, PIP
CTL2 OSLP PL 20.0 120.0 35.0 2.33 ! phosphate
CTL3 OSLP PL 20.0 120.0 35.0 2.33 ! phosphate
HOL OHL PL 30.0 115.0 40.0 2.30 ! phosphate
OSL PL OSL 80.0 104.3 ! phosphate
OSL PL O2L 98.9 111.6 ! phosphate
OSL PL OHL 48.1 108.0 ! phosphate
OSLP PL OSLP 80.0 104.3 ! phosphate
OSLP PL O2L 98.9 111.6 ! phosphate
OSLP PL OHL 48.1 108.0 ! phosphate
O2L PL O2L 120.0 120.0 ! phosphate
O2L PL OHL 98.9 108.23 ! phosphate
NTL CTL2 HL 40.0 109.5 27. 2.13 ! tetramethylammonium
NTL CTL5 HL 40.0 109.5 27. 2.13 ! tetramethylammonium
HL CTL2 HL 24.0 109.50 28. 1.767 ! tetramethylammonium
HL CTL5 HL 24.0 109.50 28. 1.767 ! tetramethylammonium
CTL2 NTL CTL2 60.0 109.5 26. 2.466 ! tetraethylammonium, from CTL5 NTL CTL2
CTL5 NTL CTL2 60.0 109.5 26. 2.466 ! tetramethylammonium
CTL5 NTL CTL5 60.0 109.5 26. 2.466 ! tetramethylammonium
HL CTL2 CTL2 33.430 110.10 22.53 2.179 ! alkane
HL CTL2 CTL3 33.430 110.10 22.53 2.179 ! alkane
HAL1 CTL1 CTL1 34.500 110.10 22.53 2.179 ! alkane, 3/92
HAL1 CTL1 CTL2 34.500 110.10 22.53 2.179 ! alkane, 3/92
HAL1 CTL1 CTL3 34.500 110.10 22.53 2.179 ! alkane, 3/92
HAL2 CTL2 CTL1 26.500 110.10 22.53 2.179 ! alkane, 4/98
HAL2 CTL2 CTL2 26.500 110.10 22.53 2.179 ! alkane, 4/98
HAL2 CTL2 CTL3 34.600 110.10 22.53 2.179 ! alkane, 4/98
HAL3 CTL3 CTL1 33.430 110.10 22.53 2.179 ! alkane, 4/98
HAL3 CTL3 CTL2 34.600 110.10 22.53 2.179 ! alkane, 4/98
HAL3 CTL3 CTL3 37.500 110.10 22.53 2.179 ! alkane, 4/98
HBL CTL1 CCL 50.000 109.50 ! for POPS
HBL CTL1 CTL2 35.000 111.00 ! for POPS
NTL CTL2 CTL2 67.7 115.00 ! tetramethylammonium
NTL CTL2 CTL3 67.7 115.00 ! tetramethylammonium
HCL NH3L CTL2 33.0 109.50 4.00 2.056 ! ethanolamine
HCL NH3L CTL1 30.0 109.50 20.00 2.074 ! for POPS
HCL NH3L HCL 41.0 109.50 ! ethanolamine
NH3L CTL2 CTL2 67.7 110.00 ! ethanolamine
NH3L CTL2 HAL2 45.0 107.50 35.00 2.0836 ! ethanolamine
CTL1 CTL1 CTL1 53.350 111.00 8.00 2.561 ! alkane, 3/92
NH3L CTL1 CCL 43.7 110.00 ! for POPS
NH3L CTL1 CTL2 67.7 110.00 ! for POPS
NH3L CTL1 HBL 51.5 107.50 ! for POPS
CTL1 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol
CTL1 CTL1 CTL3 53.350 108.50 8.00 2.561 ! alkane, 3/92
CTL1 CTL2 CTL1 58.350 113.50 11.16 2.561 ! glycerol
CTL1 CTL2 CTL2 58.350 113.50 11.16 2.561 ! glycerol
CTL1 CTL2 CTL3 58.350 113.50 11.16 2.561 ! glycerol
CTL2 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol
CTL2 CTL1 CTL3 58.350 113.50 11.16 2.561 ! glycerol
CTL2 CTL2 CTL2 58.350 113.60 11.16 2.561 ! alkane, 3/92
CTL2 CTL2 CTL3 58.000 115.00 8.00 2.561 ! alkane, 3/92
CTL3 CTL1 CTL3 58.350 113.50 11.16 2.561 ! glycerol
HOL OHL CTL1 57.500 106.00 ! glycerol
HOL OHL CTL2 57.500 106.00 ! glycerol
HOL OHL CTL3 57.500 106.00 ! glycerol
OHL CTL1 CTL1 75.700 110.10 ! glycerol, PIP
OHL CTL1 CTL2 75.700 110.10 ! glycerol
OHL CTL2 CTL1 75.700 110.10 ! glycerol
OHL CTL2 CTL2 75.700 110.10 ! glycerol
OHL CTL2 CTL3 75.700 110.10 ! glycerol
OHL CTL1 HAL1 45.900 108.89 ! glycerol
OHL CTL2 HAL2 45.900 108.89 ! glycerol
OHL CTL3 HAL3 45.900 108.89 ! glycerol
O2L SL O2L 130.0 109.47 35.0 2.45 ! methylsulfate
O2L SL OSL 85.0 98.0 ! methylsulfate
