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Unverified Commit 698769b9 authored by qiuzy's avatar qiuzy Committed by GitHub
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fix Charmm NBThole calculation bug and Improper dihedral parameter match issue (#2952) 

* nbthole

* Update charmmpsffile.py

* Update charmmpsffile.py

* Update charmmparameterset.py

fix multiple dihedral with the same periodicity and add a warning reminder for improper dihedral

* add test example for NBTHole

add system files of CYT-GUA-CYT DNA segment for testing NBThole

* Update TestCharmmFiles.py
parent b5b39611
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Showing with 3939 additions and 11 deletions
wrappers/python/simtk/openmm/app/charmmparameterset.py
View file @ 698769b9
...@@ -387,7 +387,7 @@ class CharmmParameterSet(object): ...@@ -387,7 +387,7 @@ class CharmmParameterSet(object):
if dtype != dihedral: if dtype != dihedral:
warnings.warn('Replacing dihedral %r with %r' % warnings.warn('Replacing dihedral %r with %r' %
(dtype, dihedral)) (dtype, dihedral))
self.dihedral_types[key] self.dihedral_types[key][i]=dihedral
replaced = True replaced = True
break break
if not replaced: if not replaced:
...@@ -413,10 +413,20 @@ class CharmmParameterSet(object): ...@@ -413,10 +413,20 @@ class CharmmParameterSet(object):
theteq = tmp theteq = tmp
except IndexError: except IndexError:
pass # Do nothing pass # Do nothing
# Improper types seem not to have the central atom defined in if type1 < type4:
# the first place, so just have the key a fully sorted list. We key = (type1, type2, type3, type4)
# still depend on the PSF having properly ordered improper atoms elif type1 > type4:
key = tuple(sorted([type1, type2, type3, type4])) key = (type4, type3, type2, type1)
else:
# OK, we need to sort by the middle atoms now
if type2 < type3:
key = (type1, type2, type3, type4)
else:
key = (type4, type3, type2, type1)
# check repeat improper dihedral
if key in self.improper_types:
warnings.warn('Repeat improper dihedral found %r and New param. k: %f ,thetaq: %f will use' %
(key,k,theteq))
self.improper_types[key] = ImproperType(k, theteq) self.improper_types[key] = ImproperType(k, theteq)
continue continue
if section == 'CMAP': if section == 'CMAP':
......
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 698769b9
...@@ -677,13 +677,12 @@ class CharmmPsfFile(object): ...@@ -677,13 +677,12 @@ class CharmmPsfFile(object):
# Store the atoms # Store the atoms
a1, a2, a3, a4 = imp.atom1, imp.atom2, imp.atom3, imp.atom4 a1, a2, a3, a4 = imp.atom1, imp.atom2, imp.atom3, imp.atom4
at1, at2, at3, at4 = a1.attype, a2.attype, a3.attype, a4.attype at1, at2, at3, at4 = a1.attype, a2.attype, a3.attype, a4.attype
key = tuple(sorted([at1, at2, at3, at4])) key = min((at1,at2,at3,at4), (at4,at3,at2,at1))
if not key in parmset.improper_types: if not key in parmset.improper_types:
# Check for wild-cards key = min((at1,'X', 'X',at4),(at4,'X','X',at1))
for anchor in (at2, at3, at4): if not key in parmset.improper_types:
key = tuple(sorted([at1, anchor, 'X', 'X'])) raise MissingParameter('No improper dihedral parameters found for '
if key in parmset.improper_types: '%r' % imp)
break # This is the right key
try: try:
imp.improper_type = parmset.improper_types[key] imp.improper_type = parmset.improper_types[key]
except KeyError: except KeyError:
...@@ -1490,6 +1489,31 @@ class CharmmPsfFile(object): ...@@ -1490,6 +1489,31 @@ class CharmmPsfFile(object):
ii, jj, q, eps, sig = force.getExceptionParameters(i) ii, jj, q, eps, sig = force.getExceptionParameters(i)
nbtforce.addExclusion(ii, jj) nbtforce.addExclusion(ii, jj)
# Using CustomBondForce to Calculate 1-4 atom pairs' NBThole interaction which have been excluded
if has_drude_particle and has_nbthole_terms:
nbt14force=mm.CustomBondForce('-138.935456*charge_prod*(1.0+0.5*screen*r)*exp(-1.0*screen*r)/r')
nbt14force.addPerBondParameter("charge_prod")
nbt14force.addPerBondParameter("screen")
nbt14force.setForceGroup(self.NONBONDED_FORCE_GROUP)
num_nbt14=0
for dih in self.dihedral_list:
a1, a4 = dih.atom1, dih.atom4
idx_a1, idx_a4 = a1.idx, a4.idx
at1, at4 = self.atom_list[idx_a1].type, self.atom_list[idx_a4].type
if at1.nbthole and at4.nbthole:
name_a4 = at4.name
nbt_value = at1.nbthole.get(name_a4,0)
if abs(nbt_value)>TINY:
q1, q4 = a1.charge, a4.charge
alpha1= pow(-1*self.drudeconsts_list[idx_a1][0],-1./6.)
alpha4= pow(-1*self.drudeconsts_list[idx_a4][0],-1./6.)
qij=q1*q4
screen=nbt_value*alpha1*alpha4*10.0
nbt14force.addBond(idx_a1,idx_a4,[qij,screen])
num_nbt14+=1
if num_nbt14>0:
system.addForce(nbt14force)
# Add GB model if we're doing one # Add GB model if we're doing one
if implicitSolvent is not None: if implicitSolvent is not None:
if verbose: print('Adding GB parameters...') if verbose: print('Adding GB parameters...')
......
wrappers/python/tests/TestCharmmFiles.py
View file @ 698769b9
...@@ -147,6 +147,26 @@ class TestCharmmFiles(unittest.TestCase): ...@@ -147,6 +147,26 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole) ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15559.71602, delta=0.05) self.assertAlmostEqual(ene, 15559.71602, delta=0.05)
def test_NBThole(self):
"""Tests CHARMM system with NBTHole"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/cyt-gua-cyt.psf')
crd = CharmmCrdFile('systems/cyt-gua-cyt.crd')
params = CharmmParameterSet('systems/toppar_drude_master_protein_2013e.str','systems/toppar_drude_nucleic_acid_2017b.str')
# Box dimensions (cubic box)
psf.setBox(30.0*angstroms, 30.0*angstroms, 30.0*angstroms)
# Now compute the full energy
plat = Platform.getPlatformByName('Reference')
system = psf.createSystem(params, nonbondedMethod=PME, ewaldErrorTolerance=0.00005)
integrator = DrudeLangevinIntegrator(300*kelvin, 1.0/picosecond, 1*kelvin, 10/picosecond, 0.001*picoseconds)
con = Context(system, integrator, plat)
con.setPositions(crd.positions)
state = con.getState(getEnergy=True, enforcePeriodicBox=True)
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, -292.73015, delta=1.0)
def test_Drude(self): def test_Drude(self):
"""Test CHARMM systems with Drude force field""" """Test CHARMM systems with Drude force field"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning) warnings.filterwarnings('ignore', category=CharmmPSFWarning)
......
wrappers/python/tests/systems/cyt-gua-cyt.crd 0 → 100644
View file @ 698769b9
* GENERATE PSF WITH OPTIMIZED
* DRUDE PROTEIN FORCE FIELD
* DATE: 12/18/20 21: 0:51 CREATED BY USER: qiuzy
*
176 EXT
1 1 CYT H5T 9.2932028107 10.8307655966 18.0403805565 DNA 1 0.0000000000
2 1 CYT O5' 9.7405057857 10.9593876058 17.1900208161 DNA 1 0.0000000000
3 1 CYT DO5' 9.7443608855 10.9701534822 17.2167747416 DNA 1 0.0000000000
4 1 CYT C5' 9.3378314770 9.8642782612 16.3526854601 DNA 1 0.0000000000
5 1 CYT DC5' 9.3228652453 9.8708543183 16.3690757578 DNA 1 0.0000000000
6 1 CYT H5' 8.2433627306 9.8918886167 16.1409964005 DNA 1 0.0000000000
7 1 CYT H5'' 9.6966975882 8.8884478625 16.7528768866 DNA 1 0.0000000000
8 1 CYT LP5A 10.0329938722 10.8762904825 17.3633574304 DNA 1 0.0000000000
9 1 CYT LP5B 9.5216068682 11.2291939395 17.1477383635 DNA 1 0.0000000000
10 1 CYT N1 10.7047933306 13.5599274596 14.7217834187 DNA 1 0.0000000000
11 1 CYT DN1 10.7171602569 13.6006466854 14.9192228159 DNA 1 0.0000000000
12 1 CYT C6 10.8458690961 13.7526817274 16.0576344359 DNA 1 0.0000000000
13 1 CYT DC6 10.8742308520 13.8393255725 16.2925497977 DNA 1 0.0000000000
14 1 CYT H6 11.0900286235 12.8603303781 16.6355660785 DNA 1 0.0000000000
15 1 CYT C2 10.4015820054 14.6360827853 13.9005309947 DNA 1 0.0000000000
16 1 CYT DC2 10.4344031214 14.4646101275 13.8938155983 DNA 1 0.0000000000
17 1 CYT O2 10.2742291657 14.4537442986 12.6812447655 DNA 1 0.0000000000
18 1 CYT DO2 10.2610055335 14.5122753146 12.6878191455 DNA 1 0.0000000000
19 1 CYT LP2A 10.1984600236 14.7561982490 12.5222459092 DNA 1 0.0000000000
20 1 CYT LP2B 10.3278830615 14.1165289212 12.6043873723 DNA 1 0.0000000000
21 1 CYT N3 10.2435796272 15.8610716979 14.4576865192 DNA 1 0.0000000000
22 1 CYT DN3 10.2437225105 15.8053678902 14.3999071713 DNA 1 0.0000000000
23 1 CYT LP3 10.1648888158 16.1402345268 14.2617889112 DNA 1 0.0000000000
24 1 CYT C4 10.3889844094 16.0095613165 15.7699689627 DNA 1 0.0000000000
25 1 CYT DC4 10.3689407643 16.0448179651 15.6964577735 DNA 1 0.0000000000
26 1 CYT N4 10.2283490971 17.2280334028 16.3036245770 DNA 1 0.0000000000
27 1 CYT DN4 10.2227494101 17.2231155259 16.3074327496 DNA 1 0.0000000000
28 1 CYT H41 10.0031070134 18.0034261022 15.6923653660 DNA 1 0.0000000000
29 1 CYT H42 10.3330975496 17.3759830496 17.2998472449 DNA 1 0.0000000000
30 1 CYT C5 10.7021146086 14.9326311974 16.6125891448 DNA 1 0.0000000000
31 1 CYT DC5 10.6453773081 15.1266438450 16.5340012782 DNA 1 0.0000000000
32 1 CYT H5 10.8113110875 15.0954944323 17.6785470341 DNA 1 0.0000000000
33 1 CYT C4' 10.0035522446 10.0080707962 14.9870200987 DNA 1 0.0000000000
34 1 CYT DC4' 9.9902769466 10.0171203034 15.0014752810 DNA 1 0.0000000000
35 1 CYT H4' 9.6476214004 9.2236148313 14.3044738544 DNA 1 0.0000000000
36 1 CYT O4' 9.6512896821 11.2937564245 14.4216418735 DNA 1 0.0000000000
37 1 CYT DO4' 9.6440196904 11.3024029738 14.4049072086 DNA 1 0.0000000000
38 1 CYT LPRA 9.4961560382 11.4451319342 14.6964490800 DNA 1 0.0000000000
39 1 CYT LPRB 9.5814265433 11.2022962211 14.0911056684 DNA 1 0.0000000000
40 1 CYT LPX 9.7452677830 11.2687306852 14.4449190658 DNA 1 0.0000000000
41 1 CYT C1' 10.8929563473 12.1549888049 14.2510602770 DNA 1 0.0000000000
42 1 CYT DC1' 10.8869695971 12.1749540876 14.3150932056 DNA 1 0.0000000000
43 1 CYT H1' 11.1148810267 12.1990133142 13.1737975513 DNA 1 0.0000000000
44 1 CYT C2' 11.9986965375 11.4386489370 14.9958450658 DNA 1 0.0000000000
45 1 CYT DC2' 11.9603418629 11.4091724259 14.9717319705 DNA 1 0.0000000000
46 1 CYT H2'' 12.0887188971 11.8273479133 16.0182936981 DNA 1 0.0000000000
47 1 CYT H2' 12.9011995827 11.5889332288 14.4182512845 DNA 1 0.0000000000
48 1 CYT C3' 11.5288612740 10.0002924476 15.0123701837 DNA 1 0.0000000000
49 1 CYT DC3' 11.4149102348 9.9714169074 15.0447839793 DNA 1 0.0000000000
50 1 CYT H3' 11.9181626566 9.5626986208 15.9340285594 DNA 1 0.0000000000
51 1 CYT O3' 12.1192972201 9.2744376379 13.9250283861 DNA 1 0.0000000000
52 1 CYT DO3' 12.1261589188 9.2661927690 13.9105780491 DNA 1 0.0000000000
53 2 GUA P 13.6126892952 9.6666210188 13.4629397870 DNA 2 0.0000000000
54 2 GUA DP 13.5974540487 9.6533261933 13.4695461097 DNA 2 0.0000000000
55 2 GUA O1P 14.3391933902 10.3706743189 14.5560757832 DNA 2 0.0000000000
56 2 GUA DO1P 14.3130879412 10.3755078794 14.5483045279 DNA 2 0.0000000000
57 2 GUA O2P 14.2928034370 8.4583505968 12.9560628695 DNA 2 0.0000000000
58 2 GUA DO2P 14.2601877114 8.4431802852 12.9519335310 DNA 2 0.0000000000
59 2 GUA O5' 13.2927290918 10.6646658107 12.2542919090 DNA 2 0.0000000000
60 2 GUA DO5' 13.3001859458 10.6516009153 12.2945931388 DNA 2 0.0000000000
61 2 GUA C5' 12.3255169585 10.2802735866 11.2592370529 DNA 2 0.0000000000
62 2 GUA DC5' 12.2784190645 10.3146328091 11.1969012214 DNA 2 0.0000000000
63 2 GUA H5' 11.3455988541 10.7637231239 11.4848189715 DNA 2 0.0000000000
64 2 GUA H5'' 12.3132363236 9.1724445338 11.1579130414 DNA 2 0.0000000000
65 2 GUA N9 14.2853219132 13.7140499534 10.7654868469 DNA 2 0.0000000000
66 2 GUA DN9 14.2899554574 13.7172067956 10.7816395213 DNA 2 0.0000000000
67 2 GUA C4 14.1524568617 15.0605474808 10.5730753810 DNA 2 0.0000000000
68 2 GUA DC4 14.1649106805 15.0054544872 10.5752232966 DNA 2 0.0000000000
69 2 GUA N3 13.7491120066 15.6815990748 9.4421527763 DNA 2 0.0000000000
70 2 GUA DN3 13.7360685150 15.7529761787 9.4097745025 DNA 2 0.0000000000
71 2 GUA LP3 13.6587790568 15.5177332886 9.1463691374 DNA 2 0.0000000000
72 2 GUA C2 13.7302328868 17.0003966115 9.5701584905 DNA 2 0.0000000000
73 2 GUA DC2 13.7227402073 17.0046526985 9.5511129244 DNA 2 0.0000000000
74 2 GUA N1 14.0807487539 17.6732976817 10.7201620363 DNA 2 0.0000000000
75 2 GUA DN1 14.0627115270 17.6465944960 10.6619374053 DNA 2 0.0000000000
76 2 GUA H1 14.0287779671 18.6927448983 10.7075555782 DNA 2 0.0000000000
77 2 GUA N2 13.3503674517 17.7614398450 8.5335320211 DNA 2 0.0000000000
78 2 GUA DN2 13.3553271002 17.7713609867 8.5668692806 DNA 2 0.0000000000
79 2 GUA H21 13.2968624269 18.7727575459 8.5124912562 DNA 2 0.0000000000
80 2 GUA H22 13.0920597792 17.2727798656 7.6846907042 DNA 2 0.0000000000
81 2 GUA C6 14.5003198368 17.0563104684 11.8976081222 DNA 2 0.0000000000
82 2 GUA DC6 14.5259159765 17.0987750347 11.9785124763 DNA 2 0.0000000000
83 2 GUA O6 14.7956844322 17.7477450787 12.8829408850 DNA 2 0.0000000000
84 2 GUA DO6 14.7917319313 17.8061191042 12.8767425584 DNA 2 0.0000000000
85 2 GUA LP6A 14.8934339064 17.5419459565 13.1486321131 DNA 2 0.0000000000
86 2 GUA LP6B 14.7551520534 18.0871117248 12.8075261572 DNA 2 0.0000000000
87 2 GUA C5 14.5278071260 15.6568038635 11.7877178782 DNA 2 0.0000000000
88 2 GUA DC5 14.5000396903 15.7508093104 11.7051855005 DNA 2 0.0000000000
89 2 GUA N7 14.8797436890 14.6807561178 12.7083471274 DNA 2 0.0000000000
90 2 GUA DN7 14.8766912897 14.7103509970 12.7044716189 DNA 2 0.0000000000
91 2 GUA LP7 14.9882728859 14.7142830797 13.0394020363 DNA 2 0.0000000000
92 2 GUA C8 14.7192773375 13.5467101380 12.0659958660 DNA 2 0.0000000000
93 2 GUA DC8 14.7425557965 13.5929339133 12.1054368597 DNA 2 0.0000000000
94 2 GUA H8 14.9033162906 12.5596516591 12.4860473455 DNA 2 0.0000000000
95 2 GUA C4' 12.7277309043 10.8108599613 9.8877167788 DNA 2 0.0000000000
96 2 GUA DC4' 12.7438817170 10.8346838104 9.8877710838 DNA 2 0.0000000000
97 2 GUA H4' 11.9506671233 10.5889220202 9.1461387754 DNA 2 0.0000000000
98 2 GUA O4' 12.8557684975 12.2504316438 9.9686210551 DNA 2 0.0000000000
99 2 GUA DO4' 12.8507403809 12.2808297908 9.9532822079 DNA 2 0.0000000000
100 2 GUA LPRA 12.8404675862 12.3077460638 10.3135570415 DNA 2 0.0000000000
101 2 GUA LPRB 12.7025076665 12.3560597038 9.6722195786 DNA 2 0.0000000000
102 2 GUA LPX 12.9261747260 12.1823726023 9.9483486197 DNA 2 0.0000000000
103 2 GUA C1' 14.0283796572 12.6802528899 9.7487568163 DNA 2 0.0000000000
104 2 GUA DC1' 14.0390432208 12.6774344674 9.7732426765 DNA 2 0.0000000000
105 2 GUA H1' 13.9472002408 13.1109923452 8.7500546339 DNA 2 0.0000000000
106 2 GUA C2' 14.9588835678 11.4939001558 9.7907882024 DNA 2 0.0000000000
107 2 GUA DC2' 14.9289493218 11.4779058946 9.7551466797 DNA 2 0.0000000000
108 2 GUA H2'' 15.3190287466 11.3600063764 10.8263915554 DNA 2 0.0000000000
109 2 GUA H2' 15.7594485925 11.6898635537 9.0692736025 DNA 2 0.0000000000
110 2 GUA C3' 14.0778992403 10.3185542158 9.3800840181 DNA 2 0.0000000000
111 2 GUA DC3' 13.9889255398 10.3232402275 9.4205990746 DNA 2 0.0000000000
112 2 GUA H3' 14.4074286571 9.4078482179 9.8880277398 DNA 2 0.0000000000
113 2 GUA O3' 14.0980339496 10.0296238206 7.9690998225 DNA 2 0.0000000000
114 2 GUA DO3' 14.1146819989 10.0448192638 7.9505848037 DNA 2 0.0000000000
115 3 CYT P 15.4966170410 10.0938838835 7.1918910281 DNA 3 0.0000000000
116 3 CYT DP 15.4836399688 10.1031335338 7.1847270552 DNA 3 0.0000000000
117 3 CYT O1P 16.6229278056 9.9925107749 8.1513568435 DNA 3 0.0000000000
118 3 CYT DO1P 16.6111838437 10.0044139080 8.1425933569 DNA 3 0.0000000000
119 3 CYT O2P 15.4906389094 9.1079356850 6.0839560838 DNA 3 0.0000000000
120 3 CYT DO2P 15.4765392685 9.1239667455 6.0776773089 DNA 3 0.0000000000
121 3 CYT O5' 15.4346054024 11.5733075922 6.5847093535 DNA 3 0.0000000000
122 3 CYT DO5' 15.4519788279 11.5678505389 6.5887656871 DNA 3 0.0000000000
123 3 CYT C5' 14.2338598934 12.0130780210 5.9257131423 DNA 3 0.0000000000
124 3 CYT DC5' 14.2111689293 12.1030513281 5.8671113193 DNA 3 0.0000000000
125 3 CYT H5' 13.6204792008 12.6218050524 6.6309700635 DNA 3 0.0000000000
126 3 CYT H5'' 13.7239592375 11.1436712533 5.4556045276 DNA 3 0.0000000000
127 3 CYT N1 17.3708056866 14.4608685106 6.0097116886 DNA 3 0.0000000000
128 3 CYT DN1 17.4203492444 14.3553473746 6.1074347207 DNA 3 0.0000000000
129 3 CYT C6 17.7486704262 13.3834882119 6.7507287024 DNA 3 0.0000000000
130 3 CYT DC6 17.8422204842 13.2485891489 6.8625115562 DNA 3 0.0000000000
131 3 CYT H6 17.3551904410 12.4227311459 6.4178716941 DNA 3 0.0000000000
132 3 CYT C2 17.8125111743 15.7276359939 6.3606523658 DNA 3 0.0000000000
133 3 CYT DC2 17.7393456039 15.6861706337 6.2507192796 DNA 3 0.0000000000
134 3 CYT O2 17.4582142016 16.7029252059 5.6833800347 DNA 3 0.0000000000
135 3 CYT DO2 17.4823852380 16.7291225596 5.7093687830 DNA 3 0.0000000000
136 3 CYT LP2A 17.5969375809 16.9963582397 5.8143489998 DNA 3 0.0000000000
137 3 CYT LP2B 17.2497034812 16.5981279767 5.4225336730 DNA 3 0.0000000000
138 3 CYT N3 18.6268101784 15.8622185658 7.4350789294 DNA 3 0.0000000000
139 3 CYT DN3 18.5947384591 15.8784239185 7.3885152736 DNA 3 0.0000000000
140 3 CYT LP3 18.7463878437 16.1762493490 7.5329862820 DNA 3 0.0000000000
141 3 CYT C4 18.9802228242 14.7868435055 8.1320599344 DNA 3 0.0000000000
142 3 CYT DC4 18.9870091079 14.8585067416 8.1229937342 DNA 3 0.0000000000
143 3 CYT N4 19.7864744345 14.9401995876 9.1898012835 DNA 3 0.0000000000
144 3 CYT DN4 19.7866937645 14.9393993105 9.1808664532 DNA 3 0.0000000000
145 3 CYT H41 20.1033764306 15.8712950208 9.4324417474 DNA 3 0.0000000000
146 3 CYT H42 20.0743759378 14.1414660314 9.7422126367 DNA 3 0.0000000000
147 3 CYT C5 18.5390480055 13.5009015570 7.7916740087 DNA 3 0.0000000000
148 3 CYT DC5 18.6209207426 13.6671676446 7.8694584559 DNA 3 0.0000000000
149 3 CYT H5 18.8495836014 12.6474195141 8.3854454556 DNA 3 0.0000000000
150 3 CYT C4' 14.5722314767 12.9565858746 4.7755511076 DNA 3 0.0000000000
151 3 CYT DC4' 14.6194174088 12.9635294021 4.7584711128 DNA 3 0.0000000000
152 3 CYT H4' 13.6560182500 13.3575640701 4.3237067537 DNA 3 0.0000000000
153 3 CYT O4' 15.3257382340 14.0751333230 5.3008850585 DNA 3 0.0000000000
154 3 CYT DO4' 15.3477066283 14.1106197174 5.2926783427 DNA 3 0.0000000000
155 3 CYT LPRA 15.3993012990 13.9694635208 5.6263422485 DNA 3 0.0000000000
156 3 CYT LPRB 15.1827201512 14.3469961423 5.1331459238 DNA 3 0.0000000000
157 3 CYT LPX 15.3547485097 14.0057166575 5.2350084152 DNA 3 0.0000000000
158 3 CYT C1' 16.5090637148 14.1652005249 4.8501869155 DNA 3 0.0000000000
159 3 CYT DC1' 16.5394182353 14.1052888689 4.8817584318 DNA 3 0.0000000000
160 3 CYT H1' 16.4432368719 15.0044008711 4.1578092390 DNA 3 0.0000000000
161 3 CYT C2' 16.8215342471 12.8624066509 4.1409839134 DNA 3 0.0000000000
162 3 CYT DC2' 16.8128948543 12.8643513095 4.1128661256 DNA 3 0.0000000000
163 3 CYT H2'' 17.2662180915 12.1629946284 4.8704358638 DNA 3 0.0000000000
164 3 CYT H2' 17.4790335660 13.0958740418 3.2958046285 DNA 3 0.0000000000
165 3 CYT C3' 15.4585303431 12.3528659759 3.6925173585 DNA 3 0.0000000000
166 3 CYT DC3' 15.4514728155 12.3606673045 3.6595919964 DNA 3 0.0000000000
167 3 CYT H3' 15.4458356826 11.2592702770 3.7034164728 DNA 3 0.0000000000
168 3 CYT O3' 15.0970628016 12.7444525649 2.3568327224 DNA 3 0.0000000000
169 3 CYT DO3' 15.0957402485 12.7465137953 2.3513381103 DNA 3 0.0000000000
170 3 CYT H3T 15.7208194811 12.3189037559 1.7477869821 DNA 3 0.0000000000
171 3 CYT LP3A 14.8631284962 12.5197425709 2.2253786739 DNA 3 0.0000000000
172 3 CYT LP3B 15.2621617862 13.0406278765 2.2701003881 DNA 3 0.0000000000
173 4 SOD SOD 8.0012643510 8.0008164757 3.0004178332 SOD 1 0.0000000000
174 4 SOD DSOD 7.9995263949 7.9996931111 2.9998442918 SOD 1 0.0000000000
175 5 SOD SOD 12.0044661566 5.0069237907 13.0004600645 SOD 2 0.0000000000
176 5 SOD DSOD 11.9983799335 4.9975433225 12.9998323610 SOD 2 0.0000000000
wrappers/python/tests/systems/cyt-gua-cyt.psf 0 → 100644
View file @ 698769b9
PSF EXT CMAP CHEQ DRUDE XPLOR
3 !NTITLE
* GENERATE PSF WITH OPTIMIZED
* DRUDE PROTEIN FORCE FIELD
* DATE: 12/18/20 18:53:46 CREATED BY USER: qiuzy
176 !NATOM
1 DNA 1 CYT H5T HDP1A 0.360000 1.00800 0 0.00000 0.00000
2 DNA 1 CYT O5' OD31A 1.75950 15.5990 0 -1.02800 1.30000
3 DNA 1 CYT DO5' DRUD -1.75950 0.400000 0 0.00000 0.00000
4 DNA 1 CYT C5' CD32A 1.67530 11.6110 0 -1.00000 1.30000
5 DNA 1 CYT DC5' DRUD -1.73530 0.400000 0 0.00000 0.00000
6 DNA 1 CYT H5' HDA2A 0.800000E-01 1.00800 0 0.00000 0.00000
7 DNA 1 CYT H5'' HDA2A 0.800000E-01 1.00800 0 0.00000 0.00000
8 DNA 1 CYT LP5A LPD -0.230000 0.00000 -1 0.00000 0.00000
9 DNA 1 CYT LP5B LPD -0.230000 0.00000 -1 0.00000 0.00000
10 DNA 1 CYT N1 ND2R6C 1.81230 13.6070 0 -1.11000 0.822000
11 DNA 1 CYT DN1 DRUD -1.82830 0.400000 0 0.00000 0.00000
12 DNA 1 CYT C6 CD2R6H 2.15790 11.6110 0 -1.75200 2.00400
13 DNA 1 CYT DC6 DRUD -2.29690 0.400000 0 0.00000 0.00000
14 DNA 1 CYT H6 HDR6B 0.251000 1.00800 0 0.00000 0.00000
15 DNA 1 CYT C2 CD2O4A 2.55030 11.6110 0 -1.58000 2.06400
16 DNA 1 CYT DC2 DRUD -2.18130 0.400000 0 0.00000 0.00000
17 DNA 1 CYT O2 OD2C1B 1.42990 15.5994 0 -0.679000 0.675000
18 DNA 1 CYT DO2 DRUD -1.42990 0.400000 0 0.00000 0.00000
19 DNA 1 CYT LP2A LPDNA1 -0.180000 0.00000 -1 0.00000 0.00000
20 DNA 1 CYT LP2B LPDNA1 -0.266000 0.00000 -1 0.00000 0.00000
21 DNA 1 CYT N3 ND2R6B 1.23810 13.6070 0 -0.509000 0.737000
22 DNA 1 CYT DN3 DRUD -1.23810 0.400000 0 0.00000 0.00000
23 DNA 1 CYT LP3 LPDNA1 -0.491000 0.00000 -1 0.00000 0.00000
24 DNA 1 CYT C4 CD2R6B 2.43030 11.6110 0 -1.14300 1.24500
25 DNA 1 CYT DC4 DRUD -1.85530 0.400000 0 0.00000 0.00000
26 DNA 1 CYT N4 ND2B1 1.56610 13.6070 0 -1.62200 0.277000
27 DNA 1 CYT DN4 DRUD -2.21010 0.400000 0 0.00000 0.00000
28 DNA 1 CYT H41 HDP1A 0.346000 1.00800 0 0.00000 0.00000
29 DNA 1 CYT H42 HDP1A 0.346000 1.00800 0 0.00000 0.00000
30 DNA 1 CYT C5 CD2R6J 2.08510 11.6110 0 -1.85600 0.783000
31 DNA 1 CYT DC5 DRUD -2.36410 0.400000 0 0.00000 0.00000
32 DNA 1 CYT H5 HDR6A 0.128000 1.00800 0 0.00000 0.00000
33 DNA 1 CYT C4' CD315B 2.31880 11.6110 0 -1.56200 1.10300
34 DNA 1 CYT DC4' DRUD -2.16880 0.400000 0 0.00000 0.00000
35 DNA 1 CYT H4' HDA1R5 0.550000E-01 1.00800 0 0.00000 0.00000
36 DNA 1 CYT O4' OD305A 1.36420 15.5994 0 -0.618000 1.54500
37 DNA 1 CYT DO4' DRUD -1.36420 0.400000 0 0.00000 0.00000
38 DNA 1 CYT LPRA LPD -0.152000 0.00000 -1 0.00000 0.00000
39 DNA 1 CYT LPRB LPD -0.152000 0.00000 -1 0.00000 0.00000
40 DNA 1 CYT LPX LPD 0.00000 0.00000 -1 0.00000 0.00000
41 DNA 1 CYT C1' CD315A 2.31280 11.6110 0 -1.56200 1.10300
42 DNA 1 CYT DC1' DRUD -2.16880 0.400000 0 0.00000 0.00000
43 DNA 1 CYT H1' HDA1R5 0.550000E-01 1.00800 0 0.00000 0.00000
44 DNA 1 CYT C2' CD325B 2.06270 11.6110 0 -1.61700 1.10300
45 DNA 1 CYT DC2' DRUD -2.20670 0.400000 0 0.00000 0.00000
46 DNA 1 CYT H2'' HDA2R5 0.720000E-01 1.00800 0 0.00000 0.00000
47 DNA 1 CYT H2' HDA2R5 0.720000E-01 1.00800 0 0.00000 0.00000
48 DNA 1 CYT C3' CD315B 2.14820 11.6110 0 -1.64200 0.862000
49 DNA 1 CYT DC3' DRUD -2.22370 0.400000 0 0.00000 0.00000
50 DNA 1 CYT H3' HDA1R5 0.260000E-01 1.00800 0 0.00000 0.00000
51 DNA 1 CYT O3' OD30BN 1.17720 15.5994 0 -0.901000 0.181000
52 DNA 1 CYT DO3' DRUD -1.64720 0.400000 0 0.00000 0.00000
53 DNA 2 GUA P PD1AN 2.90360 30.5740 0 -0.974000 2.09800
54 DNA 2 GUA DP DRUD -1.71260 0.400000 0 0.00000 0.00000
55 DNA 2 GUA O1P OD2C2C 0.898400 15.5994 0 -0.931000 1.08300
56 DNA 2 GUA DO1P DRUD -1.67440 0.400000 0 0.00000 0.00000
57 DNA 2 GUA O2P OD2C2C 0.898400 15.5994 0 -0.931000 1.08300
58 DNA 2 GUA DO2P DRUD -1.67440 0.400000 0 0.00000 0.00000
59 DNA 2 GUA O5' OD30BN 1.17720 15.5994 0 -0.901000 0.181000
60 DNA 2 GUA DO5' DRUD -1.64720 0.400000 0 0.00000 0.00000
61 DNA 2 GUA C5' CD32C 2.42220 11.6110 0 -1.64200 0.862000
62 DNA 2 GUA DC5' DRUD -2.22370 0.400000 0 0.00000 0.00000
63 DNA 2 GUA H5' HDA2A 0.260000E-01 1.00800 0 0.00000 0.00000
64 DNA 2 GUA H5'' HDA2A 0.260000E-01 1.00800 0 0.00000 0.00000
65 DNA 2 GUA N9 ND2R5F 1.82490 13.6070 0 -0.880000 1.35100
66 DNA 2 GUA DN9 DRUD -1.62790 0.400000 0 0.00000 0.00000
67 DNA 2 GUA C4 CD2R6F 2.17410 11.6110 0 -1.25900 0.797000
68 DNA 2 GUA DC4 DRUD -1.94710 0.400000 0 0.00000 0.00000
69 DNA 2 GUA N3 ND2R6B 1.52370 13.6070 0 -0.771000 0.865000
70 DNA 2 GUA DN3 DRUD -1.52370 0.400000 0 0.00000 0.00000
71 DNA 2 GUA LP3 LPDNA1 -0.459000 0.00000 -1 0.00000 0.00000
72 DNA 2 GUA C2 CD2R6C 2.41450 11.6110 0 -1.10900 1.62800
73 DNA 2 GUA DC2 DRUD -1.82750 0.400000 0 0.00000 0.00000
74 DNA 2 GUA N1 ND2R6C 1.80700 13.6070 0 -1.56800 0.271000
75 DNA 2 GUA DN1 DRUD -2.17300 0.400000 0 0.00000 0.00000
76 DNA 2 GUA H1 HDP1A 0.287000 1.00800 0 0.00000 0.00000
77 DNA 2 GUA N2 ND2B1 1.32020 13.6070 0 -1.40400 0.298000
78 DNA 2 GUA DN2 DRUD -2.05620 0.400000 0 0.00000 0.00000
79 DNA 2 GUA H21 HDP1A 0.327000 1.00800 0 0.00000 0.00000
80 DNA 2 GUA H22 HDP1A 0.327000 1.00800 0 0.00000 0.00000
81 DNA 2 GUA C6 CD2O4A 1.95720 11.6110 0 -0.943000 1.94000
82 DNA 2 GUA DC6 DRUD -1.68520 0.400000 0 0.00000 0.00000
83 DNA 2 GUA O6 OD2C1B 1.36310 15.5994 0 -0.617000 1.53900
84 DNA 2 GUA DO6 DRUD -1.36310 0.400000 0 0.00000 0.00000
85 DNA 2 GUA LP6A LPDNA1 -0.259000 0.00000 -1 0.00000 0.00000
86 DNA 2 GUA LP6B LPDNA1 -0.138000 0.00000 -1 0.00000 0.00000
87 DNA 2 GUA C5 CD2R6F 2.32440 11.6110 0 -1.78800 1.03300
88 DNA 2 GUA DC5 DRUD -2.32040 0.400000 0 0.00000 0.00000
89 DNA 2 GUA N7 ND2R5E 1.39910 13.6070 0 -0.650000 0.946000
90 DNA 2 GUA DN7 DRUD -1.39910 0.400000 0 0.00000 0.00000
91 DNA 2 GUA LP7 LPDNA1 -0.322000 0.00000 -1 0.00000 0.00000
92 DNA 2 GUA C8 CD2R5F 1.96000 11.6110 0 -1.42700 1.30900
93 DNA 2 GUA DC8 DRUD -2.07300 0.400000 0 0.00000 0.00000
94 DNA 2 GUA H8 HDR5B 0.165000 1.00800 0 0.00000 0.00000
95 DNA 2 GUA C4' CD315B 2.31880 11.6110 0 -1.56200 1.10300
96 DNA 2 GUA DC4' DRUD -2.16880 0.400000 0 0.00000 0.00000
97 DNA 2 GUA H4' HDA1R5 0.550000E-01 1.00800 0 0.00000 0.00000
98 DNA 2 GUA O4' OD305A 1.36420 15.5994 0 -0.618000 1.54500
99 DNA 2 GUA DO4' DRUD -1.36420 0.400000 0 0.00000 0.00000
100 DNA 2 GUA LPRA LPD -0.152000 0.00000 -1 0.00000 0.00000
101 DNA 2 GUA LPRB LPD -0.152000 0.00000 -1 0.00000 0.00000
102 DNA 2 GUA LPX LPD 0.00000 0.00000 -1 0.00000 0.00000
103 DNA 2 GUA C1' CD315A 2.31280 11.6110 0 -1.56200 1.10300
104 DNA 2 GUA DC1' DRUD -2.16880 0.400000 0 0.00000 0.00000
105 DNA 2 GUA H1' HDA1R5 0.550000E-01 1.00800 0 0.00000 0.00000
106 DNA 2 GUA C2' CD325B 2.06270 11.6110 0 -1.61700 1.10300
107 DNA 2 GUA DC2' DRUD -2.20670 0.400000 0 0.00000 0.00000
108 DNA 2 GUA H2'' HDA2R5 0.720000E-01 1.00800 0 0.00000 0.00000
109 DNA 2 GUA H2' HDA2R5 0.720000E-01 1.00800 0 0.00000 0.00000
110 DNA 2 GUA C3' CD315B 2.14820 11.6110 0 -1.64200 0.862000
111 DNA 2 GUA DC3' DRUD -2.22370 0.400000 0 0.00000 0.00000
112 DNA 2 GUA H3' HDA1R5 0.260000E-01 1.00800 0 0.00000 0.00000
113 DNA 2 GUA O3' OD30BN 1.17720 15.5994 0 -0.901000 0.181000
114 DNA 2 GUA DO3' DRUD -1.64720 0.400000 0 0.00000 0.00000
115 DNA 3 CYT P PD1AN 2.90360 30.5740 0 -0.974000 2.09800
116 DNA 3 CYT DP DRUD -1.71260 0.400000 0 0.00000 0.00000
117 DNA 3 CYT O1P OD2C2C 0.898400 15.5994 0 -0.931000 1.08300
118 DNA 3 CYT DO1P DRUD -1.67440 0.400000 0 0.00000 0.00000
119 DNA 3 CYT O2P OD2C2C 0.898400 15.5994 0 -0.931000 1.08300
120 DNA 3 CYT DO2P DRUD -1.67440 0.400000 0 0.00000 0.00000
121 DNA 3 CYT O5' OD30BN 1.17720 15.5994 0 -0.901000 0.181000
122 DNA 3 CYT DO5' DRUD -1.64720 0.400000 0 0.00000 0.00000
123 DNA 3 CYT C5' CD32C 2.42220 11.6110 0 -1.64200 0.862000
124 DNA 3 CYT DC5' DRUD -2.22370 0.400000 0 0.00000 0.00000
125 DNA 3 CYT H5' HDA2A 0.260000E-01 1.00800 0 0.00000 0.00000
126 DNA 3 CYT H5'' HDA2A 0.260000E-01 1.00800 0 0.00000 0.00000
127 DNA 3 CYT N1 ND2R6C 1.81230 13.6070 0 -1.11000 0.822000
128 DNA 3 CYT DN1 DRUD -1.82830 0.400000 0 0.00000 0.00000