CTL2 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate
CTL3 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate
CEL1 CEL1 CTL2 48.00 123.50 ! from 2-butene, yin,adm jr., 12/95
CEL1 CEL1 CTL3 48.00 123.50 ! 2-butene, yin,adm jr., 12/95
CEL2 CEL1 CTL2 48.00 126.00 ! 1-butene; from propene, yin,adm jr., 12/95
CEL2 CEL1 CTL3 47.00 125.20 ! propene, yin,adm jr., 12/95
HEL1 CEL1 CEL1 52.00 119.50 ! 2-butene, yin,adm jr., 12/95
HEL1 CEL1 CEL2 42.00 118.00 ! propene, yin,adm jr., 12/95
HEL1 CEL1 CTL2 40.00 116.00 ! 1-butene; from propene, yin,adm jr., 12/95
HEL1 CEL1 CTL3 22.00 117.00 ! propene, yin,adm jr., 12/95
HEL2 CEL2 CEL1 45.00 120.50 ! propene, yin,adm jr., 12/95
HEL2 CEL2 CEL2 55.50 120.50 ! ethene, yin,adm jr., 12/95
HEL2 CEL2 HEL2 19.00 119.00 ! propene, yin,adm jr., 12/95
CEL1 CTL2 CTL2 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95
CEL1 CTL2 CTL3 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95
HAL2 CTL2 CEL1 45.00 111.50 ! 1-butene; from propene, yin,adm jr., 12/95
HAL3 CTL3 CEL1 42.00 111.50 ! 2-butene, yin,adm jr., 12/95
CEL1 CTL2 CEL1 30.0 114.0 ! 1,4-dipentene, adm jr., 2/00
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
X CTL1 OHL X 0.14 3 0.00 ! glycerol
X CTL2 OHL X 0.14 3 0.00 ! glycerol
X CTL3 OHL X 0.14 3 0.00 ! glycerol
OCL CCL CTL1 NH3L 3.20 2 180.00 ! for POPS
OBL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid
OBL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid
OSL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid
OSL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid
OSLP CL CTL2 HAL2 0.00 6 180.00 ! acetic acid
OSLP CL CTL3 HAL3 0.00 6 180.00 ! acetic acid
OBL CL OSL CTL1 0.965 1 180.00 ! methyl acetate
OBL CL OSL CTL1 3.85 2 180.00 ! methyl acetate
OBL CL OSL CTL2 0.965 1 180.00 ! methyl acetate
OBL CL OSL CTL2 3.85 2 180.00 ! methyl acetate
OBL CL OSL CTL3 0.965 1 180.00 ! methyl acetate
OBL CL OSL CTL3 3.85 2 180.00 ! methyl acetate
X CL OSL X 2.05 2 180.00 ! methyl acetate
X CTL2 CL X 0.05 6 180.00 ! methyl acetate
X CTL3 CL X 0.05 6 180.00 ! methyl acetate
X CL OHL X 2.05 2 180.00 ! acetic acid
X CTL1 CCL X 0.05 6 180.00 ! for POPS
HAL2 CTL2 CL OHL 0.00 6 180.00
HAL3 CTL3 CL OHL 0.00 6 180.00
PL OSLP CTL2 CTL1 0.407 2 0.00 ! Phos-gly, 8/05
PL OSLP CTL2 CTL1 0.241 1 180.00 ! Phos-gly, 8/05
PL OSLP CTL2 CTL2 0.407 2 0.00 ! Phos-gly, 8/05
PL OSLP CTL2 CTL2 0.241 1 180.00 ! Phos-gly, 8/05
OSL PL OSL CTL1 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSL PL OSL CTL1 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSL PL OSL CTL1 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSLP PL OSLP CTL1 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSLP PL OSLP CTL1 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSLP PL OSLP CTL1 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSLP PL OSLP CTL2 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr.
OSLP PL OSLP CTL2 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr.
OSLP PL OSLP CTL2 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr.