129 DNA 3 CYT C6 CD2R6H 2.15790 11.6110 0 -1.75200 2.00400
130 DNA 3 CYT DC6 DRUD -2.29690 0.400000 0 0.00000 0.00000
131 DNA 3 CYT H6 HDR6B 0.251000 1.00800 0 0.00000 0.00000
132 DNA 3 CYT C2 CD2O4A 2.55030 11.6110 0 -1.58000 2.06400
133 DNA 3 CYT DC2 DRUD -2.18130 0.400000 0 0.00000 0.00000
134 DNA 3 CYT O2 OD2C1B 1.42990 15.5994 0 -0.679000 0.675000
135 DNA 3 CYT DO2 DRUD -1.42990 0.400000 0 0.00000 0.00000
136 DNA 3 CYT LP2A LPDNA1 -0.180000 0.00000 -1 0.00000 0.00000
137 DNA 3 CYT LP2B LPDNA1 -0.266000 0.00000 -1 0.00000 0.00000
138 DNA 3 CYT N3 ND2R6B 1.23810 13.6070 0 -0.509000 0.737000
139 DNA 3 CYT DN3 DRUD -1.23810 0.400000 0 0.00000 0.00000
140 DNA 3 CYT LP3 LPDNA1 -0.491000 0.00000 -1 0.00000 0.00000
141 DNA 3 CYT C4 CD2R6B 2.43030 11.6110 0 -1.14300 1.24500
142 DNA 3 CYT DC4 DRUD -1.85530 0.400000 0 0.00000 0.00000
143 DNA 3 CYT N4 ND2B1 1.56610 13.6070 0 -1.62200 0.277000
144 DNA 3 CYT DN4 DRUD -2.21010 0.400000 0 0.00000 0.00000
145 DNA 3 CYT H41 HDP1A 0.346000 1.00800 0 0.00000 0.00000
146 DNA 3 CYT H42 HDP1A 0.346000 1.00800 0 0.00000 0.00000
147 DNA 3 CYT C5 CD2R6J 2.08510 11.6110 0 -1.85600 0.783000
148 DNA 3 CYT DC5 DRUD -2.36410 0.400000 0 0.00000 0.00000
149 DNA 3 CYT H5 HDR6A 0.128000 1.00800 0 0.00000 0.00000
150 DNA 3 CYT C4' CD315B 2.31880 11.6110 0 -1.56200 1.10300
151 DNA 3 CYT DC4' DRUD -2.16880 0.400000 0 0.00000 0.00000
152 DNA 3 CYT H4' HDA1R5 0.550000E-01 1.00800 0 0.00000 0.00000
153 DNA 3 CYT O4' OD305A 1.36420 15.5994 0 -0.618000 1.54500
154 DNA 3 CYT DO4' DRUD -1.36420 0.400000 0 0.00000 0.00000
155 DNA 3 CYT LPRA LPD -0.152000 0.00000 -1 0.00000 0.00000
156 DNA 3 CYT LPRB LPD -0.152000 0.00000 -1 0.00000 0.00000
157 DNA 3 CYT LPX LPD 0.00000 0.00000 -1 0.00000 0.00000
158 DNA 3 CYT C1' CD315A 2.31280 11.6110 0 -1.56200 1.10300
159 DNA 3 CYT DC1' DRUD -2.16880 0.400000 0 0.00000 0.00000
160 DNA 3 CYT H1' HDA1R5 0.550000E-01 1.00800 0 0.00000 0.00000
161 DNA 3 CYT C2' CD325B 2.06270 11.6110 0 -1.61700 1.10300
162 DNA 3 CYT DC2' DRUD -2.20670 0.400000 0 0.00000 0.00000
163 DNA 3 CYT H2'' HDA2R5 0.720000E-01 1.00800 0 0.00000 0.00000
164 DNA 3 CYT H2' HDA2R5 0.720000E-01 1.00800 0 0.00000 0.00000
165 DNA 3 CYT C3' CD315B 1.93390 11.6110 0 -1.24200 1.10300
166 DNA 3 CYT DC3' DRUD -1.93390 0.400000 0 0.00000 0.00000
167 DNA 3 CYT H3' HDA1R5 0.100000 1.00800 0 0.00000 0.00000
168 DNA 3 CYT O3' OD31G 1.37520 15.5990 0 -0.628000 0.181000
169 DNA 3 CYT DO3' DRUD -1.37520 0.400000 0 0.00000 0.00000
170 DNA 3 CYT H3T HDP1A 0.260000 1.00800 0 0.00000 0.00000
171 DNA 3 CYT LP3A LPD -0.230000 0.00000 -1 0.00000 0.00000
172 DNA 3 CYT LP3B LPD -0.230000 0.00000 -1 0.00000 0.00000
173 SOD 1 SOD SOD SODD 1.68760 22.6000 0 -0.157000 1.30000
174 SOD 1 SOD DSOD DRUD -0.687600 0.400000 0 0.00000 0.00000
175 SOD 2 SOD SOD SODD 1.68760 22.6000 0 -0.157000 1.30000
176 SOD 2 SOD DSOD DRUD -0.687600 0.400000 0 0.00000 0.00000
180 !NBOND: bonds
2 3 4 5 2 1 2 8
2 9 10 11 12 13 15 16
17 18 21 22 24 25 26 27
30 31 33 34 36 37 41 42
44 45 48 49 51 52 10 15
15 21 21 24 24 30 30 12
12 10 15 17 24 26 26 28
26 29 30 32 12 14 19 17
20 17 23 21 10 41 41 43
41 44 44 46 44 48 48 50
48 51 48 33 33 36 36 41
33 4 33 35 4 6 4 7
4 2 51 53 36 38 36 39
36 40 53 54 55 56 57 58
59 60 61 62 65 66 67 68
69 70 72 73 74 75 77 78
81 82 83 84 87 88 89 90
92 93 95 96 98 99 103 104
106 107 110 111 113 114 65 67
67 69 69 72 72 74 74 81
81 87 87 67 65 92 92 89
87 89 92 94 81 83 74 76
72 77 77 79 77 80 71 69
91 89 85 83 86 83 65 103
103 105 103 106 106 108 106 110
110 112 110 113 110 95 95 98
98 103 95 61 95 97 61 63
61 64 61 59 59 53 53 55
53 57 113 115 98 100 98 101
98 102 115 116 117 118 119 120
121 122 123 124 127 128 129 130
132 133 134 135 138 139 141 142
143 144 147 148 150 151 153 154
158 159 161 162 165 166 168 169
127 132 132 138 138 141 141 147
147 129 129 127 132 134 141 143
143 145 143 146 147 149 129 131
136 134 137 134 140 138 127 158
158 160 158 161 161 163 161 165
165 167 165 168 165 150 150 153
153 158 150 123 150 152 123 125
123 126 123 121 121 115 115 117
115 119 153 155 153 156 153 157
168 170 168 171 168 172 44 47
106 109 161 164 173 174 175 176
175 !NTHETA: angles
1 2 4 2 4 6 2 4 7
2 4 33 6 4 7 6 4 33
7 4 33 12 10 15 12 10 41
15 10 41 10 12 14 10 12 30
14 12 30 10 15 17 10 15 21
17 15 21 15 21 24 21 24 26
21 24 30 26 24 30 24 26 28
24 26 29 28 26 29 12 30 24
12 30 32 24 30 32 4 33 35
4 33 36 4 33 48 35 33 36
35 33 48 36 33 48 33 36 41
10 41 36 10 41 43 10 41 44
36 41 43 36 41 44 43 41 44
41 44 46 41 44 47 41 44 48
46 44 47 46 44 48 47 44 48
33 48 44 33 48 50 33 48 51
44 48 50 44 48 51 50 48 51
48 51 53 51 53 55 51 53 57
51 53 59 55 53 57 55 53 59
57 53 59 53 59 61 59 61 63
59 61 64 59 61 95 63 61 64
63 61 95 64 61 95 67 65 92
67 65 103 92 65 103 65 67 69
65 67 87 69 67 87 67 69 72
69 72 74 69 72 77 74 72 77
72 74 76 72 74 81 76 74 81
72 77 79 72 77 80 79 77 80
74 81 83 74 81 87 83 81 87
67 87 81 67 87 89 81 87 89
87 89 92 65 92 89 65 92 94
89 92 94 61 95 97 61 95 98
61 95 110 97 95 98 97 95 110
98 95 110 95 98 103 65 103 98
65 103 105 65 103 106 98 103 105
98 103 106 105 103 106 103 106 108
103 106 109 103 106 110 108 106 109
108 106 110 109 106 110 95 110 106
95 110 112 95 110 113 106 110 112
106 110 113 112 110 113 110 113 115
113 115 117 113 115 119 113 115 121
117 115 119 117 115 121 119 115 121
115 121 123 121 123 125 121 123 126
121 123 150 125 123 126 125 123 150
126 123 150 129 127 132 129 127 158
132 127 158 127 129 131 127 129 147
131 129 147 127 132 134 127 132 138
134 132 138 132 138 141 138 141 143
138 141 147 143 141 147 141 143 145
141 143 146 145 143 146 129 147 141
129 147 149 141 147 149 123 150 152
123 150 153 123 150 165 152 150 153
152 150 165 153 150 165 150 153 158
127 158 153 127 158 160 127 158 161
153 158 160 153 158 161 160 158 161
158 161 163 158 161 164 158 161 165
163 161 164 163 161 165 164 161 165
150 165 161 150 165 167 150 165 168
161 165 167 161 165 168 167 165 168
165 168 170
258 !NPHI: dihedrals
1 2 4 6 1 2 4 7
1 2 4 33 2 4 33 35
2 4 33 36 2 4 33 48
4 33 36 41 4 33 48 44
4 33 48 50 4 33 48 51
6 4 33 35 6 4 33 36
6 4 33 48 7 4 33 35
7 4 33 36 7 4 33 48
10 12 30 24 10 12 30 32
10 15 21 24 10 41 36 33
10 41 44 46 10 41 44 47
10 41 44 48 12 10 15 17
12 10 15 21 12 10 41 36
12 10 41 43 12 10 41 44
12 30 24 21 12 30 24 26
14 12 10 15 14 12 10 41
14 12 30 24 14 12 30 32
15 10 12 30 15 10 41 36
15 10 41 43 15 10 41 44
15 21 24 26 15 21 24 30
17 15 10 41 17 15 21 24
21 15 10 41 21 24 26 28
21 24 26 29 21 24 30 32
26 24 30 32 28 26 24 30
29 26 24 30 30 12 10 41
33 36 41 43 33 36 41 44
33 48 44 41 33 48 44 46
33 48 44 47 33 48 51 53
35 33 36 41 35 33 48 44
35 33 48 50 35 33 48 51
36 33 48 44 36 33 48 50
36 33 48 51 36 41 44 46
36 41 44 47 36 41 44 48
41 36 33 48 41 44 48 50
41 44 48 51 43 41 44 46
43 41 44 47 43 41 44 48
44 48 51 53 46 44 48 50
46 44 48 51 47 44 48 50
47 44 48 51 48 51 53 55
48 51 53 57 48 51 53 59
50 48 51 53 51 53 59 61
53 59 61 63 53 59 61 64
53 59 61 95 55 53 59 61
57 53 59 61 59 61 95 97
59 61 95 98 59 61 95 110
61 95 98 103 61 95 110 106
61 95 110 112 61 95 110 113
63 61 95 97 63 61 95 98
63 61 95 110 64 61 95 97
64 61 95 98 64 61 95 110
65 67 69 72 65 67 87 81
65 67 87 89 65 92 89 87
65 103 98 95 65 103 106 108
65 103 106 109 65 103 106 110
67 65 92 89 67 65 92 94
67 65 103 98 67 65 103 105
67 65 103 106 67 69 72 74
67 69 72 77 67 87 81 74
67 87 81 83 67 87 89 92
69 67 65 92 69 67 65 103
69 67 87 81 69 67 87 89
69 72 74 76 69 72 74 81
69 72 77 79 69 72 77 80
72 69 67 87 72 74 81 83
72 74 81 87 74 72 77 79
74 72 77 80 74 81 87 89
76 74 72 77 76 74 81 83
76 74 81 87 77 72 74 81
81 87 89 92 83 81 87 89
87 67 65 92 87 67 65 103
87 89 92 94 89 92 65 103
92 65 103 98 92 65 103 105
92 65 103 106 94 92 65 103
95 98 103 105 95 98 103 106
95 110 106 103 95 110 106 108
95 110 106 109 95 110 113 115
97 95 98 103 97 95 110 106
97 95 110 112 97 95 110 113
98 95 110 106 98 95 110 112
98 95 110 113 98 103 106 108
98 103 106 109 98 103 106 110
103 98 95 110 103 106 110 112
103 106 110 113 105 103 106 108
105 103 106 109 105 103 106 110
106 110 113 115 108 106 110 112
108 106 110 113 109 106 110 112
109 106 110 113 110 113 115 117
110 113 115 119 110 113 115 121
112 110 113 115 113 115 121 123
115 121 123 125 115 121 123 126
115 121 123 150 117 115 121 123
119 115 121 123 121 123 150 152
121 123 150 153 121 123 150 165
123 150 153 158 123 150 165 161
123 150 165 167 123 150 165 168
125 123 150 152 125 123 150 153
125 123 150 165 126 123 150 152
126 123 150 153 126 123 150 165
127 129 147 141 127 129 147 149
127 132 138 141 127 158 153 150
127 158 161 163 127 158 161 164
127 158 161 165 129 127 132 134
129 127 132 138 129 127 158 153
129 127 158 160 129 127 158 161
129 147 141 138 129 147 141 143
131 129 127 132 131 129 127 158
131 129 147 141 131 129 147 149
132 127 129 147 132 127 158 153
132 127 158 160 132 127 158 161
132 138 141 143 132 138 141 147
134 132 127 158 134 132 138 141
138 132 127 158 138 141 143 145
138 141 143 146 138 141 147 149
143 141 147 149 145 143 141 147
146 143 141 147 147 129 127 158
150 153 158 160 150 153 158 161
150 165 161 158 150 165 161 163
150 165 161 164 150 165 168 170
152 150 153 158 152 150 165 161
152 150 165 167 152 150 165 168
153 150 165 161 153 150 165 167
153 150 165 168 153 158 161 163
153 158 161 164 153 158 161 165
158 153 150 165 158 161 165 167
158 161 165 168 160 158 161 163
160 158 161 164 160 158 161 165
161 165 168 170 163 161 165 167
163 161 165 168 164 161 165 167
164 161 165 168 167 165 168 170
9 !NIMPHI: impropers
15 10 21 17 24 21 30 26
26 24 28 29 72 69 74 77
81 74 87 83 77 79 72 80
132 127 138 134 141 138 147 143
143 141 145 146
9 !NDON: donors
2 1 26 28 26 29 74 76
77 79 77 80 143 145 143 146
168 170
20 !NACC: acceptors
2 0 17 15 21 0 36 0
51 0 55 53 57 53 59 0
69 0 83 81 89 0 98 0
113 0 117 115 119 115 121 0
134 132 138 0 153 0 168 0
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 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 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
19 0 !NGRP NST2
0 1 0 9 1 0 32 2 0
43 1 0 47 2 0 50 2 0
52 2 0 64 1 0 94 2 0
105 1 0 109 2 0 112 2 0
114 2 0 126 1 0 149 2 0
160 1 0 164 2 0 172 2 0
174 2 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 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 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
23 92 !NUMLP NUMLPH
3 1 F 0.350000 110.000 91.0000
3 5 F 0.350000 110.000 269.000
3 9 F 0.350000 110.000 180.000
3 13 F 0.350000 110.000 180.000
3 17 F -0.350000 179.990 179.990
3 21 F -0.350000 110.000 90.0000
3 25 F -0.350000 110.000 270.000
3 29 F -0.100000 0.00000 0.00000
3 33 F -0.350000 179.990 179.990
3 37 F 0.350000 110.000 180.000
3 41 F 0.350000 110.000 180.000
3 45 F -0.350000 179.990 179.990
3 49 F -0.350000 110.000 90.0000
3 53 F -0.350000 110.000 270.000
3 57 F -0.100000 0.00000 0.00000
3 61 F 0.350000 110.000 180.000
3 65 F 0.350000 110.000 180.000
3 69 F -0.350000 179.990 179.990
3 73 F -0.350000 110.000 90.0000
3 77 F -0.350000 110.000 270.000
3 81 F -0.100000 0.00000 0.00000
3 85 F 0.350000 110.000 91.0000
3 89 F 0.350000 110.000 269.000
8 2 4 1 9 2 4 1
19 17 15 10 20 17 15 21
23 21 15 24 38 36 41 33
39 36 41 33 40 36 41 33
71 69 72 67 85 83 81 74
86 83 81 87 91 89 87 92
100 98 103 95 101 98 103 95
102 98 103 95 136 134 132 127
137 134 132 138 140 138 132 141
155 153 158 150 156 153 158 150
157 153 158 150 171 168 165 170
172 168 165 170
20 !NUMANISO
102.800 -102.758 13.8746
256.226 -51.3020 -38.6603
0.227374E-12 -257.540 118.812
0.00000 -153.395 62.4930
0.227374E-12 -257.540 118.812
256.226 -51.3020 -38.6603
0.227374E-12 -257.540 118.812
0.00000 -153.395 62.4930
142.857 476.190 -142.857
476.190 142.857 -142.857
476.190 142.857 -142.857
256.226 -51.3020 -38.6603
0.227374E-12 -257.540 118.812
0.00000 -153.395 62.4930
142.857 476.190 -142.857
476.190 142.857 -142.857
476.190 142.857 -142.857
102.800 -102.758 13.8746
142.857 476.190 -142.857
142.857 476.190 -142.857
2 4 8 9 17 15 10 21
21 23 24 15 36 40 38 39
69 71 67 72 83 81 87 74
89 91 92 87 98 102 100 101
59 55 51 57 55 53 59 51
57 53 51 59 134 132 127 138
138 140 141 132 153 157 155 156
121 117 113 119 117 115 121 113
119 115 113 121 168 165 171 172
51 57 59 55 113 119 121 117
0 !NCRTERM: cross-terms
wrappers/python/tests/systems/toppar_drude_nucleic_acid_2017b.str 0 → 100644
View file @ 698769b9
* DRUDE topology and parameter stream file
* Nucleic acids
*
! jal: contains initial RNA parameter set, not fully tested yet
!requires toppar_drude_master*.str
!nucleic acids
!references
!
!Lemkul, J.A. and MacKerell, A.D., Jr., "Polarizable Force Field for
!DNA Based on the Classical Drude Oscillator: I. Refinement using
!Quantum Mechanical Base Stacking and Conformational Energetics,"
!J. Chem. Theory Comput., In Press, 2017, DOI: 10.1021/acs.jctc.7b00067
!
!Lemkul, J.A. and MacKerell, A.D., Jr., "Polarizable Force Field for
!DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular
!Dynamics Simulations of Duplex DNA," J. Chem. Theory Comput.,
!In Press, 2017, DOI: 10.1021/acs.jctc.7b00068
!
!Savelyev, A. and MacKerell, A.D., Jr., "All-Atom Polarizable Force
!Field for DNA Based on the Classical Drude Oscillator Model," Journal
!of Computational Chemistry, 35; 1219-1239, 2014, DOI: 10.1002/jcc.23611,
!NIHMSID #585697
!
!Nucleic Acid Bases
!Baker, C.M., Anisimov, V.M., and MacKerell, A.D., Jr., "Development of
!CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the
!Classical Drude Oscillator Model," Journal of Physical Chemistry B,
!115; 580-596, 2011, PMC3166616
!
read rtf card append
* Topology for Drude nucleic acids
*
38
!
DECL +P
DECL +O1P
DECL +O2P
DECL +O5'
DECL -O3'
DEFA FIRS 5TER LAST 3TER
AUTOGENERATE ANGLES DIHEDRALS DRUDE
RESI CYT -1.000 ! Cytosine, jal update 06/15
!