O2L PL OSLP CTL2 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr.
O2L PL OSL CTL2 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr.
OSLP PL OSLP CTL3 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr.
OSLP PL OSLP CTL3 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr.
OSLP PL OSLP CTL3 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr.
O2L PL OSLP CTL1 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr., PIP
O2L PL OSL CTL1 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr., PIP
O2L PL OSLP CTL3 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr.
O2L PL OSL CTL3 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr.
OHL PL OSL CTL1 0.95 2 0.00 ! terminal phosphate, PIP
OHL PL OSL CTL1 0.50 3 0.00 ! terminal phosphate, PIP
OHL PL OSL CTL2 0.95 2 0.00 ! terminal phosphate
OHL PL OSL CTL2 0.50 3 0.00 ! terminal phosphate
OHL PL OSL CTL3 0.95 2 0.00 ! terminal phosphate
OHL PL OSL CTL3 0.50 3 0.00 ! terminal phosphate
OHL PL OSLP CTL2 0.95 2 0.00 ! terminal phosphate
OHL PL OSLP CTL2 0.50 3 0.00 ! terminal phosphate
OHL PL OSLP CTL3 0.95 2 0.00 ! terminal phosphate
OHL PL OSLP CTL3 0.50 3 0.00 ! terminal phosphate
X OHL PL X 0.30 3 0.00 ! terminal phosphate
X CTL1 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
X CTL2 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
X CTL3 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
X CTL1 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
X CTL2 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
X CTL3 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
CTL1 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92
CTL1 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92
CTL2 CTL2 CL OSL 0.000 6 0.00 ! glycerol & propl ester, 6/07
CTL2 CTL2 CL OSL 0.030 3 180.00 ! glycerol & propl ester, 6/07
CTL2 CTL2 CL OSL 0.432 2 180.00 ! glycerol & propl ester, 6/07
CTL2 CTL2 CL OSL 0.332 1 0.00 ! glycerol & propl ester, 6/07
CTL3 CTL2 CL OSL 0.000 6 0.00 ! glycerol & propl ester, 6/07
CTL3 CTL2 CL OSL 0.030 3 180.00 ! glycerol & propl ester, 6/07
CTL3 CTL2 CL OSL 0.432 2 180.00 ! glycerol & propl ester, 6/07
CTL3 CTL2 CL OSL 0.332 1 0.00 ! glycerol & propl ester, 6/07
CTL3 CTL2 CTL2 CL 0.000 5 180.00 ! propyl ester, 6/07
CTL3 CTL2 CTL2 CL 0.317 3 180.00 ! propyl ester, 6/07
CTL3 CTL2 CTL2 CL 0.557 2 0.00 ! propyl ester, 6/07
CTL3 CTL2 CTL2 CL 0.753 1 0.00 ! propyl ester, 6/07
CTL2 CTL2 CTL2 CL 0.000 5 180.00 ! propyl ester, 6/07
CTL2 CTL2 CTL2 CL 0.317 3 180.00 ! propyl ester, 6/07
CTL2 CTL2 CTL2 CL 0.557 2 0.00 ! propyl ester, 6/07
CTL2 CTL2 CTL2 CL 0.753 1 0.00 ! propyl ester, 6/07
OSL CTL2 CTL1 OSL -0.429 4 60.00 ! glycerol, 8/08
OSL CTL2 CTL1 OSL 0.614 3 0.00 ! glycerol, 8/08
OSL CTL2 CTL1 OSL -0.115 2 60.00 ! glycerol, 8/08
OSL CTL2 CTL1 OSL 0.703 1 180.00 ! glycerol, 8/08
OSLP CTL2 CTL1 OSL 0.000 4 0.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL1 OSL 0.607 3 180.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL1 OSL 0.254 2 60.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL1 OSL 2.016 1 180.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL2 OSL 0.000 4 0.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL2 OSL 0.607 3 180.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL2 OSL 0.254 2 60.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL2 OSL 2.016 1 180.00 ! Fit to QM, theta2, 07/08 jbk