! H42 H41
! \ /
! N4
! |
! C4
! / \\
! H5-C5 N3
! || |
! H6-C6 C2
! \ / \\
! N1 O2
! /
! O1P H5' H4' O4' /
! | | \ / \ /
! -P-O5'-C5'----C4' C1'-H1'
! | | \ /
! O2P H5'' C3'-C2'-H2''
! / \ \
! O3' H3' O2'-H2'
!GROUP
ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 ! DMP
ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O5' OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM C5' CD32C 0.1985 ALPHA -1.642 THOLE 0.862
ATOM H5' HDA2A 0.026
ATOM H5'' HDA2A 0.026
GROUP !!NA base
ATOM N1 ND2R6C -0.016 ALPHA -1.110 THOLE 0.822
ATOM C6 CD2R6H -0.139 ALPHA -1.752 THOLE 2.004
ATOM H6 HDR6B 0.251
ATOM C2 CD2O4A 0.369 ALPHA -1.580 THOLE 2.064
ATOM O2 OD2C1B 0.000 ALPHA -0.679 THOLE 0.675
ATOM LP2A LPDNA1 -0.180
ATOM LP2B LPDNA1 -0.266
ATOM N3 ND2R6B 0.000 ALPHA -0.509 THOLE 0.737
ATOM LP3 LPDNA1 -0.491
ATOM C4 CD2R6B 0.575 ALPHA -1.143 THOLE 1.245
ATOM N4 ND2B1 -0.644 ALPHA -1.622 THOLE 0.277
ATOM H41 HDP1A 0.346
ATOM H42 HDP1A 0.346
ATOM C5 CD2R6J -0.279 ALPHA -1.856 THOLE 0.783
ATOM H5 HDR6A 0.128
GROUP !! THF
ATOM C4' CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H4' HDA1R5 0.055
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H1' HDA1R5 0.055
GROUP !! PRO2, changed from EtOH - jal 7/18/2014
!! jal 7/18/2014
ATOM C2' CD315B 0.000 ALPHA -1.242 THOLE 1.103 ! neutralize group charge
ATOM H2'' HDA1R5 0.100
ATOM O2' OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2' HDP1A 0.260
ATOM LPHA LPD -0.180
ATOM LPHB LPD -0.180
GROUP
ATOM C3' CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e
ATOM H3' HDA1R5 0.026
ATOM O3' OD30BR -0.470 ALPHA -0.901 THOLE 0.181
BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1
BOND C2 O2 C4 N4 N4 H41 N4 H42 C5 H5 C6 H6
BOND LP2A O2 LP2B O2
BOND LP3 N3
BOND N1 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2'
BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1'
BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P
BOND P O2P O3' +P
BOND O4' LPRA O4' LPRB
BOND O4' LPX
BOND O2' LPHA O2' LPHB
IMPR C2 N1 N3 O2 C4 N3 C5 N4
IMPR N4 C4 H41 H42
! Base lone pairs
LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
! O4' Lone pairs
LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
! O2' Lone pairs
LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0
!Anisotropies
! Base anisotropies
ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
!O4' Anisotropy
ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222
!O2' anisotropy
ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162
!Phosphate Anisotropy
ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000
DONO H42 N4
DONO H2' O2'
DONO H41 N4
ACCE O2 C2
ACCE N3
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364
IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337
IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356
IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237
IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334
IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337
IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01
IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01
IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
RESI THY -1.000 ! Thymine, jal update 06/15
!
! H51 O4
! | ||
! H52-C5M C4 H3
! | \ / \ /
! H53 C5 N3
! || |
! H6-C6 C2
! \ / \\
! N1 O2
! /
! O1P H5' H4' O4' /
! | | \ / \ /
! -P-O5'-C5'----C4' C1'-H1'
! | | \ /
! O2P H5'' C3'-C2'-H2''
! / \ \
! O3' H3' O2'-H2'
!
GROUP
ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 ! DMP
ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O5' OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM C5' CD32C 0.1985 ALPHA -1.642 THOLE 0.862
ATOM H5' HDA2A 0.026
ATOM H5'' HDA2A 0.026
GROUP
ATOM N1 ND2R6D -0.192 ALPHA -0.979 THOLE 1.057 !! jal atom type
ATOM C6 CD2R6H 0.138 ALPHA -1.545 THOLE 0.534
ATOM H6 HDR6B 0.282
ATOM C2 CD2O4A 0.524 ALPHA -0.985 THOLE 1.928
ATOM O2 OD2C1B 0.000 ALPHA -0.587 THOLE 1.945
ATOM LP2A LPDNA1 -0.131
ATOM LP2B LPDNA1 -0.229
ATOM N3 ND2R6C -0.506 ALPHA -0.766 THOLE 1.447
ATOM H3 HDP1A 0.297
ATOM C4 CD2O4A 0.493 ALPHA -1.013 THOLE 0.566
ATOM O4 OD2C1B 0.000 ALPHA -1.556 THOLE 1.924
ATOM LP4A LPDNA1 -0.302
ATOM LP4B LPDNA1 -0.168
ATOM C5 CD2R6J -0.174 ALPHA -1.209 THOLE 1.848
ATOM C5M CD33A -0.173 ALPHA -1.545 THOLE 0.326
ATOM H51 HDA3A 0.047
ATOM H52 HDA3A 0.047
ATOM H53 HDA3A 0.047
GROUP !! THF
ATOM C4' CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H4' HDA1R5 0.055
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H1' HDA1R5 0.055
GROUP !! PRO2, changed from EtOH - jal 7/18/2014
!! jal 7/18/2014
ATOM C2' CD315B 0.000 ALPHA -1.242 THOLE 1.103 ! neutralize group charge
ATOM H2'' HDA1R5 0.100
ATOM O2' OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2' HDP1A 0.260
ATOM LPHA LPD -0.180
ATOM LPHB LPD -0.180
GROUP
ATOM C3' CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e
ATOM H3' HDA1R5 0.026
ATOM O3' OD30BR -0.470 ALPHA -0.901 THOLE 0.181
BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6
BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 C5M
BOND C5M H51 C5M H52 C5M H53 C6 H6
BOND LP2A O2 LP2B O2
BOND LP4A O4 LP4B O4
BOND N1 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2'
BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1'
BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P
BOND P O2P O3' +P
BOND O4' LPRA O4' LPRB
BOND O4' LPX
BOND O2' LPHA O2' LPHB
IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M
! Base lone pairs
LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0
! O4' Lone pairs
LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
! O2' Lone pairs
LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0
!Anisotropies
! Base anisotropies
ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA
!O4' Anisotropy
ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222
!O2' anisotropy
ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162
!Phosphate Anisotropy
ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000
DONO H3 N3
ACCE O2 C2
ACCE O4 C4
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704
IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432
IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813
IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191
IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795
IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327
IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900
IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0
IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0
IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0
RESI URA -1.000 ! Uracil
!
! O4
! ||
! C4 H3
! / \ /
! H5-C5 N3
! || |
! H6-C6 C2
! \ / \\
! N1 O2
! /
! O1P H5' H4' O4' /
! | | \ / \ /
! -P-O5'-C5'----C4' C1'-H1'
! | | \ /
! O2P H5'' C3'-C2'-H2''
! / \ \
! O3' H3' O2'-H2'
!
GROUP
ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 ! DMP
ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O5' OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM C5' CD32C 0.1985 ALPHA -1.642 THOLE 0.862
ATOM H5' HDA2A 0.026
ATOM H5'' HDA2A 0.026
GROUP
ATOM N1 ND2R6C -0.240 ALPHA -1.192 THOLE 1.639
ATOM C6 CD2R6H 0.095 ALPHA -0.500 THOLE 0.544 !!!CB
ATOM H6 HDR6B 0.341
ATOM C2 CD2O4A 0.636 ALPHA -1.072 THOLE 1.120
ATOM O2 OD2C1B 0.000 ALPHA -0.799 THOLE 1.076
ATOM LP2A LPDNA1 -0.126
ATOM LP2B LPDNA1 -0.229
ATOM N3 ND2R6C -0.593 ALPHA -1.631 THOLE 1.574
ATOM H3 HDP1A 0.317
ATOM C4 CD2O4A 0.557 ALPHA -1.072 THOLE 1.079
ATOM O4 OD2C1B 0.000 ALPHA -0.657 THOLE 1.156
ATOM LP4A LPDNA1 -0.254
ATOM LP4B LPDNA1 -0.192
ATOM C5 CD2R6J -0.321 ALPHA -1.949 THOLE 1.307
ATOM H5 HDR6A 0.009
GROUP !! THF
ATOM C4' CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H4' HDA1R5 0.055
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H1' HDA1R5 0.055
GROUP !! PRO2, changed from EtOH - jal 7/18/2014
!! jal 7/18/2014
ATOM C2' CD315B 0.000 ALPHA -1.242 THOLE 1.103 ! neutralize group charge
ATOM H2'' HDA1R5 0.100
ATOM O2' OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2' HDP1A 0.260
ATOM LPHA LPD -0.180
ATOM LPHB LPD -0.180
GROUP
ATOM C3' CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e
ATOM H3' HDA1R5 0.026
ATOM O3' OD30BR -0.470 ALPHA -0.901 THOLE 0.181
BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6
BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 H5
BOND C6 H6
BOND LP2A O2 LP2B O2
BOND LP4A O4 LP4B O4
BOND N1 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2'
BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1'
BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P
BOND P O2P O3' +P
BOND O4' LPRA O4' LPRB
BOND O4' LPX
BOND O2' LPHA O2' LPHB
IMPR C2 N1 N3 O2 C4 N3 C5 O4
! Base lone pairs
LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0
! O4' Lone pairs
LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
! O2' Lone pairs
LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0
!Anisotropies
! Base anisotropies
ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA
!O4' Anisotropy
ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222
!O2' anisotropy
ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162
!Phosphate Anisotropy
ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000
DONO H3 N3
DONO H2' O2'
ACCE O2 C2
ACCE O4 C4
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160
IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284
IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212
IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001
IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251
IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896
IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746
IC C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379
IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338
IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373
IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218
IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383
IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227
IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03
IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
RESI ADE -1.000 ! Adenine, jal update 06/15
!
! H61 H62
! \ /
! N6
! |
! C6
! // \
! N1 C5--N7\\
! | || C8-H8
! C2 C4--N9/
! / \\ / \
! H2 N3 \
! \
! /
! O1P H5' H4' O4' /
! | | \ / \ /
! -P-O5'-C5'----C4' C1'-H1'
! | | \ /
! O2P H5'' C3'-C2'-H2''
! / \ \
! O3' H3' O2'-H2'
!
GROUP
ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 ! DMP
ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O5' OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM C5' CD32C 0.1985 ALPHA -1.642 THOLE 0.862
ATOM H5' HDA2A 0.026
ATOM H5'' HDA2A 0.026
GROUP
ATOM N9 ND2R5D 0.066 ALPHA -0.676 THOLE 0.935
ATOM C4 CD2R6F 0.227 ALPHA -1.045 THOLE 1.100
ATOM N3 ND2R6B 0.000 ALPHA -1.602 THOLE 0.006
ATOM LP3 LPDNA1 -0.507
ATOM C2 CD2R6C 0.208 ALPHA -1.120 THOLE 1.469
ATOM H2 HDR6C 0.176
ATOM N1 ND2R6B 0.000 ALPHA -1.507 THOLE 0.967
ATOM LP1 LPDNA1 -0.472
ATOM C6 CD2R6C 0.402 ALPHA -1.454 THOLE 0.557
ATOM N6 ND2B1 -0.742 ALPHA -1.330 THOLE 0.465
ATOM H61 HDP1A 0.373
ATOM H62 HDP1A 0.373
ATOM C5 CD2R6F -0.118 ALPHA -1.238 THOLE 1.854
ATOM N7 ND2R5E 0.000 ALPHA -1.462 THOLE 0.252
ATOM LP7 LPDNA1 -0.189
ATOM C8 CD2R5F 0.038 ALPHA -1.357 THOLE 1.402
ATOM H8 HDR5B 0.165
GROUP !! THF
ATOM C4' CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H4' HDA1R5 0.055
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H1' HDA1R5 0.055
GROUP !! PRO2, changed from EtOH - jal 7/18/2014
!! jal 7/18/2014
ATOM C2' CD315B 0.000 ALPHA -1.242 THOLE 1.103 ! neutralize group charge
ATOM H2'' HDA1R5 0.100
ATOM O2' OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2' HDP1A 0.260
ATOM LPHA LPD -0.180
ATOM LPHB LPD -0.180
GROUP
ATOM C3' CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e
ATOM H3' HDA1R5 0.026
ATOM O3' OD30BR -0.470 ALPHA -0.901 THOLE 0.181
BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6
BOND C6 C5 C5 C4 N9 C8 C8 N7 N7 C5
BOND C8 H8 C6 N6 N6 H61 N6 H62 C2 H2
BOND LP1 N1 !LP1 C2 LP1 C6
BOND LP3 N3 !LP3 C2 LP3 C4
BOND LP7 N7 !LP7 C5 LP7 C8
BOND N9 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2'
BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1'
BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P
BOND P O2P O3' +P
BOND O4' LPRA O4' LPRB !C1' LPRA C1' LPRB C4' LPRA C4' LPRB
BOND O4' LPX !C1' LPX C4' LPX
BOND O2' LPHA O2' LPHB !C2' LPHA C2' LPHB
! Base lone pairs
LONEPAIR bisector LP1 N1 C2 C6 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99
! O4' Lone pairs
LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
! O2' Lone pairs
LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0
!Anisotropies
! Base anisotropies
ANISOTROPY N1 LP1 C6 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID
!O4' Anisotropy
ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222
!O2' anisotropy
ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162
!Phosphate Anisotropy
ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000
IMPR N6 C6 H61 H62 C6 N1 C5 N6
DONO H61 N6
DONO H62 N6
DONO H2' O2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367
IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312
IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382
IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0
IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0
IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0
IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342
IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337
IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01
IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01
IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337
IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01
IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01
IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
RESI GUA -1.000 ! Guanine, jal update 06/15
!
! O6
! ||
! C6
! / \
! H1-N1 C5--N7\\
! | || C8-H8
! C2 C4--N9/
! / \\ / \
! H21-N2 N3 \
! | \
! H22 \
! \
! /
! O1P H5' H4' O4' /
! | | \ / \ /
! -P-O5'-C5'----C4' C1'-H1'
! | | \ /
! O2P H5'' C3'-C2'-H2''
! / \ \
! O3' H3' O2'-H2'
! |
GROUP
ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 ! DMP
ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O5' OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM C5' CD32C 0.1985 ALPHA -1.642 THOLE 0.862
ATOM H5' HDA2A 0.026
ATOM H5'' HDA2A 0.026
GROUP
ATOM N9 ND2R5F 0.197 ALPHA -0.880 THOLE 1.351
ATOM C4 CD2R6F 0.227 ALPHA -1.259 THOLE 0.797
ATOM N3 ND2R6B 0.000 ALPHA -0.771 THOLE 0.865
ATOM LP3 LPDNA1 -0.459
ATOM C2 CD2R6C 0.587 ALPHA -1.109 THOLE 1.628
ATOM N1 ND2R6C -0.366 ALPHA -1.568 THOLE 0.271
ATOM H1 HDP1A 0.287
ATOM N2 ND2B1 -0.736 ALPHA -1.404 THOLE 0.298
ATOM H21 HDP1A 0.327
ATOM H22 HDP1A 0.327
ATOM C6 CD2O4A 0.272 ALPHA -0.943 THOLE 1.940
ATOM O6 OD2C1B 0.000 ALPHA -0.617 THOLE 1.539
ATOM LP6A LPDNA1 -0.259
ATOM LP6B LPDNA1 -0.138
ATOM C5 CD2R6F 0.004 ALPHA -1.788 THOLE 1.033
ATOM N7 ND2R5E 0.000 ALPHA -0.650 THOLE 0.946
ATOM LP7 LPDNA1 -0.322
ATOM C8 CD2R5F -0.113 ALPHA -1.427 THOLE 1.309
ATOM H8 HDR5B 0.165
GROUP !! THF
ATOM C4' CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H4' HDA1R5 0.055
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H1' HDA1R5 0.055
GROUP !! PRO2, changed from EtOH - jal 7/18/2014
!! jal 7/18/2014
ATOM C2' CD315B 0.000 ALPHA -1.242 THOLE 1.103 ! neutralize group charge
ATOM H2'' HDA1R5 0.100
ATOM O2' OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2' HDP1A 0.260
ATOM LPHA LPD -0.180
ATOM LPHB LPD -0.180
GROUP
ATOM C3' CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e
ATOM H3' HDA1R5 0.026
ATOM O3' OD30BR -0.470 ALPHA -0.901 THOLE 0.181
BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6 C6 C5
BOND C5 C4 N9 C8 C8 N7 C5 N7 C8 H8 C6 O6
BOND N1 H1 C2 N2 N2 H21 N2 H22
BOND LP3 N3 !LP3 C2 LP3 C4
BOND LP7 N7 !LP7 C5 LP7 C8
BOND LP6A O6 LP6B O6 !LP6A C6 LP6B C6
BOND N9 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2'
BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1'
BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P
BOND P O2P O3' +P
BOND O4' LPRA O4' LPRB !C1' LPRA C1' LPRB C4' LPRA C4' LPRB
BOND O4' LPX !C1' LPX C4' LPX
BOND O2' LPHA O2' LPHB !C2' LPHA C2' LPHB
IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22
! Base lone pairs
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR relative LP6A O6 C6 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP6B O6 C6 C5 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99
! O4' Lone pairs
LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
! O2' Lone pairs
LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0
!Anisotropies
! Base anisotropies
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY O6 C6 C5 N1 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID
!O4' Anisotropy
ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222
!O2' anisotropy
ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162
!Phosphate Anisotropy
ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000
DONO H21 N2
DONO H22 N2
DONO H1 N1
DONO H2' O2'
ACCE O6 C6
ACCE N3
ACCE N7
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
! Chi and sugar-phosphate backbone in B-DNA ike conformation
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374
IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304
IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377
IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355
IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327
IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375
IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341
IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01
IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01
IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393
IC C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03
IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239
IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
PRES 5TER 0.000 ! 5-terminal HYDROXYL patch, from MeOH
!
! Base
! H5T1 H4' O4' /
! | \ / \ /
! H5T-O5T-C5T----C4' C1'-H1'
! | \ /
! H5T2 C3'-C2D-H2D
! / \ \
! O3' H3' H2Da
! |
DELETE ATOM P
DELETE ATOM O1P
DELETE ATOM O2P
DELETE ATOM DP
DELETE ATOM DO1P
DELETE ATOM DO2P
DELETE ATOM DO5'
DELETE ATOM DC5'
GROUP
ATOM H5T HDP1A 0.360
ATOM O5' OD31A 0.000 ALPHA -1.028 THOLE 1.3
ATOM C5' CD32A -0.060 ALPHA -1.000 THOLE 1.3
ATOM H5' HDA2A 0.080
ATOM H5'' HDA2A 0.080
ATOM LP5A LPD -0.230
ATOM LP5B LPD -0.230
BOND O5' H5T
BOND O5' LP5A O5' LP5B
LONEPAIR relative LP5A O5' C5' H5T distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP5B O5' C5' H5T distance 0.35 angle 110.0 dihe 269.0
ANISOTROPY O5' C5' LP5A LP5B A11 0.8108 A22 1.2162
DONO H5T O5'
IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000
PRES 3TER -0.100 ! 3-terminal HYDROXYL patch, from PRO2 (jal 7/18/2014)
!
! \
! C3T-
! / \
! O3T H3'
! |
! H3T
GROUP
ATOM C3' CD315B 0.000 ALPHA -1.242 THOLE 1.103 ! neutralize group charge
ATOM H3' HDA1R5 0.100
ATOM O3' OD31G 0.000 ALPHA -0.628 THOLE 0.181
ATOM H3T HDP1A 0.260
ATOM LP3A LPD -0.230
ATOM LP3B LPD -0.230
BOND O3' H3T
BOND O3' LP3A O3' LP3B
LONEPAIR relative LP3A O3' C3' H3T distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP3B O3' C3' H3T distance 0.35 angle 110.0 dihe 269.0
ANISOTROPY O3' C3' LP3A LP3B A11 0.8108 A22 1.2162
DONO H3T O3'
IC H3T O3' C3' C4' 0.0000 0.00 -180.00 0.00 0.0000
PRES DEOX -0.470 ! Patch to make DEOXYribose from default ribose bases
! modified by jal 7/18/2014 due to RNA-specific atom type for O3'
DELETE ATOM O2'
DELETE ATOM LPHA
DELETE ATOM LPHB
DELETE ATOM DO2'
DELETE ANISOTROPY O3' +O2P +O5' +O1P A11 1.0000 A22 0.6000
GROUP
ATOM O3' OD30BN -0.470 ALPHA -0.901 THOLE 0.181
GROUP
ATOM C2' CD325B -0.144 ALPHA -1.617 THOLE 1.103 !neutralize group charge
ATOM H2' HDA2R5 0.072
ATOM H2'' HDA2R5 0.072
BOND C2' H2'
BOND C3' O3'
BOND O3' +P
ANISOTROPY O3' +O2P +O5' +O1P A11 1.0000 A22 0.6000
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C1' C3' *C2' H2' 0.0000 0.0000 -115.00 0.0000 0.0000
PRES DEO3 0.000 ! for the 3'-terminal DNA nucleotides
DELETE ATOM O2'
DELETE ATOM LPHA
DELETE ATOM LPHB
DELETE ATOM DO2'
GROUP
ATOM C2' CD325B -0.144 ALPHA -1.617 THOLE 1.103 !neutralize group charge
ATOM H2' HDA2R5 0.072
ATOM H2'' HDA2R5 0.072
BOND C2' H2'
BOND C3' O3'
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C1' C3' *C2' H2' 0.0000 0.0000 -115.00 0.0000 0.0000
!! jal - for making nucleotides
PRES 3POM -0.6805
GROUP
ATOM P3 PD1AN 1.191 ALPHA -0.974 THOLE 2.098
ATOM O3P1 OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O3P2 OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O3T OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM C3T CD32C 0.0725 ALPHA -1.642 THOLE 0.862 ! -0.1e, jal
ATOM H3T1 HDA2A 0.026
ATOM H3T2 HDA2A 0.026
ATOM H3T3 HDA2A 0.026
BOND O3' P3
BOND P3 O3P1 P3 O3P2 P3 O3T
BOND O3T C3T
BOND C3T H3T1 C3T H3T2 C3T H3T3
ANISOTROPY O3T O3P1 O3' O3P2 A11 1.0000 A22 0.6000
ANISOTROPY O3' O3P2 O3T O3P1 A11 1.0000 A22 0.6000
ANISOTROPY O3P1 P3 O3T O3' A11 0.6000 A22 1.0000
ANISOTROPY O3P2 P3 O3' O3T A11 0.6000 A22 1.0000
IC P3 O3' C3' C4' 0.0000 000.00 180.00 000.00 0.0000
IC C3' O3' P3 O3T 0.0000 000.00 -95.22 000.00 0.0000
IC O3T O3' *P3 O3P1 0.0000 000.00 -115.82 000.00 0.0000
IC O3T O3' *P3 O3P2 0.0000 000.00 115.90 000.00 0.0000
IC C3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000
IC H3T1 C3T O3T P3 0.0000 000.00 180.00 000.00 0.0000
IC H3T2 C3T O3T P3 0.0000 000.00 60.00 000.00 0.0000
IC H3T3 C3T O3T P3 0.0000 000.00 -60.00 000.00 0.0000
PRES 5POM -0.3195
GROUP
ATOM O5T OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM C5T CD33C 0.0725 ALPHA -1.642 THOLE 0.862 ! -0.1e
ATOM H5T1 HDA3A 0.026
ATOM H5T2 HDA3A 0.026
ATOM H5T3 HDA3A 0.026
BOND P O5T
BOND O5T C5T
BOND C5T H5T1 C5T H5T2 C5T H5T3
ANISOTROPY O5T O1P O5' O2P A11 1.0000 A22 0.6000
ANISOTROPY O5' O2P O5T O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5T O5' A11 0.6000 A22 1.0000
ANISOTROPY O2P P O5' O5T A11 0.6000 A22 1.0000
IC O5T P O5' C5' 1.5837 102.73 72.47 116.87 1.4386
IC O5' P O5T C5T 1.5843 102.73 72.47 116.85 1.4394
IC O1P P O5T C5T 1.4910 107.70 -41.57 116.85 1.4394
IC O2P P O5' C5' 1.4906 107.67 -41.56 116.87 1.4386
IC H5T1 C5T O5T P 1.1128 110.79 -42.95 116.85 1.5837
IC H5T2 C5T O5T P 1.1118 109.92 77.01 116.85 1.5837
IC H5T3 C5T O5T P 1.1095 109.84 -163.26 116.85 1.5837
IC O5' O5T *P O1P 1.5843 102.73 -114.04 107.70 1.4910
IC O5' O5T *P O2P 1.5843 102.73 113.68 108.15 1.4906
IC P O5T C5T H5T1 1.5837 116.85 -42.95 110.79 1.1128
IC H5T1 O5T *C5T H5T2 1.1128 110.79 119.96 109.92 1.1118
IC H5T1 O5T *C5T H5T3 1.1128 110.79 -120.31 109.84 1.1095
!nucleic acid model compounds
RESI CYTB 0.000 ! Cytosine base, jal update 06/15
!
! H42 H41
! \ /
! N4
! |
! C4
! / \\
! H5-C5 N3
! || |
! H6-C6 C2
! \ / \\
! N1 O2
! |
! H1
!
GROUP
ATOM N1 ND2R6C -0.218 ALPHA -1.110 THOLE 0.822
ATOM C6 CD2R6H -0.139 ALPHA -1.752 THOLE 2.004
ATOM H6 HDR6B 0.251
ATOM C2 CD2O4A 0.369 ALPHA -1.580 THOLE 2.064
ATOM O2 OD2C1B 0.000 ALPHA -0.679 THOLE 0.675
ATOM LP2A LPDNA1 -0.180
ATOM LP2B LPDNA1 -0.266
ATOM N3 ND2R6B 0.000 ALPHA -0.509 THOLE 0.737
ATOM LP3 LPDNA1 -0.491
ATOM C4 CD2R6B 0.575 ALPHA -1.143 THOLE 1.245
ATOM N4 ND2B1 -0.644 ALPHA -1.622 THOLE 0.277
ATOM H41 HDP1A 0.346
ATOM H42 HDP1A 0.346
ATOM C5 CD2R6J -0.279 ALPHA -1.856 THOLE 0.783
ATOM H5 HDR6A 0.128
ATOM H1 HDP1A 0.202
BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1
BOND C2 O2 C4 N4 N4 H41 N4 H42 C5 H5 C6 H6 N1 H1
BOND LP2A O2 LP2B O2
BOND LP3 N3
IMPR C2 N1 N3 O2 C4 N3 C5 N4
IMPR N4 C4 H41 H42 N1 C6 C2 H1
LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
DONO H42 N4
DONO H41 N4
ACCE O2 C2
ACCE N3
IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337
IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356
IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237
IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334
IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337
IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01
IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01
IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC H1 N1 C2 N3 0.0 0.0 180.0 0.0 0.0
RESI MCYT 0.000 ! 1-Me-Cytosine, jal update 06/15
!
! H42 H41
! \ /
! N4
! |
! C4
! / \\
! H5-C5 N3
! || |
! H6-C6 C2
! \ / \\
! N1 O2
! |
! C1 H11,H12,H13
!
GROUP
ATOM N1 ND2R6C -0.218 ALPHA -1.110 THOLE 0.822
ATOM C6 CD2R6H -0.139 ALPHA -1.752 THOLE 2.004
ATOM H6 HDR6B 0.251
ATOM C2 CD2O4A 0.369 ALPHA -1.580 THOLE 2.064
ATOM O2 OD2C1B 0.000 ALPHA -0.679 THOLE 0.675
ATOM LP2A LPDNA1 -0.180
ATOM LP2B LPDNA1 -0.266
ATOM N3 ND2R6B 0.000 ALPHA -0.509 THOLE 0.737
ATOM LP3 LPDNA1 -0.491
ATOM C4 CD2R6B 0.575 ALPHA -1.143 THOLE 1.245
ATOM N4 ND2B1 -0.644 ALPHA -1.622 THOLE 0.277
ATOM H41 HDP1A 0.346
ATOM H42 HDP1A 0.346
ATOM C5 CD2R6J -0.279 ALPHA -1.856 THOLE 0.783
ATOM H5 HDR6A 0.128
ATOM C1 CD33A -0.146 ALPHA -1.324 THOLE 0.477
ATOM H11 HDA3A 0.116
ATOM H12 HDA3A 0.116
ATOM H13 HDA3A 0.116
BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1
BOND C2 O2 C4 N4 N4 H41 N4 H42 C5 H5 C6 H6
BOND N1 C1 C1 H11 C1 H12 C1 H13
BOND LP2A O2 LP2B O2
BOND LP3 N3
IMPR C2 N1 N3 O2 C4 N3 C5 N4
IMPR N4 C4 H41 H42 N1 C6 C2 C1
LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
DONO H42 N4
DONO H41 N4
ACCE O2 C2
ACCE N3
IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337
IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356
IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237
IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334
IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337
IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01
IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01
IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C2 C6 *N1 C1 0.0 0.0 180.0 0.0 0.0
IC C6 N1 C1 H11 0.0 0.0 180.0 0.0 0.0
IC H11 N1 *C1 H12 0.0 0.0 120.0 0.0 0.0
IC H11 N1 *C1 H13 0.0 0.0 -120.0 0.0 0.0
PRES CYTM 0.202 ! Me-CYT patch onto CYTB
! use as "LAST CYTM" in generate statement or as "PRES CYTM" in patch statement
DELE ATOM H1
ATOM C1 CD33A -0.146 ALPHA -1.324 THOLE 0.477
ATOM H11 HDA3A 0.116
ATOM H12 HDA3A 0.116
ATOM H13 HDA3A 0.116
BOND N1 C1 C1 H11 C1 H12 C1 H13
IMPR N1 C6 C2 C1
IC C2 C6 *N1 C1 0.0 0.0 180.0 0.0 0.0
IC C6 N1 C1 H11 0.0 0.0 180.0 0.0 0.0
IC H11 N1 *C1 H12 0.0 0.0 120.0 0.0 0.0
IC H11 N1 *C1 H13 0.0 0.0 240.0 0.0 0.0
RESI THYB 0.000 ! Thymine base, jal update 06/15
!
! H51 O4
! | ||
! H52-C5M C4 H3
! | \ / \ /
! H53 C5 N3
! || |
! H6-C6 C2
! \ / \\
! N1 O2
! |
! H1
!
GROUP
ATOM N1 ND2R6C -0.432 ALPHA -0.979 THOLE 1.057
ATOM C6 CD2R6H 0.138 ALPHA -1.545 THOLE 0.534
ATOM H6 HDR6B 0.282
ATOM C2 CD2O4A 0.524 ALPHA -0.985 THOLE 1.928
ATOM O2 OD2C1B 0.000 ALPHA -0.587 THOLE 1.945
ATOM LP2A LPDNA1 -0.131
ATOM LP2B LPDNA1 -0.229
ATOM N3 ND2R6C -0.506 ALPHA -0.766 THOLE 1.447
ATOM H3 HDP1A 0.297
ATOM C4 CD2O4A 0.493 ALPHA -1.013 THOLE 0.566
ATOM O4 OD2C1B 0.000 ALPHA -1.556 THOLE 1.924
ATOM LP4A LPDNA1 -0.302
ATOM LP4B LPDNA1 -0.168
ATOM C5 CD2R6J -0.174 ALPHA -1.209 THOLE 1.848
ATOM C5M CD33A -0.173 ALPHA -1.545 THOLE 0.326
ATOM H51 HDA3A 0.047
ATOM H52 HDA3A 0.047
ATOM H53 HDA3A 0.047
ATOM H1 HDP1A 0.240
BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6
BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 C5M
BOND C5M H51 C5M H52 C5M H53 C6 H6 N1 H1
BOND LP2A O2 LP2B O2
BOND LP4A O4 LP4B O4
IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M
IMPR N1 C6 C2 H1
LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0
ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA
DONO H3 N3
ACCE O2 C2
ACCE O4 C4
IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432
IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813
IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191
IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795
IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327
IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900
IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0
IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0
IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0
IC C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0
RESI MTHY 0.000 ! 1-Me-Thymine, jal update 06/15
!
! H51 O4
! | ||
! H52-C5M C4 H3
! | \ / \ /
! H53 C5 N3
! || |
! H6-C6 C2
! \ / \\
! N1 O2
! |
! C1 H11,H12,H13
!
GROUP
ATOM N1 ND2R6C -0.432 ALPHA -0.979 THOLE 1.057
ATOM C6 CD2R6H 0.138 ALPHA -1.545 THOLE 0.534
ATOM H6 HDR6B 0.282
ATOM C2 CD2O4A 0.524 ALPHA -0.985 THOLE 1.928
ATOM O2 OD2C1B 0.000 ALPHA -0.587 THOLE 1.945
ATOM LP2A LPDNA1 -0.131
ATOM LP2B LPDNA1 -0.229
ATOM N3 ND2R6C -0.506 ALPHA -0.766 THOLE 1.447
ATOM H3 HDP1A 0.297
ATOM C4 CD2O4A 0.493 ALPHA -1.013 THOLE 0.566
ATOM O4 OD2C1B 0.000 ALPHA -1.556 THOLE 1.924
ATOM LP4A LPDNA1 -0.302
ATOM LP4B LPDNA1 -0.168
ATOM C5 CD2R6J -0.174 ALPHA -1.209 THOLE 1.848
ATOM C5M CD33A -0.173 ALPHA -1.545 THOLE 0.326
ATOM H51 HDA3A 0.047
ATOM H52 HDA3A 0.047
ATOM H53 HDA3A 0.047
ATOM C1 CD33A -0.018 ALPHA -1.250 THOLE 0.436
ATOM H11 HDA3A 0.086
ATOM H12 HDA3A 0.086
ATOM H13 HDA3A 0.086
BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6
BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 C5M
BOND C5M H51 C5M H52 C5M H53 C6 H6 N1 C1
BOND C1 H11 C1 H12 C1 H13
BOND LP2A O2 LP2B O2
BOND LP4A O4 LP4B O4
IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M
IMPR N1 C6 C2 C1
LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0
ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA
DONO H3 N3
ACCE O2 C2
ACCE O4 C4
IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432
IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813
IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191
IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795
IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327
IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900
IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0
IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0
IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0
IC C2 C6 *N1 C1 0.0 0.0 180.0 0.0 0.0
IC C6 N1 C1 H11 0.0 0.0 180.0 0.0 0.0
IC H11 N1 *C1 H12 0.0 0.0 120.0 0.0 0.0
IC H11 N1 *C1 H13 0.0 0.0 -120.0 0.0 0.0
PRES THYM 0.240 ! Me-THY patch with THYB
! use as "LAST THYM" in generate statement or as "PRES THYM" in patch statement
DELE ATOM H1
ATOM C1 CD33A -0.018 ALPHA -1.250 THOLE 0.436
ATOM H11 HDA3A 0.086
ATOM H12 HDA3A 0.086
ATOM H13 HDA3A 0.086
BOND N1 C1 C1 H11 C1 H12 C1 H13
IC C5 C6 N1 C1 0.0 0.0 180.0 0.0 0.0
IC C6 N1 C1 H11 0.0 0.0 180.0 0.0 0.0
IC H11 N1 *C1 H12 0.0 0.0 120.0 0.0 0.0
IC H11 N1 *C1 H13 0.0 0.0 240.0 0.0 0.0
RESI URAB 0.000 ! Uracil base; modified cmb 04/10
!
! O4
! ||
! C4 H3
! / \ /
! H5-C5 N3
! || |
! H6-C6 C2
! \ / \\
! N1 O2
! |
! H1
!
GROUP
ATOM N1 ND2R6C -0.239 ALPHA -1.192 THOLE 1.639
ATOM C6 CD2R6H 0.095 ALPHA -0.500 THOLE 0.544 !!!CB
ATOM H6 HDR6B 0.341
ATOM C2 CD2O4A 0.636 ALPHA -1.072 THOLE 1.120
ATOM O2 OD2C1B 0.000 ALPHA -0.799 THOLE 1.076
ATOM LP2A LPDNA1 -0.126
ATOM LP2B LPDNA1 -0.229
ATOM N3 ND2R6C -0.593 ALPHA -1.631 THOLE 1.574
ATOM H3 HDP1A 0.317
ATOM C4 CD2O4A 0.557 ALPHA -1.072 THOLE 1.079
ATOM O4 OD2C1B 0.000 ALPHA -0.657 THOLE 1.156
ATOM LP4A LPDNA1 -0.254
ATOM LP4B LPDNA1 -0.192
ATOM C5 CD2R6J -0.321 ALPHA -1.949 THOLE 1.307
ATOM H5 HDR6A 0.009
ATOM H1 HDP1A -0.001
BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6
BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 H5
BOND C6 H6 N1 H1
BOND LP2A O2 LP2B O2
BOND LP4A O4 LP4B O4
IMPR C2 N1 N3 O2 C4 N3 C5 O4
LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0
ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA
DONO H3 N3
ACCE O2 C2
ACCE O4 C4
IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338
IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373
IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218
IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383
IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227
IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03
IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0
PRES URAM -0.001 ! Me-URA patch with URAB
! use as "LAST URAM" in generate statement or as "PRES URAM" in patch statement
DELE ATOM H1
ATOM C1 CD33A -0.364 ALPHA -1.863 THOLE 0.686
ATOM H11 HDA3A 0.121
ATOM H12 HDA3A 0.121
ATOM H13 HDA3A 0.121
BOND N1 C1 C1 H11 C1 H12 C1 H13
IC C5 C6 N1 C1 0.0 0.0 180.0 0.0 0.0
IC C6 N1 C1 H11 0.0 0.0 180.0 0.0 0.0
IC H11 N1 *C1 H12 0.0 0.0 120.0 0.0 0.0
IC H11 N1 *C1 H13 0.0 0.0 240.0 0.0 0.0
RESI ADEB 0.000 ! Adenine base, jal update 06/15
!
! H61 H62
! \ /
! N6
! |
! C6
! // \
! N1 C5--N7\\
! | || C8-H8
! C2 C4--N9/
! / \\ / \
! H2 N3 H9
!
GROUP
ATOM N9 ND2R5D -0.215 ALPHA -0.676 THOLE 0.935
ATOM C4 CD2R6F 0.227 ALPHA -1.045 THOLE 1.100
ATOM N3 ND2R6B 0.000 ALPHA -1.602 THOLE 0.006
ATOM LP3 LPDNA1 -0.507
ATOM C2 CD2R6C 0.208 ALPHA -1.120 THOLE 1.469
ATOM H2 HDR6C 0.176
ATOM N1 ND2R6B 0.000 ALPHA -1.507 THOLE 0.967
ATOM LP1 LPDNA1 -0.472
ATOM C6 CD2R6C 0.402 ALPHA -1.454 THOLE 0.557
ATOM N6 ND2B1 -0.742 ALPHA -1.330 THOLE 0.465
ATOM H61 HDP1A 0.373
ATOM H62 HDP1A 0.373
ATOM C5 CD2R6F -0.118 ALPHA -1.238 THOLE 1.854
ATOM N7 ND2R5E 0.000 ALPHA -1.462 THOLE 0.252
ATOM LP7 LPDNA1 -0.189
ATOM C8 CD2R5F 0.038 ALPHA -1.357 THOLE 1.402
ATOM H8 HDR5B 0.165
ATOM H9 HDP1A 0.281
BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6
BOND C6 C5 C5 C4 N9 C8 C8 N7 N7 C5
BOND C8 H8 C6 N6 N6 H61 N6 H62 C2 H2 N9 H9
BOND LP1 N1 LP3 N3 LP7 N7
LONEPAIR bisector LP1 N1 C2 C6 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99
ANISOTROPY N1 LP1 C6 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID
IMPR N6 C6 H61 H62 C6 N1 C5 N6
DONO H61 N6
DONO H62 N6
ACCE N3
ACCE N7
ACCE N1
IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312
IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382
IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0
IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0
IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0
IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342
IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337
IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01
IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01
IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337
IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01
IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01
IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0
IC C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0
RESI MADE 0.000 ! 9-Me-Adenine, jal update 06/15
!
! H61 H62
! \ /
! N6
! |
! C6
! // \
! N1 C5--N7\\
! | || C8-H8
! C2 C4--N9/
! / \\ / \
! H2 N3 C9 H91,H92,H93
!