CTL3 CTL1 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3
CTL2 CTL1 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3
CTL3 CTL2 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3
CTL2 CTL2 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3
CL OSL CTL1 CTL2 0.000 4 0.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL2 0.150 3 180.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL2 1.453 2 180.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL2 0.837 1 180.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL3 0.000 4 0.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL3 0.150 3 180.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL3 1.453 2 180.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL3 0.837 1 180.00 ! glycerol, beta1 6/07
CL OSL CTL2 CTL1 0.267 3 180.00 ! glycerol, gamma1 6/07
CL OSL CTL2 CTL1 0.173 2 0.00 ! glycerol, gamma1 6/07
CL OSL CTL2 CTL1 0.781 1 180.00 ! glycerol, gamma1 6/07
X CTL2 NTL X 0.26 3 0.00 ! tetramethylammonium
X CTL5 NTL X 0.23 3 0.00 ! tetramethylammonium
X CTL1 NH3L X 0.10 3 0.00 ! for POPS
X CTL2 NH3L X 0.10 3 0.00 ! ethanolamine
NH3L CTL2 CTL2 OHL 0.7 1 180.00 ! ethanolamine
NH3L CTL2 CTL2 OSLP 0.7 1 180.00 ! ethanolamine
NTL CTL2 CTL2 OHL 4.3 1 180.00 ! choline, 12/92
NTL CTL2 CTL2 OHL -0.4 3 180.00 ! choline, 12/92
NTL CTL2 CTL2 OSLP 3.3 1 180.00 ! choline, 12/92
NTL CTL2 CTL2 OSLP -0.4 3 180.00 ! choline, 12/92
X CTL1 CTL1 X 0.200 3 0.00 ! alkane, 3/92
X CTL1 CTL2 X 0.200 3 0.00 ! alkane, 3/92
X CTL1 CTL3 X 0.200 3 0.00 ! alkane, 3/92
X CTL2 CTL2 X 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell
X CTL2 CTL3 X 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell
X CTL3 CTL3 X 0.1525 3 0.00 ! alkane, 4/98, yin and mackerell
!alkane CCCC dihedrals based on pentane, heptane and hexane vdz/vqz/ccsd(t) QM data
CTL3 CTL2 CTL2 CTL3 0.060 2 0.00 ! alkane, 7/08, jbk
CTL3 CTL2 CTL2 CTL3 0.035 5 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL3 0.162 2 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL3 0.047 3 180.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL3 0.105 4 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL3 0.177 5 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL2 0.101 2 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL2 0.142 3 180.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL2 0.074 4 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL2 0.097 5 0.00 ! alkane, 7/08, jbk
HAL3 CTL3 OSL SL 0.00 3 0.00 ! methylsulfate
CTL2 OSL SL O2L 0.00 3 0.00 ! methylsulfate
CTL3 OSL SL O2L 0.00 3 0.00 ! methylsulfate
HEL1 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update
CTL3 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update
X CEL1 CEL1 X 0.4500 1 180.00 ! 2-butene, adm jr., 4/04
X CEL1 CEL1 X 8.5000 2 180.00 !