GROUP
ATOM N9 ND2R5D -0.215 ALPHA -0.676 THOLE 0.935
ATOM C4 CD2R6F 0.227 ALPHA -1.045 THOLE 1.100
ATOM N3 ND2R6B 0.000 ALPHA -1.602 THOLE 0.006
ATOM LP3 LPDNA1 -0.507
ATOM C2 CD2R6C 0.208 ALPHA -1.120 THOLE 1.469
ATOM H2 HDR6C 0.176
ATOM N1 ND2R6B 0.000 ALPHA -1.507 THOLE 0.967
ATOM LP1 LPDNA1 -0.472
ATOM C6 CD2R6C 0.402 ALPHA -1.454 THOLE 0.557
ATOM N6 ND2B1 -0.742 ALPHA -1.330 THOLE 0.465
ATOM H61 HDP1A 0.373
ATOM H62 HDP1A 0.373
ATOM C5 CD2R6F -0.118 ALPHA -1.238 THOLE 1.854
ATOM N7 ND2R5E 0.000 ALPHA -1.462 THOLE 0.252
ATOM LP7 LPDNA1 -0.189
ATOM C8 CD2R5F 0.038 ALPHA -1.357 THOLE 1.402
ATOM H8 HDR5B 0.165
ATOM C9 CD33A -0.175 ALPHA -1.403 THOLE 0.403
ATOM H91 HDA3A 0.152
ATOM H92 HDA3A 0.152
ATOM H93 HDA3A 0.152
BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6
BOND C6 C5 C5 C4 N9 C8 C8 N7 N7 C5
BOND C8 H8 C6 N6 N6 H61 N6 H62 C2 H2
BOND N9 C9 C9 H91 C9 H92 C9 H93
!DOUB N1 C6 C2 N3 C4 C5 N7 C8
BOND LP1 N1
BOND LP3 N3
BOND LP7 N7
LONEPAIR bisector LP1 N1 C2 C6 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99
ANISOTROPY N1 LP1 C6 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID
IMPR N6 C6 H61 H62 C6 N1 C5 N6
DONO H61 N6
DONO H62 N6
ACCE N3
ACCE N7
ACCE N1
IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312
IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382
IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0
IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0
IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0
IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342
IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337
IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01
IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01
IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337
IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01
IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01
IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0
IC C4 C8 *N9 C9 0.0 0.0 180.0 0.0 0.0
IC C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0
IC H91 N9 *C9 H92 0.0 0.0 120.0 0.0 0.0
IC H91 N9 *C9 H93 0.0 0.0 -120.0 0.0 0.0
PRES ADEM 0.281 ! Me-ADE patch with ADEB
! use as "LAST ADEM" in generate statement or as "PRES ADEM" in patch statement
DELE ATOM H9
ATOM C9 CD33A -0.175 ALPHA -1.403 THOLE 0.403
ATOM H91 HDA3A 0.152
ATOM H92 HDA3A 0.152
ATOM H93 HDA3A 0.152
BOND N9 C9 C9 H91 C9 H92 C9 H93
IC C4 C8 *N9 C9 0.0 0.0 180.0 0.0 0.0
IC C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0
IC H91 N9 *C9 H92 0.0 0.0 120.0 0.0 0.0
IC H91 N9 *C9 H93 0.0 0.0 -120.0 0.0 0.0
RESI GUAB 0.000 ! Guanine base, jal update 06/15
!
! O6
! ||
! C6
! / \
! H1-N1 C5--N7\\
! | || C8-H8
! C2 C4--N9/
! / \\ / \
! H21-N2 N3 H9
! |
! H22
GROUP
ATOM N9 ND2R5D -0.019 ALPHA -0.880 THOLE 1.351
ATOM C4 CD2R6F 0.227 ALPHA -1.259 THOLE 0.797
ATOM N3 ND2R6B 0.000 ALPHA -0.771 THOLE 0.865
ATOM LP3 LPDNA1 -0.459
ATOM C2 CD2R6C 0.587 ALPHA -1.109 THOLE 1.628
ATOM N1 ND2R6C -0.366 ALPHA -1.568 THOLE 0.271
ATOM H1 HDP1A 0.287
ATOM N2 ND2B1 -0.736 ALPHA -1.404 THOLE 0.298
ATOM H21 HDP1A 0.327
ATOM H22 HDP1A 0.327
ATOM C6 CD2O4A 0.272 ALPHA -0.943 THOLE 1.940
ATOM O6 OD2C1B 0.000 ALPHA -0.617 THOLE 1.539
ATOM LP6A LPDNA1 -0.259
ATOM LP6B LPDNA1 -0.138
ATOM C5 CD2R6F 0.004 ALPHA -1.788 THOLE 1.033
ATOM N7 ND2R5E 0.000 ALPHA -0.650 THOLE 0.946
ATOM LP7 LPDNA1 -0.322
ATOM C8 CD2R5F -0.113 ALPHA -1.427 THOLE 1.309
ATOM H8 HDR5B 0.165
ATOM H9 HDP1A 0.216
BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6 C6 C5
BOND C5 C4 N9 C8 C8 N7 C5 N7 C8 H8 C6 O6
BOND N1 H1 C2 N2 N2 H21 N2 H22 N9 H9
BOND LP3 N3 LP7 N7
BOND LP6A O6 LP6B O6
IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR relative LP6A O6 C6 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP6B O6 C6 C5 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY O6 C6 C5 N1 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID
DONO H21 N2
DONO H22 N2
DONO H1 N1
ACCE O6 C6
ACCE N3
ACCE N7
IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304
IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377
IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355
IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327
IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375
IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341
IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01
IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01
IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393
IC C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03
IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239
IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
IC C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0
RESI MGUA 0.000 ! me-Guanine base, jal update 6/15
!
! O6
! ||
! C6
! / \
! H1-N1 C5--N7\\
! | || C8-H8
! C2 C4--N9/
! / \\ / \
! H21-N2 N3 C9-H9[123]
! |
! H22
GROUP
ATOM N9 ND2R5D -0.019 ALPHA -0.880 THOLE 1.351
ATOM C4 CD2R6F 0.227 ALPHA -1.259 THOLE 0.797
ATOM N3 ND2R6B 0.000 ALPHA -0.771 THOLE 0.865
ATOM LP3 LPDNA1 -0.459
ATOM C2 CD2R6C 0.587 ALPHA -1.109 THOLE 1.628
ATOM N1 ND2R6C -0.366 ALPHA -1.568 THOLE 0.271
ATOM H1 HDP1A 0.287
ATOM N2 ND2B1 -0.736 ALPHA -1.404 THOLE 0.298
ATOM H21 HDP1A 0.327
ATOM H22 HDP1A 0.327
ATOM C6 CD2O4A 0.272 ALPHA -0.943 THOLE 1.940
ATOM O6 OD2C1B 0.000 ALPHA -0.617 THOLE 1.539
ATOM LP6A LPDNA1 -0.259
ATOM LP6B LPDNA1 -0.138
ATOM C5 CD2R6F 0.004 ALPHA -1.788 THOLE 1.033
ATOM N7 ND2R5E 0.000 ALPHA -0.650 THOLE 0.946
ATOM LP7 LPDNA1 -0.322
ATOM C8 CD2R5F -0.113 ALPHA -1.427 THOLE 1.309
ATOM H8 HDR5B 0.165
ATOM C9 CD33A -0.264 ALPHA -1.793 THOLE 0.571
ATOM H91 HDA3A 0.160
ATOM H92 HDA3A 0.160
ATOM H93 HDA3A 0.160
BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6 C6 C5
BOND C5 C4 N9 C8 C8 N7 C5 N7 C8 H8 C6 O6
BOND N1 H1 C2 N2 N2 H21 N2 H22
BOND N9 C9 C9 H91 C9 H92 C9 H93
BOND LP3 N3 LP7 N7
BOND LP6A O6 LP6B O6
IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR relative LP6A O6 C6 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP6B O6 C6 C5 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY O6 C6 C5 N1 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID
DONO H21 N2
DONO H22 N2
DONO H1 N1
ACCE O6 C6
ACCE N3
ACCE N7
IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304
IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377
IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355
IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327
IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375
IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341
IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01
IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01
IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393
IC C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03
IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239
IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
IC C4 C8 *N9 C9 0.0 0.0 180.0 0.0 0.0
IC C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0
IC H91 N9 *C9 H92 0.0 0.0 120.0 0.0 0.0
IC H91 N9 *C9 H93 0.0 0.0 -120.0 0.0 0.0
PRES GUAM 0.216 ! Me-GUA patch with GUAB
! use as "LAST GUAM" in generate statement or as "PRES GUAM" in patch statement
DELE ATOM H9
ATOM C9 CD33A -0.264 ALPHA -1.793 THOLE 0.571
ATOM H91 HDA3A 0.160
ATOM H92 HDA3A 0.160
ATOM H93 HDA3A 0.160
BOND N9 C9 C9 H91 C9 H92 C9 H93
IC C4 C8 *N9 C9 0.0 0.0 180.0 0.0 0.0
IC C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0
IC H91 N9 *C9 H92 0.0 0.0 120.0 0.0 0.0
IC H91 N9 *C9 H93 0.0 0.0 -120.0 0.0 0.0
PRES GUAE 0.216 ! Ethyl-GUA patch with GUAB
! use as "LAST GUAE" in generate statement or as "PRES GUAE" in patch statement
DELE ATOM H9
ATOM C9 CD32A -0.104 ALPHA -1.162 THOLE 0.571
ATOM H91 HDA2A 0.160
ATOM H92 HDA2A 0.160
GROUP
ATOM C10 CD33A -0.177 ALPHA -1.436 THOLE 1.3
ATOM H11 HDA3A 0.059
ATOM H12 HDA3A 0.059
ATOM H13 HDA3A 0.059
BOND N9 C9 C9 H91 C9 H92 C9 C10
BOND C10 H11 C10 H12 C10 H13
IC C4 C8 *N9 C9 0.0 0.0 180.0 0.0 0.0
IC C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0
IC H91 N9 *C9 H92 0.0 0.0 120.0 0.0 0.0
IC H91 N9 *C9 C10 0.0 0.0 -120.0 0.0 0.0
IC N9 C9 C10 H11 0.0 0.0 180.0 0.0 0.0
IC H11 C9 *C10 H12 0.0 0.0 120.0 0.0 0.0
IC H11 C9 *C10 H13 0.0 0.0 -120.0 0.0 0.0
! backbone model compounds
RESI T3PS -1.000 ! 3-phosphate-tetrahydrofuran (phosphate -1)
! capped with a furan
!
! H41a O41 H11a
! \ / \ /
! H42a--C4a C11--H12a
! | |
! H31a--C3a--C2a--H21a
! / \
! O3a H22a
! |
! O1P==P==O2P
! |
! O5b (-1) H4b1 O4b H1b1
! \ \ / \ /
! C5b-------C4b C1b-H1b2
! / \ | |
! H5b1 H5b2 C3b----C2b-H2b2
! / | \
! H3b1 H3b2 H2b1
!
!
GROUP
ATOM O4A OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LP1 LPD -0.152
ATOM LP2 LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1A CD315A 0.092 ALPHA -1.562 THOLE 1.103 ! neutralize group charge !+ 0.05e
ATOM H11A HDA2R5 0.055
ATOM H12A HDA2R5 0.055
ATOM C4A CD315B 0.092 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H41A HDA2R5 0.055
ATOM H42A HDA2R5 0.055
GROUP
ATOM C2A CD325B -0.144 ALPHA -1.617 THOLE 1.103 ! neutralize group charge
ATOM H21A HDA2R5 0.072
ATOM H22A HDA2R5 0.072
GROUP
ATOM C3A CD315B -0.0755 ALPHA -1.642 THOLE 0.862 ! DMP, charge to yield unit charge ! -0.3e
ATOM H31A HDA1R5 0.026
ATOM O3A OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098
ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O5B OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM C5B CD32C 0.1985 ALPHA -1.642 THOLE 0.862
ATOM H5B1 HDA2A 0.026
ATOM H5B2 HDA2A 0.026
GROUP
ATOM O4B OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LPA LPD -0.152
ATOM LPB LPD -0.152
ATOM LPX2 LPD 0.000 !dummy for anisotropic polarizability
ATOM C4B CD315B 0.097 ALPHA -1.562 THOLE 1.103 ! neutralize group charge
ATOM H4B1 HDA1R5 0.055
ATOM C1B CD315A 0.042 ALPHA -1.562 THOLE 1.103
ATOM H1B1 HDA2R5 0.055
ATOM H1B2 HDA2R5 0.055
GROUP
ATOM C2B CD325B -0.144 ALPHA -1.617 THOLE 1.103 ! neutralize group charge
ATOM H2B1 HDA2R5 0.072
ATOM H2B2 HDA2R5 0.072
GROUP
ATOM C3B CD315B -0.144 ALPHA -1.617 THOLE 1.103 ! neutralize group charge
ATOM H3B1 HDA2R5 0.072
ATOM H3B2 HDA2R5 0.072
BOND C1A O4A C1A C2A C2A C3A C3A C4A C4A O4A C3A O3A
BOND C1A H11A C1A H12A C2A H21A C2A H22A C3A H31A C4A H41A
BOND C4A H42A O3A P P O1P P O2P P O5B O5B C5B
BOND C5B H5B1 C5B H5B2 C5B C4B C4B O4B O4B C1B C1B C2B
BOND C2B C3B C3B C4B C4B H4B1 C1B H1B1 C1B H1B2 C2B H2B1
BOND C2B H2B2 C3B H3B1 C3B H3B2
BOND O4A LP1 O4A LP2 O4A LPX
BOND O4B LPA O4B LPB O4B LPX2
! O4A Lone pairs
LONEPAIR bisector LP1 O4A C1A C4A distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LP2 O4A C1A C4A distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4A C1A C4A distance 0.10 angle 0.0 dihe 0.0
ANISOTROPY O4A LPX LP1 LP2 A11 0.8889 A22 1.2222
! O4B Lone pairs
LONEPAIR bisector LPA O4B C1B C4B distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPB O4B C1B C4B distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX2 O4B C1B C4B distance 0.10 angle 0.0 dihe 0.0
ANISOTROPY O4B LPX2 LPA LPB A11 0.8889 A22 1.2222
ANISOTROPY O5B O1P O3A O2P A11 1.0000 A22 0.6000
ANISOTROPY O3A O2P O5B O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5B O3A A11 0.6000 A22 1.0000
ANISOTROPY O2P P O3A O5B A11 0.6000 A22 1.0000
IC C4a O4a C1a C2a 1.4055 108.09 -21.00 106.18 1.5457 !0.0 for c3aendo (north) pucker
IC O4a C1a C2a C3a 1.4127 106.18 30.00 103.11 1.5346 !
IC C1a C2a C3a C4a 1.5457 103.11 -30.00 100.86 1.5211 !0.0 for o4aendo barrier
IC C2a C3a C4a O4a 1.5346 100.86 20.00 103.15 1.4055
IC C3a C4a O4a C1a 1.5211 103.15 0.00 108.09 1.4127
IC C2a O4a *C1a H11a 0.0000 0.00 120.00 0.00 0.0000
IC C2a O4a *C1a H12a 0.0000 0.00 -120.00 0.00 0.0000
IC C3a C1a *C2a H22a 0.0000 0.00 120.00 0.00 0.0000
IC C3a C1a *C2a H21a 0.0000 0.00 -120.00 0.00 0.0000
IC C1a C2a O2T H2T 0.0000 0.00 180.00 0.00 0.0000
IC C2a C4a *C3a O3a 0.0000 0.00 -120.00 0.00 0.0000
IC C2a C4a *C3a H31a 0.0000 0.00 120.00 0.00 0.0000
IC O4a C3a *C4a H41a 0.0000 0.00 120.00 0.00 0.0000
IC O4a C3a *C4a H42a 0.0000 0.00 -120.00 0.00 0.0000
IC C4a C3a O3a P 0.0000 000.00 -164.29 000.00 0.0000 !epsilon bi:-164.29,bii:-92.78
IC C3a O3a P O5b 0.0000 000.00 -89.68 000.00 0.0000 !zeta bi:-89.68,bii:159.19
IC O5b O3a *P O1P 0.0000 000.00 -115.82 000.00 0.0000
IC O5b O3a *P O2P 0.0000 000.00 115.90 000.00 0.0000
IC O3a P O5b C5b 0.0000 000.00 -46.90 000.00 0.0000 !alpha+1:A:291, B:298
IC P O5B C5B C4B 0.0000 0.00 180.00 0.00 0.0000 !beta+1:A:175, B:168
IC H5b1 C5b O5b P 0.0000 000.00 180.00 000.00 0.0000
IC H5b2 C5b O5b P 0.0000 000.00 60.00 000.00 0.0000
IC O3a P O5B C5B 0.0000 0.00 180.00 0.00 0.0000
IC C4B O5B *C5B H5B1 0.0000 0.00 120.00 0.00 0.0000
IC C4B O5B *C5B H5B2 0.0000 0.00 -120.00 0.00 0.0000
IC O5B C5B C4B C3B 0.0000 0.00 180.00 0.00 0.0000 !gamma+1,A:57, B:51
IC C5B C4B C3B C2B 0.0000 0.00 -108.00 0.00 0.0000 !-155:c3aendo(north) -108:c2aendo(south)
IC C4B C3B C2B C1B 0.0000 0.00 -40.00 0.00 0.0000 !40:c3aendo(north) -40:c2aendo(south)
IC C3B C2B C1B O4B 0.0000 0.00 40.00 0.00 0.0000 !-40:c3aendo(north) 40:c2aendo(south)
!following IC is used to define C3'endo in surfaces, but commented due to redundancy
!IC C4B O4B C1B C2B 0.0000 0.00 25.00 0.00 0.0000 !0.0: c3aendo(north) 25:c2aendo(south)
IC O4B C3B *C4B H4B1 0.0000 0.00 120.00 0.00 0.0000
IC C2B O4B *C1B H1B1 0.0000 0.00 120.00 0.00 0.0000
IC C2B O4B *C1B H1B2 0.0000 0.00 -120.00 0.00 0.0000
IC C3B C1B *C2B H2B1 0.0000 0.00 -120.00 0.00 0.0000
IC C3B C1B *C2B H2B2 0.0000 0.00 120.00 0.00 0.0000
IC C2B C4B *C3B H3B1 0.0000 0.00 120.00 0.00 0.0000
IC C2B C4B *C3B H3B2 0.0000 0.00 -120.00 0.00 0.0000
PATC FIRS NONE LAST NONE
RESI R3PS -1.000 ! RNA model compound, jal 7/5/2014
!
!
! H41' O4' H11'
! \ / \ /
! H42'-C4' C1'-H12'
! \ /
! H31'-C3'-C2'-H21'
! / \
! O3' O2T-H2T
! |
! O1P==P==O2P
! | (-)
! O5b
! |
! H5b1--C5b--H5b2
! \ O4b H1b1
! \ / \ /
! C4b C1b-H1b2
! /\ /
! H4b1 C3b-C2b-H2b1
! / \ \
! H3b1 H3b2 O2Tb-H2Tb
!