X CEL2 CEL2 X 4.9000 2 180.00 ! ethene, yin,adm jr., 12/95
CTL2 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95
CTL3 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95
HEL1 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95
!alkene update, 2004,2009
CEL1 CEL1 CTL2 HAL2 0.3000 3 180.00 !2-butene, adm jr., 4/04
CEL1 CEL1 CTL3 HAL3 0.3000 3 180.00 !2-butene, adm jr., 4/04
!CEL1 CEL1 CTL2 CTL3 0.9000 1 180.00 !2-pentene and 3-heptene
!CEL1 CEL1 CTL2 CTL3 0.2000 2 180.00 !2-pentene and 3-heptene
CEL1 CEL1 CTL2 CTL3 0.9100 1 180.0 !2-hexene, adm jr., 11/09, end fix jbk
CEL1 CEL1 CTL2 CTL3 0.1800 2 180.0 !2-hexene, adm jr., 11/09
CEL1 CEL1 CTL2 CTL3 0.1700 3 180.0 !2-hexene, adm jr., 11/09
CEL1 CEL1 CTL2 CTL2 0.9100 1 180.0 !2-hexene, adm jr., 11/09
CEL1 CEL1 CTL2 CTL2 0.1800 2 180.0 !2-hexene, adm jr., 11/09
CEL1 CEL1 CTL2 CTL2 0.1700 3 180.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CL 0.1400 1 180.0 !2-hexene, adm jr., 11/09, add jbk for DHA
CEL1 CTL2 CTL2 CL 0.1700 2 0.0 !2-hexene, adm jr., 11/09, add jbk for DHA
CEL1 CTL2 CTL2 CL 0.0500 3 180.0 !2-hexene, adm jr., 11/09, add jbk for DHA
CEL1 CTL2 CTL2 CTL2 0.1400 1 180.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CTL2 0.1700 2 0.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CTL2 0.0500 3 180.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CTL3 0.1400 1 180.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CTL3 0.1700 2 0.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CTL3 0.0500 3 180.0 !2-hexene, adm jr., 11/09
CEL2 CEL1 CTL2 CTL2 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update
CEL2 CEL1 CTL2 CTL2 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update
CEL2 CEL1 CTL2 CTL3 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update
CEL2 CEL1 CTL2 CTL3 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update
CEL2 CEL1 CTL2 HAL2 0.1200 3 0.00 ! 1-butene, yin,adm jr., 12/95
CEL2 CEL1 CTL3 HAL3 0.0500 3 180.00 ! propene, yin,adm jr., 12/95
HEL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! butene, yin,adm jr., 12/95
HEL1 CEL1 CTL2 CTL3 0.1200 3 0.00 ! butene, yin,adm jr., 12/95
HEL1 CEL1 CTL2 HAL2 0.0000 3 0.00 ! butene, adm jr., 2/00 update
HEL1 CEL1 CTL3 HAL3 0.0000 3 0.00 ! butene, adm jr., 2/00 update
! 1,4-dipentene, adm jr., 2/00
CEL2 CEL1 CTL2 CEL1 1.200 1 180.00 !1,4-dipentene
CEL2 CEL1 CTL2 CEL1 0.400 2 180.00 !1,4-dipentene
CEL2 CEL1 CTL2 CEL1 1.300 3 180.00 !1,4-dipentene
CEL1 CTL2 CEL1 HEL1 0.000 2 0.00 !1,4-dipentene
CEL1 CTL2 CEL1 HEL1 0.000 3 0.00 !1,4-dipentene