GROUP !! from T3PS
ATOM C4' CD315B 0.092 ALPHA -1.562 THOLE 1.103 !! jal orig alpha -1.562
ATOM H41' HDA2R5 0.055 ! THF
ATOM H42' HDA2R5 0.055 ! THF
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LP1A LPD -0.152
ATOM LP1B LPD -0.152
ATOM LPX1 LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.092 ALPHA -1.562 THOLE 1.103 ! from T3PS
ATOM H11' HDA2R5 0.055 ! THF
ATOM H12' HDA2R5 0.055 ! THF
GROUP !! jal - changed from EtOH to PRO2 charges
ATOM C2' CD315B 0.000 ALPHA -1.242 THOLE 1.103 ! neutralize group charge
ATOM H21' HDA1R5 0.100
ATOM O2T OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2T HDP1A 0.260
ATOM LP21 LPD -0.180
ATOM LP22 LPD -0.180
GROUP
ATOM C3' CD315B -0.0755 ALPHA -1.642 THOLE 0.862 !! jal orig alpha -1.642
ATOM H31' HDA1R5 0.026
ATOM O3' OD30BR -0.470 ALPHA -0.901 THOLE 0.181
GROUP
ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098 ! DMP
ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O5b OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM C5b CD32C 0.1985 ALPHA -1.642 THOLE 0.862 !! jal orig alpha -1.642
ATOM H5b1 HDA2A 0.026
ATOM H5b2 HDA2A 0.026
GROUP !! THF
ATOM C4b CD315B 0.097 ALPHA -1.562 THOLE 1.103 !! jal orig alpha -1.562
ATOM H4b1 HDA1R5 0.055
ATOM O4b OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LP2A LPD -0.152
ATOM LP2B LPD -0.152
ATOM LPX2 LPD 0.000 !dummy for anisotropic polarizability
ATOM C1b CD315A 0.042 ALPHA -1.562 THOLE 1.103 ! straight from THF
ATOM H1b1 HDA2R5 0.055 ! THF
ATOM H1b2 HDA2R5 0.055 ! THF
GROUP !! jal - changed from EtOH to PRO2 charges
ATOM C2b CD315B 0.000 ALPHA -1.242 THOLE 1.103 ! neutralize group charge
ATOM H2b1 HDA1R5 0.100
ATOM O2Tb OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2Tb HDP1A 0.260
ATOM LP23 LPD -0.180
ATOM LP24 LPD -0.180
GROUP
ATOM C3b CD315B -0.144 ALPHA -1.617 THOLE 1.103 ! from T3PS
ATOM H3b1 HDA2R5 0.072 ! THF
ATOM H3b2 HDA2R5 0.072 ! THF
! First ring and phosphate
BOND C1' H11' C1' H12' C1' C2' C2' H21' C2' O2T O2T H2T
BOND C2' C3' C3' H31' C3' O3' C3' C4' C4' O4' O4' C1'
BOND C4' H41' C4' H42'
BOND O4' LP1A O4' LP1B
BOND O4' LPX1
BOND O2T LP21 O2T LP22
BOND O3' P P O1P P O2P
BOND P O5b O5b C5b
! Second ring
BOND C1b H1b1 C1b H1b2 C1b C2b C2b H2b1 C2b O2Tb O2Tb H2Tb
BOND C2b C3b C3b H3b1 C3b H3b2 C3b C4b C4b O4b O4b C1b
BOND C4b H4b1 C4b C5b C5b H5b1 C5b H5b2
BOND O4b LP2A O4b LP2B O4b LPX2
BOND O2Tb LP23 O2Tb LP24
! O4' Lone pairs
! first ring
LONEPAIR bisector LP1A O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LP1B O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX1 O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
! second ring
LONEPAIR bisector LP2A O4b C1b C4b distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LP2B O4b C1b C4b distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX2 O4b C1b C4b distance 0.10 angle 0.0 dihe 0.0
! O2' Lone pairs
! first ring
LONEPAIR relative LP21 O2T C2' H2T distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP22 O2T C2' H2T distance 0.35 angle 110.0 dihe 269.0
! second ring
LONEPAIR relative LP23 O2Tb C2b H2Tb distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP24 O2Tb C2b H2Tb distance 0.35 angle 110.0 dihe 269.0
!Anisotropies
!O4' Anisotropy
ANISOTROPY O4' LPX1 LP1A LP1B A11 0.8889 A22 1.2222
ANISOTROPY O4b LPX2 LP2A LP2B A11 0.8889 A22 1.2222
!O2' anisotropy
ANISOTROPY O2T C2' LP21 LP22 A11 0.8108 A22 1.2162
ANISOTROPY O2Tb C2b LP23 LP24 A11 0.8108 A22 1.2162
!Phosphate Anisotropy
ANISOTROPY O5b O1P O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY O3' O2P O5b O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5b O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P O3' O5b A11 0.6000 A22 1.0000
DONO H2T O2T
ACCE O1P P
ACCE O2P P
ACCE O2T
ACCE O3'
ACCE O4'
DONO H2Tb O2Tb
ACCE O2Tb
ACCE O4b
ACCE O5b
!!! IC table taken from R3PS in toppar_all36_na_model.str
IC C4' O4' C1' C2' 1.4055 108.09 0.00 106.18 1.5457 !0.0 for c3'endo (south) pucker
IC O4' C1' C2' C3' 1.4127 106.18 -30.00 103.11 1.5346
IC C1' C2' C3' C4' 1.5457 103.11 45.00 100.86 1.5211
IC C2' C3' C4' O4' 1.5346 100.86 -45.00 103.15 1.4055
IC C3' C4' O4' C1' 1.5211 103.15 30.00 108.09 1.4127
IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346
IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346
IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211
IC O2T C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211
IC C1' C2' O2T H2T 0.0000 0.00 180.00 0.00 0.0000
IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055
IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127
IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127
IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055
IC C4' C3' O3' P 0.0000 000.00 -164.29 000.00 0.0000 !epsilon bi:-164.29,bii:-92.78
IC C3' O3' P O5b 0.0000 000.00 -89.68 000.00 0.0000 !zeta bi:-89.68,bii:159.19
IC O5b O3' *P O1P 0.0000 000.00 -115.82 000.00 0.0000
IC O5b O3' *P O2P 0.0000 000.00 115.90 000.00 0.0000
IC O3' P O5b C5b 0.0000 000.00 -46.90 000.00 0.0000 !alpha+1:A:291, b:298
IC P O5b C5b C4b 0.0000 0.00 180.00 0.00 0.0000 !beta+1:A:175, b:168
IC H5b1 C5b O5b P 0.0000 000.00 180.00 000.00 0.0000
IC H5b2 C5b O5b P 0.0000 000.00 60.00 000.00 0.0000
IC C4b O5b *C5b H5b1 0.0000 0.00 120.00 0.00 0.0000
IC H5b1 O5b *C5b H5b2 0.0000 0.00 -120.00 0.00 0.0000
IC O5b C5b C4b C3b 0.0000 0.00 180.00 0.00 0.0000 !gamma+1,A:57, b:51
IC C5b C4b C3b C2b 0.0000 0.00 -155.00 0.00 0.0000 !-155:c3'endo(north) -108:c2'endo(south)
IC C4b C3b C2b C1b 0.0000 0.00 40.00 0.00 0.0000 !40:c3'endo(north) -40:c2'endo(south)
IC C3b C2b C1b O4b 0.0000 0.00 -40.00 0.00 0.0000 !-40:c3'endo(north) 40:c2'endo(south)
!following IC is used to define C3'endo in surfaces, but commented due to redundancy
IC O4b C5b *C4b H4b1 0.0000 0.00 -120.00 0.00 0.0000
IC C2b O4b *C1b H1b1 0.0000 0.00 120.00 0.00 0.0000
IC C2b O4b *C1b H1b2 0.0000 0.00 -120.00 0.00 0.0000
IC C3b C1b *C2b H2b1 0.0000 0.00 -120.00 0.00 0.0000
IC C3b C1b *C2b O2Tb 0.0000 0.00 120.00 0.00 0.0000
IC C1b C2b O2Tb H2Tb 0.0000 0.00 180.00 0.00 0.0000
IC C2b C4b *C3b H3b1 0.0000 0.00 120.00 0.00 0.0000
IC C2b C4b *C3b H3b2 0.0000 0.00 -120.00 0.00 0.0000
PATC FIRS NONE LAST NONE
RESI T3PM -1.000 ! 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -1)
! capped with a methyl group. This is to investigate the differences
! between BI and BII forms of DNA
!
! H41' O4' H11'
! \ / \ /
! H42'--C4' C1'--H12'
! | |
! H31'--C3'--C2'--H21'
! / \
! O3' H22'
! |
! O1P==P==O2P
! |
! O3T (-1)
! \
! C3T--H3T3
! / \
! H3T1 H3T2
!
GROUP
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LP1 LPD -0.152
ATOM LP2 LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.092 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H11' HDA2R5 0.055
ATOM H12' HDA2R5 0.055
ATOM C4' CD315B 0.092 ALPHA -1.562 THOLE 1.103 ! neutralize group charge ! +0.05e
ATOM H41' HDA2R5 0.055
ATOM H42' HDA2R5 0.055
GROUP
ATOM C2' CD325B -0.144 ALPHA -1.617 THOLE 1.103
ATOM H21' HDA2R5 0.072
ATOM H22' HDA2R5 0.072
GROUP
ATOM C3' CD315B -0.0755 ALPHA -1.617 THOLE 1.103 ! -0.3e
ATOM H31' HDA1R5 0.026
ATOM O3' OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098
ATOM O1P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O2P OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
ATOM O3T OD30BN -0.470 ALPHA -0.901 THOLE 0.181
ATOM C3T CD32C 0.1725 ALPHA -1.642 THOLE 0.862
ATOM H3T1 HDA2A 0.026
ATOM H3T2 HDA2A 0.026
ATOM H3T3 HDA2A 0.026
BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'
BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41'
BOND C4' H42' O3' P P O1P P O2P P O3T O3T C3T
BOND C3T H3T1 C3T H3T2 C3T H3T3
BOND O4' LP1 O4' LP2 O4' LPX
! O4' Lone pairs
LONEPAIR bisector LP1 O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LP2 O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
ANISOTROPY O4' LPX LP1 LP2 A11 0.8889 A22 1.2222
ANISOTROPY O3T O1P O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY O3' O2P O3T O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O3T O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P O3' O3T A11 0.6000 A22 1.0000
IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457
IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346
IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211
IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055
IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127
IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346
IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346
IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211
IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211
IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055
IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127
IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127
IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055
IC P O3' C3' C4' 0.0000 000.00 180.00 000.00 0.0000
IC C3' O3' P O3T 0.0000 000.00 -95.22 000.00 0.0000
IC O3T O3' *P O1P 0.0000 000.00 -115.82 000.00 0.0000
IC O3T O3' *P O2P 0.0000 000.00 115.90 000.00 0.0000
IC C3T O3T P O3' 0.0000 000.00 -46.90 000.00 0.0000
IC H3T1 C3T O3T P 0.0000 000.00 180.00 000.00 0.0000
IC H3T2 C3T O3T P 0.0000 000.00 60.00 000.00 0.0000
IC H3T3 C3T O3T P 0.0000 000.00 -60.00 000.00 0.0000
PATC FIRS NONE LAST NONE
!!in toppar_drude_model stream file
!RESI DMPN -1.000 ! Dimethylphosphate, nucleic acids
!!
!! nucleic acid specific, differs from lipid DMP
!!
!! H11
!! |
!! H13- C1-H12
!! \
!! O13 O11
!! \\ /
!! (-) P1
!! // \
!! O14 O12
!! /
!! H23-C2-H22
!! |
!! H21
!!
!GROUP
!ATOM P PD1AN 1.191 ALPHA -0.974 THOLE 2.098
!ATOM O13 OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
!ATOM O14 OD2C2C -0.776 ALPHA -0.931 THOLE 1.083 ! +0.1e
!ATOM O11 OD30BN -0.470 ALPHA -0.901 THOLE 0.181
!ATOM O12 OD30BN -0.470 ALPHA -0.901 THOLE 0.181
!ATOM C1 CD33C 0.0725 ALPHA -1.642 THOLE 0.862 ! -0.1e
!ATOM H11 HDA3A 0.026
!ATOM H12 HDA3A 0.026
!ATOM H13 HDA3A 0.026
!ATOM C2 CD33C 0.0725 ALPHA -1.642 THOLE 0.862 ! -0.1e
!ATOM H21 HDA3A 0.026
!ATOM H22 HDA3A 0.026
!ATOM H23 HDA3A 0.026
!
!BOND P O11 P O12 P O13 P O14
!BOND O11 C1 O12 C2
!BOND C1 H11 C1 H12 C1 H13
!BOND C2 H21 C2 H22 C2 H23
!
!ANISOTROPY O11 O13 O12 O14 A11 1.0000 A22 0.6000
!ANISOTROPY O12 O14 O11 O13 A11 1.0000 A22 0.6000
!ANISOTROPY O13 P O11 O12 A11 0.6000 A22 1.0000
!ANISOTROPY O14 P O12 O11 A11 0.6000 A22 1.0000
!
!IC O11 P O12 C2 1.5837 102.73 72.47 116.87 1.4386
!IC O12 P O11 C1 1.5843 102.73 72.47 116.85 1.4394
!IC O13 P O11 C1 1.4910 107.70 -41.57 116.85 1.4394
!IC O14 P O12 C2 1.4906 107.67 -41.56 116.87 1.4386
!IC H11 C1 O11 P 1.1128 110.79 -42.95 116.85 1.5837
!IC H12 C1 O11 P 1.1118 109.92 77.01 116.85 1.5837
!IC H13 C1 O11 P 1.1095 109.84 -163.26 116.85 1.5837
!IC H21 C2 O12 P 1.1125 110.79 -42.95 116.87 1.5843
!IC H22 C2 O12 P 1.1123 109.91 77.00 116.87 1.5843
!IC H23 C2 O12 P 1.1094 109.84 -163.30 116.87 1.5843
!IC O12 O11 *P O13 1.5843 102.73 -114.04 107.70 1.4910
!IC O12 O11 *P O14 1.5843 102.73 113.68 108.15 1.4906
!IC P O11 C1 H11 1.5837 116.85 -42.95 110.79 1.1128
!IC H11 O11 *C1 H12 1.1128 110.79 119.96 109.92 1.1118
!IC H11 O11 *C1 H13 1.1128 110.79 -120.31 109.84 1.1095
!IC P O12 C2 H21 1.5843 116.87 -42.95 110.79 1.1125
!IC H21 O12 *C2 H22 1.1125 110.79 119.95 109.91 1.1123
!IC H21 O12 *C2 H23 1.1125 110.79 -120.35 109.84 1.1094
!patch first none last none
RESI BRIBN 0.000 ! beta-Ribose
!
! HO5--O5
! \ O4
! H51--C5 / \ O1--HO1
! / \ / \ /
! H52 C4 C1
! / \ / \
! H4 \ / H1
! C3----C2
! / \ / \
! O3 H3 O2 H2
! | |
! HO3 HO2
!
!
GROUP
ATOM O4 OD305A 0.000 ALPHA -0.618 THOLE 1.545 ! from THF
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1 CD315A 0.144 ALPHA -1.562 THOLE 1.103
ATOM H1 HDA1R5 0.055 ! from THF
ATOM O1 OD31A 0.000 ALPHA -1.028 THOLE 1.3 ! from EtOH
ATOM HO1 HDP1A 0.360
ATOM LP1A LPD -0.230
ATOM LP1B LPD -0.230
ATOM C4 CD315B 0.150 ALPHA -1.562 THOLE 1.103
ATOM H4 HDA1R5 0.055 ! from THF
GROUP
ATOM C5 CD32A -0.060 ALPHA -1.000 THOLE 1.3
ATOM H51 HDA2A 0.080
ATOM H52 HDA2A 0.080
ATOM O5 OD31A 0.000 ALPHA -1.028 THOLE 1.3
ATOM LP5A LPD -0.230
ATOM LP5B LPD -0.230
ATOM HO5 HDP1A 0.360
GROUP
ATOM C2 CD315B 0.020 ALPHA -1.000 THOLE 1.3 ! neutralize group charge
ATOM H2 HDA1R5 0.080
ATOM O2 OD31A 0.000 ALPHA -1.028 THOLE 1.3
ATOM HO2 HDP1A 0.360
ATOM LP2A LPD -0.230
ATOM LP2B LPD -0.230
GROUP
ATOM C3 CD315B 0.020 ALPHA -1.000 THOLE 1.3 ! neutralize group charge
ATOM H3 HDA1R5 0.080
ATOM O3 OD31A 0.000 ALPHA -1.028 THOLE 1.3
ATOM HO3 HDP1A 0.360
ATOM LP3A LPD -0.230
ATOM LP3B LPD -0.230
BOND O4 C1 C1 H1 C1 O1 O1 HO1
BOND C1 C2 C2 H2 C2 O2 O2 HO2
BOND C2 C3 C3 H3 C3 O3 O3 HO3
BOND C3 C4 C4 H4 C4 C5 C4 O4
BOND C5 H51 C5 H52 C5 O5 O5 HO5
BOND O4 LPRA O4 LPRB O4 LPX
BOND O1 LP1A O1 LP1B
BOND O2 LP2A O2 LP2B
BOND O3 LP3A O3 LP3B
BOND O5 LP5A O5 LP5B
LONEPAIR bisector LPRA O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0
LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0
LONEPAIR relative LP2A O2 C2 HO2 distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP2B O2 C2 HO2 distance 0.35 angle 110.0 dihe 269.0
LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0
LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0
ANISOTROPY O4 LPX LPRA LPRB A11 0.8889 A22 1.2222
ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162
ANISOTROPY O2 C2 LP2A LP2B A11 0.8108 A22 1.2162
ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162
ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162
! IC table; from crystal geometry*
IC C4 O4 C1 C2 1.4440 110.08 18.97 105.48 1.5227
IC O4 C1 C2 C3 1.4297 105.48 -35.29 101.04 1.5223
IC C1 C2 C3 C4 1.5227 101.04 37.68 102.70 1.5258
IC C3 O4 *C4 C5 1.5258 105.50 121.77 111.20 1.4950
IC C3 O4 *C4 H4 1.5258 105.50 -118.83 108.63 0.9263
IC O4 C4 C5 O5 1.4440 111.20 64.86 111.55 1.4236
IC C4 C5 O5 HO5 1.4950 111.55 -127.57 107.69 0.8505
IC O5 C4 *C5 H51 1.4236 111.55 -124.94 108.14 0.9881
IC O5 C4 *C5 H52 1.4236 111.55 119.60 108.76 0.9311
IC C2 O4 *C1 O1 1.5227 105.48 -116.55 111.30 1.3905
IC O4 C1 O1 HO1 1.4227 109.76 66.79 107.33 0.9584
IC C2 O4 *C1 H1 1.5227 105.48 122.60 106.81 0.9349
IC C3 C1 *C2 H2 1.5223 101.04 -123.72 113.32 0.9736
IC C3 C1 *C2 O2 1.5223 101.04 114.67 111.40 1.4145
IC C1 C2 O2 HO2 1.5227 111.40 80.30 105.08 0.8475
IC C2 C4 *C3 O3 1.5223 102.70 -122.33 110.28 1.4117
IC C2 C4 *C3 H3 1.5223 102.70 114.19 111.24 0.9813
IC C4 C3 O3 HO3 1.5258 110.28 -141.24 107.85 0.8418
IC C2 C4 *C3 H4 1.5223 102.70 -89.81 25.03 2.0467
RESI BDEON 0.000 ! beta-Deoxy-Ribose ! Updated C3, C5, H51, H52, H3, O1, O3, O5 as in DNA
! not used in 2017 update
!
! HO5--O5
! \ O4
! H51--C5 / \ O1--HO1
! / \ / \ /
! H52 C4 C1
! / \ / \
! H4 \ / H1
! C3----C2
! / \ / \
! O3 H3 H21 H22
! |
! HO3
!