! 2,5-diheptene, jbk., 9/2010
! for CIS double bonds in polyunsaturated lipids (default)
CEL1 CEL1 CTL2 CEL1 0.850 1 180.00 !2,5-diheptane
CEL1 CEL1 CTL2 CEL1 0.300 2 180.00 !2,5-diheptane
CEL1 CEL1 CTL2 CEL1 0.260 3 0.00 !2,5-diheptane
CEL1 CEL1 CTL2 CEL1 0.096 4 0.00 !2,5-diheptane
! for TRANS double bonds in polyunsaturated lipids
! uncomment following 4 lines and comment previous 4 lines to use
!CEL1 CEL1 CTL2 CEL1 1.200 1 180.00 !2,5-diheptane
!CEL1 CEL1 CTL2 CEL1 0.200 2 180.00 !2,5-diheptane
!CEL1 CEL1 CTL2 CEL1 1.200 3 180.00 !2,5-diheptane
!CEL1 CEL1 CTL2 CEL1 0.100 4 180.00 !2,5-diheptane
!
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!
OBL X X CL 100.00 0 0.00 ! acetic acid
HEL2 HEL2 CEL2 CEL2 3.00 0 0.00 ! ethene, yin,adm jr., 12/95
OCL X X CL 96.00 0 0.00 ! acetate
OCL X X CCL 96.00 0 0.00 ! for POPS
NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
HOL 0.0 -0.046 0.2245
HAL1 0.0 -0.022 1.3200 ! alkane, 3/92
HAL2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98
HAL3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98
HBL 0.0 -0.022 1.3200 ! for POPS
HCL 0.0 -0.046 0.2245 ! ethanolamine
HL 0.0 -0.046 0.7 ! polar H on NC4+
HEL1 0.0 -0.031 1.25 ! alkene, yin,adm jr., 12/95
HEL2 0.0 -0.026 1.26 ! alkene, yin,adm jr., 12/95
!
CL 0.0 -0.0700 2.00 ! methyl acetate update
CCL 0.0 -0.0700 2.00 ! for POPS
CTL1 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92
CTL2 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
CTL3 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
CTL5 0.0 -0.0800 2.06 0.0 -0.01 1.9 ! old CTL3
! maintained for tetramethylammonium
CEL1 0.0 -0.068 2.09 ! alkene, yin,adm jr., 12/95
CEL2 0.0 -0.064 2.08 ! alkene, yin,adm jr., 12/95
CRL1 0.0 -0.0360 2.010 0.0 -0.01 1.9 ! CGAFF, jbk add for cholesterol
CRL2 0.0 -0.0600 2.020 0.0 -0.01 1.9 ! CPEN, cyclopentane, 8/06 viv (jbk add)
!
OBL 0.0 -0.12 1.70 0.0 -0.12 1.4
OCL 0.0 -0.12 1.70
O2L 0.0 -0.12 1.70
OHL 0.0 -0.1521 1.77
OSL 0.0 -0.1000 1.6500 !viv dec06 ether parameter
OSLP 0.0 -0.1000 1.6500 !viv dec06 ether parameter
!
NH3L 0.0 -0.20 1.85 ! ethanolamine
NTL 0.0 -0.20 1.85 ! as all other nitogens
!
SL 0.0 -0.47 2.1 ! methylsulfate
PL 0.0 -0.585 2.15 ! ADM Jr.
NBFIX
! Emin Rmin
! (kcal/mol) (A)
!
HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
! READ PARAM APPEND CARD
! to append hbond parameters from the file: par_hbond.inp
END
wrappers/python/tests/systems/toppar_all36_lipid_cholesterol.str 0 → 100644
View file @ 0993868a
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