ATOM O4 OD305A 0.000 ALPHA -0.618 THOLE 1.545 ! from THF
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1 CD315A 0.144 ALPHA -1.562 THOLE 1.103 ! from THF, neutralize group charge
ATOM H1 HDA1R5 0.055 ! from THF
ATOM O1 OD31A 0.000 ALPHA -0.901 THOLE 0.18
ATOM LP1A LPD -0.230
ATOM LP1B LPD -0.230
ATOM HO1 HDP1A 0.360
ATOM C4 CD315B 0.150 ALPHA -1.562 THOLE 1.103 ! from THF
ATOM H4 HDA1R5 0.055 ! from THF
GROUP
ATOM C5 CD32A 0.1975 ALPHA -1.642 THOLE 0.862
ATOM H51 HDA2A 0.026
ATOM H52 HDA2A 0.026
ATOM O5 OD31A 0.000 ALPHA -0.901 THOLE 0.181
ATOM LP5A LPD -0.230
ATOM LP5B LPD -0.230
ATOM HO5 HDP1A 0.360
GROUP
ATOM C2 CD325B -0.144 ALPHA -1.617 THOLE 1.103
ATOM H21 HDA2R5 0.072
ATOM H22 HDA2R5 0.072
GROUP
ATOM C3 CD315B -0.0755 ALPHA -1.642 THOLE 0.862
ATOM H3 HDA1R5 0.026
!ATOM O3 OD31A 0.000 ALPHA -0.901 THOLE 0.18
ATOM O3 OD31G 0.000 ALPHA -0.901 THOLE 0.18 !note OD31G which is used for 3'termini
ATOM LP3A LPD -0.230
ATOM LP3B LPD -0.230
ATOM HO3 HDP1A 0.360
BOND O4 C1 C1 H1 C1 O1 O1 HO1
BOND C1 C2 C2 H21 C2 H22 C2 C3
BOND C3 H3 C3 O3 O3 HO3 C3 C4
BOND C4 H4 C4 O4 C4 C5 C5 H51
BOND C5 H52 C5 O5 O5 HO5
BOND O4 LPRA O4 LPRB O4 LPX
BOND O1 LP1A O1 LP1B
BOND O3 LP3A O3 LP3B
BOND O5 LP5A O5 LP5B
LONEPAIR bisector LPRA O4 C1 C4 distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4 C1 C4 distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4 C1 C4 distance 0.10 angle 0.0 dihe 0.0
LONEPAIR relative LP1A O1 C1 HO1 distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP1B O1 C1 HO1 distance 0.35 angle 110.0 dihe 269.0
LONEPAIR relative LP3A O3 C3 HO3 distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP3B O3 C3 HO3 distance 0.35 angle 110.0 dihe 269.0
LONEPAIR relative LP5A O5 C5 HO5 distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP5B O5 C5 HO5 distance 0.35 angle 110.0 dihe 269.0
ANISOTROPY O4 LPX LPRA LPRB A11 0.8889 A22 1.2222
ANISOTROPY O1 C1 LP1A LP1B A11 0.8108 A22 1.2162
ANISOTROPY O3 C3 LP3A LP3B A11 0.8108 A22 1.2162
ANISOTROPY O5 C5 LP5A LP5B A11 0.8108 A22 1.2162
! IC table; from minimized geometry*
IC C4 O4 C1 C2 1.4309 108.67 -19.01 106.25 1.5278
IC O4 C1 C2 C3 1.4258 106.25 -8.82 103.23 1.5178
IC C1 C2 C3 C4 1.5278 103.23 31.05 101.83 1.5232
IC C3 O4 *C4 C5 1.5232 101.44 124.05 113.01 1.5448
IC C3 O4 *C4 H4 1.5232 101.44 -115.42 106.74 1.1134
IC O4 C4 C5 O5 1.4309 113.01 -178.27 111.12 1.4304
IC C4 C5 O5 HO5 1.5448 111.12 -87.73 110.40 0.9643
IC O4 C4 *C5 H51 2.4824 32.04 59.71 109.84 1.1020
IC O4 C4 *C5 H52 2.4824 32.04 -58.37 108.86 1.1027
IC C2 O4 *C1 O1 1.5278 106.25 -119.87 110.66 1.3905
IC O4 C1 O1 HO1 1.4258 110.66 60.11 106.63 0.9584
IC C2 O4 *C1 H1 1.5278 106.25 119.86 107.45 1.1137
IC C3 C1 *C2 H21 1.5178 103.23 118.42 111.24 1.1030
IC C3 C1 *C2 H22 1.5178 103.23 -122.05 112.95 1.0962
IC C2 C4 *C3 O3 1.5178 101.83 -120.07 112.49 1.4116
IC C4 C3 O3 HO3 1.5232 112.49 -53.93 107.21 0.9673
IC C2 C4 *C3 H3 1.5178 101.83 117.41 109.93 1.1144
end
read para card append
* Drude polarizable FF parameters
*
BONDS
!atom type Kb b0
!============================================
! NEW GUA (N9 is ND9G)
ND2R5F CD2R5F 400.00 1.370 ! Gua, jal
ND2R5F CD2R6F 350.00 1.370 ! Gua
ND2R5F CD315B 220.00 1.456 ! N9-C1' purine glycosidic linkage
! NEW THY (N1 is ND1T)
ND2R6D CD2O4A 340.00 1.370 ! THY, jal
ND2R6D CD2R6H 420.00 1.332 ! THY
ND2R6D CD315B 220.00 1.456 ! N1-C1' pyrimidine glycosidic linkage, from additive
!!additional nucleic acid parameters: watch for conflicts with carbohydrates
CD315B CD315B 195.00 1.518 ! C1'-C2', from THF CD325B-CD325B
CD315B OD31A 350.00 1.440 ! C2'-O2', from PRO2 OD31A-CD31A
CD315B OD31G 350.00 1.440 ! C2'-O2', from PRO2 OD31A-CD31A
CD315B OD30BN 335.00 1.440 ! C3'-O3', from DMP OD30B-CD33C
CD315B CD32C 222.50 1.528 ! C4'-C5', from TF2M CD315B-CD33A
CD315B CD32A 222.50 1.528 ! C4'-C5', from TF2M CD315B-CD33A
CD32C OD30BN 335.00 1.440 ! C5'-O5', from DMP OD30B-CD33C
! C1' is CD315A
ND2R6C CD315A 220.00 1.456 ! N1-C1' pyrimidine glycosidic linkage, from additive
ND2R5D CD315A 220.00 1.456 ! N9-C1' purine glycosidic linkage
ND2R5F CD315A 220.00 1.456 ! N9-C1' purine glycosidic linkage
ND2R6D CD315A 220.00 1.456 ! N1-C1' pyrimidine glycosidic linkage, from additive
OD305A CD315A 350.00 1.425 ! TF2M, cmb
CD315A CD325B 195.00 1.518 ! TF2M, cmb
CD315A CD315B 195.00 1.518 ! TF2M, cmb
CD315B HDA2R5 307.00 1.100 ! for T3PS
CD315A HDA2R5 307.00 1.100 ! for T3PS
ANGLES
!atom types Ktheta Theta0 Kub S0
!==================================================
! C1' is CD315A
!T3PS
OD305A CD315A HDA2R5 70.00 107.30 ! THF, viv 10/21/05
HDA2R5 CD315A HDA2R5 38.50 106.80 5.40 1.802 ! CPEN 10/17/05 viv
CD325B CD315A HDA2R5 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv
CD315B CD315A HDA2R5 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv
!!CYT
CD2R6H ND2R6C CD315A 45.00 115.90 ! CYT
CD2O4A ND2R6C CD315A 45.00 120.00 ! CYT, jal
ND2R6C CD315A CD315B 110.00 113.70 ! CYT
ND2R6C CD315A HDA1R5 43.00 111.00 ! CYT
!!ADE/GUA
CD2R6F ND2R5D CD315A 45.00 126.50 ! ADE
CD2R6F ND2R5F CD315A 45.00 126.50 ! GUA
CD2R5F ND2R5D CD315A 45.00 126.30 ! ADE, jal
CD2R5F ND2R5F CD315A 45.00 126.30 ! GUA, jal
ND2R5D CD315A CD315B 110.00 111.00 ! ADE
ND2R5F CD315A CD315B 110.00 111.00 ! GUA
ND2R5D CD315A HDA1R5 43.00 111.00 ! ADE
ND2R5F CD315A HDA1R5 43.00 111.00 ! GUA
! Glycosidic linkage
ND2R6C CD315A OD305A 110.00 108.00
ND2R6C CD315A CD325B 110.00 111.70
ND2R5D CD315A OD305A 110.00 108.00
ND2R5F CD315A OD305A 110.00 108.00
ND2R5D CD315A CD325B 110.00 111.50
ND2R5F CD315A CD325B 110.00 111.50
! Repeating for new type of N1 in THY
CD2R6H ND2R6D CD315A 45.00 115.90 ! THY
CD2O4A ND2R6D CD315A 45.00 120.00 ! THY, jal
ND2R6D CD315A HDA1R5 43.00 111.00 ! THY
ND2R6D CD315A OD305A 110.00 108.00 ! THY
ND2R6D CD315A CD325B 110.00 111.70 ! THY
ND2R6D CD315A CD315B 110.00 111.70 ! THY
! Sugar group
CD315A OD305A CD315B 95.00 111.00
OD305A CD315A CD325B 45.00 111.10
CD315A CD325B CD315B 58.00 109.50 11.16 2.561
CD315A CD315B OD31A 115.00 109.70 !RNA
CD315A CD315B OD31G 115.00 109.70 !DNA
OD305A CD315A CD315B 45.00 111.10 !RNA
CD315A CD315B CD315B 58.00 109.50 11.16 2.561 !RNA
! Hydrogens
OD305A CD315A HDA1R5 70.00 107.30 ! TF2M 02/09, cmb
CD325B CD315A HDA1R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb
CD315A CD325B HDA2R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb
CD315A CD315B HDA1R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb
CD315B CD315A HDA1R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb
CD315A CD315B HDA2R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb
!! End of C1' CD315A !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!NH-2 Bases ADE/GUA/CYT!!!!!!!!!!!
CD2R6C ND2B1 HDP1A 45.00 121.50 ! ADE, va !pyramidal 45.0 115.5 ! planar 45.0 120.0, cmb 04/10
HDP1A ND2B1 HDP1A 24.00 117.00 ! NA bases, cmb 04/10
CD2R6B ND2B1 HDP1A 40.00 121.50 ! CYT, va !pyramidal 40.0 115.5 ! planar 40.0 120.0, cmb 04/10
ND2B1 CD2R6B ND2R6B 81.00 122.30 ! CYT, cmb 04/10 ! N3-C4-N4
ND2B1 CD2R6B CD2R6J 81.00 120.00 ! CYT, jal ! C5-C4-N4
OD2C1B CD2O4A CD2R6J 93.00 122.60 ! THY, jal ! C5-C4-O4
ND2R6B CD2O4A OD2C1B 130.00 125.00 ! CYT, jal ! O2-C2-N3
CD2O4A ND2R6C HDP1A 40.50 114.00 ! THY
CD2O4A ND2R6C CD2O4A 40.00 132.00 ! THY
CD2O4A ND2R6B CD2R6B 50.00 120.00 ! CYT
CD2O4A ND2R6C CD2R6H 100.00 119.00 ! THY/CYT
ND2R6C CD2O4A ND2R6C 50.00 120.00 ! THY
ND2R6B CD2O4A ND2R6C 50.00 126.00 ! CYT
ND2R6C CD2O4A CD2R6J 70.00 118.00 ! THY, jal ! N3-C4-C5
CD2O4A CD2R6J CD2R6H 100.00 118.70 ! THY, jal ! C4-C5-C6
CD2R6B CD2R6J CD2R6H 50.00 117.00 ! CYT, jal ! C4-C5-C6
ND2R6C CD2R6H CD2R6J 10.00 114.00 ! THY/CYT, jal ! N1-C6-C5
ND2B1 CD2R6C ND2R6C 95.00 116.40 ! GUA, cmb 04/10 ! N1-C2-N2
ND2B1 CD2R6C ND2R6B 45.00 127.00 ! ADE/GUA, cmb 04/10 ! N3-C2-N2/N1-C6-N6
ND2B1 CD2R6C CD2R6F 45.00 123.00 ! ADE, cmb 04/10 ! N6-C6-C51)
ND2R6C CD2O4A OD2C1B 70.00 124.40 ! THY, jal ! N1-C6-O6)
OD2C1B CD2O4A CD2R6F 50.00 125.70 ! GUA, jal ! C5-C6-O6)
ND2R5D CD2R6F ND2R6B 100.00 118.00 ! ADE/GUA, cmb 04/10 ! N3-C4-N9
ND2R5E CD2R6F CD2R6C 100.00 128.00 ! ADE, bridgeC5, cmb 04/10 ! N7-C5-C6
ND2R5E CD2R6F CD2O4A 125.00 129.00 ! GUA, jal ! N7-C5-C6
CD2R5F ND2R5D CD33A 17.00 125.80 ! ADE, jal ! C8-N9-C9
CD2R5F ND2R5F CD33A 17.00 125.80 ! GUA, jal ! C8-N9-C9
CD2R6F ND2R5D CD33A 17.00 127.90 ! ADE, cmb 04/10 ! C4-N9-C9
CD2R6F ND2R5F CD33A 17.00 127.90 ! GUA, jal ! C4-N9-C9
CD2R5F ND2R5E CD2R6F 127.91 103.00 ! ADE, jal
CD2R5F ND2R5D CD2R6F 100.00 106.30 ! ADE, jal ! C8-N9-C4
CD2R5F ND2R5F CD2R6F 100.00 106.30 ! GUA, jal ! C8-N9-C4
ND2R5E CD2R6F CD2R6F 99.82 116.50 ! ADE, cmb 04/10 ! C4-C5-N7
ND2R5D CD2R6F CD2R6F 100.00 105.00 ! ADE, cmb 04/10 ! C5-C4-N9
ND2R5F CD2R6F CD2R6F 100.00 105.00 ! GUA, jal ! C5-C4-N9
ND2R5E CD2R5F ND2R5D 130.00 109.50 ! ADE, jal ! N7-C8-N9
ND2R5E CD2R5F ND2R5F 130.00 109.50 ! GUA, jal ! N7-C8-N9
ND2R6B CD2R6C ND2R6C 70.00 130.20 ! GUA, cmb 04/10 ! N3-C2-N1
CD2R6C ND2R6B CD2R6C 90.00 111.80 ! ADE, cmb ! C2-N1-C6
CD2O4A ND2R6C CD2R6C 70.00 123.10 ! GUA, jal ! C2-N1-C6
ND2R6B CD2R6C CD2R6F 60.00 106.70 ! ADE, cmb 04/10 ! N1-C6-C5
ND2R6C CD2O4A CD2R6F 70.00 107.80 ! GUA, jal ! N1-C6-C5
CD2R6C CD2R6F CD2R6F 60.00 121.00 ! ADE, cmb 04/10 ! C6-C5-C4
CD2O4A CD2R6F CD2R6F 70.00 120.00 ! GUA, jal ! C6-C5-C4
! Repeating for new type of N9 in GUA
ND2R5F CD2R5F HDR5B 25.00 122.50 20.00 2.1400 ! GUA, jal
ND2R5F CD2R6F ND2R6B 100.00 118.00 ! GUA
! Repeating for new type of N1 in THY
CD2O4A ND2R6D CD2R6H 100.00 119.00 ! THY, jal
CD2R6H ND2R6D CD315B 45.00 115.90 ! THY
CD2O4A ND2R6D CD315B 45.00 120.00 ! THY, jal
ND2R6D CD315B HDA1R5 43.00 111.00 ! THY
ND2R6D CD315B OD305A 110.00 108.00 ! THY
ND2R6D CD315B CD325B 110.00 111.70 ! THY
ND2R6D CD2R6H HDR6B 30.00 116.00 ! THY
ND2R6D CD2R6H CD2R6J 10.00 114.00 ! THY
ND2R6D CD2O4A OD2C1B 70.00 124.40 ! THY, jal
ND2R6D CD2O4A ND2R6C 50.00 120.00 ! THY, jal
ND2R6D CD315B CD315B 110.00 113.70 ! THY
OD305A CD315A OD31A 45.00 116.50 ! for BRIB
OD305A CD315A OD31G 45.00 116.50 ! for BRIB
!! Everywhere
OD305A CD325B CD315B 45.00 111.10 ! O4'-C1'-C2', from THF
CD315B CD315B HDA1R5 35.00 111.40 ! C1'-C2'-H2'', from TF2M
CD315B OD31A HDP1A 59.00 108.00 ! C2'-O2'-H2', from PRO2 !RNA
CD315B OD31G HDP1A 59.00 108.00 ! C2'-O2'-H2', from PRO2 !DNA 3TER, jal
CD315B CD315B CD315B 58.00 109.50 11.16 2.561 ! C1'-C2'-C3', from THF
HDA1R5 CD315B OD30BN 34.50 110.10 22.53 2.179 ! H3'-C3'-O3', from TF2M
HDA1R5 CD315B OD31A 34.50 110.10 22.53 2.179 ! H2''-C2'-O2', from TF2M !RNA
HDA1R5 CD315B OD31G 34.50 110.10 22.53 2.179 ! H2''-C2'-O2', from TF2M !DNA 3TER, jal
CD325B CD315B CD32C 53.35 114.00 8.00 2.561 ! C3'-C4'-C5', from TF2M
HDA1R5 CD315B CD32C 34.50 110.10 22.53 2.179 ! H4'-C4'-C5', from TF2M
CD315B CD32C HDA2A 33.43 110.10 22.53 2.179 ! C4'-C5'-H5'', from TF2M
CD315B CD32A HDA2A 33.43 110.10 22.53 2.179 ! C4'-C5'-H5'', from TF2M
HDA2A CD32C OD30BN 60.00 109.50 ! H5'-C5'-O5', from DMP
!!CYT
CD2R6H ND2R6C CD315B 45.00 115.90 ! CYT
CD2O4A ND2R6C CD315B 45.00 120.00 ! CYT, jal
ND2R6C CD315B CD315B 110.00 113.70 ! CYT
ND2R6C CD315B HDA1R5 43.00 111.00 ! CYT
!!GUA
CD2R6F ND2R5F CD315B 45.00 126.50 ! GUA
CD2R5F ND2R5F CD315B 45.00 126.30 ! GUA, jal
ND2R5F CD315B CD315B 110.00 111.00 ! GUA
ND2R5F CD315B HDA1R5 43.00 111.00 ! GUA
!!5TER
CD32A CD315B HDA1R5 34.50 110.10 22.53 2.179 ! C5T-C4'-H4', from TF2M
! Sugar group
CD325B CD315B HDA2R5 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv
CD315B CD325B CD315B 58.00 109.50 11.16 2.561
CD325B CD315B CD315B 58.00 109.50 11.16 2.561
OD305A CD315B CD315B 45.00 111.10
CD315B OD305A CD315B 95.00 111.00
OD305A CD315B CD32C 90.00 109.20
OD305A CD315B CD32A 90.00 109.20
CD315B CD315B CD32C 45.00 111.00
CD315B CD315B CD32A 45.00 111.00
CD325B CD315B OD30BN 115.00 109.70
CD325B CD315A OD31A 115.00 109.70 ! for BDEO
CD325B CD315B OD31G 115.00 109.70 !3TER, jal
CD315B CD315B OD30BN 115.00 109.70 !RNA
CD315B CD315B OD31A 115.00 109.70 !RNA
CD315B CD315B OD31G 115.00 109.70 !DNA 3TER, jal
CD315B CD315A OD31A 115.00 109.70 ! for BRIB
! Backbone
CD315B CD32C OD30BN 70.00 108.40
OD31A CD32A CD315B 70.00 108.40
OD30BN PD1AN OD30BN 90.00 107.50
CD32C OD30BN PD1AN 40.00 124.50
CD315B OD30BN PD1AN 40.00 114.50
! Phosphate group
OD2C2C PD1AN OD2C2C 120.00 125.00
OD2C2C PD1AN OD30BN 98.90 113.00
! Glycosidic linkage
ND2R6C CD315B OD305A 110.00 108.00
ND2R6C CD315B CD325B 110.00 111.70
ND2R5D CD315B OD305A 110.00 108.00
ND2R5F CD315B OD305A 110.00 108.00
ND2R5D CD315B CD325B 110.00 111.50
ND2R5F CD315B CD325B 110.00 111.50
OD305A CD315B HDA2R5 70.00 107.30
HDA2R5 CD315B HDA2R5 38.50 106.80 5.40 1.802
CD315B CD315B HDA2R5 35.00 111.40 22.53 2.179
DIHEDRALS
!atom types Kchi n delta
!=================================================
!
!Please follow these conventions when fitting dihedral parameters
!1) use positive force constants in all cases (switch the phase...)
! (vary phase during fitting and keep force constants positive)
!2) maintain the phase at 0 or 180 if possiple. perform initial
! fitting with this contraint and, if necessary, only then
! vary the phases during fitting. note that if the phases
! are NOT 0 or 180 the parameters are NOT transferable across
! stereoisomers
!3) refit with only individual multiplicities of 1 through 6
!4) maintain the number of significant figures used below
!
! ND3A3 CD2O1A CD31C CD32B 0.200 3 0.00 ! comment
!
! C1' is CD315A
!T3PS
HDA2R5 CD315A CD325B HDA2R5 0.190 3 0.00 ! THF, viv
CD315B OD305A CD315A HDA2R5 0.300 3 0.00 ! TF2M, cmb
CD315B CD325B CD315A HDA2R5 0.190 3 0.00 ! TF2M, cmb
CD315A OD305A CD315B HDA2R5 0.300 3 0.00 ! TF2M, cmb
CD315A CD325B CD315B HDA2R5 0.190 3 0.00 ! TF2M, cmb
! Involving N1/N9 (not Chi)
ND2R6C CD315A CD325B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' !RNA
HDA2R5 CD325B CD315A ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1
HDA1R5 CD325B CD315A ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1
CD2O4A ND2R6C CD315A HDA1R5 0.000 3 0.00 ! C2-N1-C1'-H1', jal
CD2R6H ND2R6C CD315A HDA1R5 0.195 3 0.00 ! C6-N1-C1'-H1'
ND2R6C CD315A OD305A CD315B 0.000 3 180.00 ! N1-C1a-O4a-C4a, jal 06/16
ND2R6C CD315A CD325B CD315B 0.500 3 0.00 ! N1-C1a-C2D-C3a, jal 06/16
HDA2R5 CD325B CD315A ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9
HDA2R5 CD325B CD315A ND2R5F 0.000 3 0.00 ! H2'-C2'-C1'-N9
HDA1R5 CD325B CD315A ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9
HDA1R5 CD325B CD315A ND2R5F 0.000 3 0.00 ! H2'-C2'-C1'-N9
CD2R6F ND2R5D CD315A HDA1R5 0.000 3 0.00 ! C4-N9-C1'-H1'
CD2R6F ND2R5F CD315A HDA1R5 0.000 3 0.00 ! C4-N9-C1'-H1'
CD2R5F ND2R5D CD315A HDA1R5 0.195 3 0.00 ! C8-N9-C1'-H1', jal
CD2R5F ND2R5F CD315A HDA1R5 0.195 3 0.00 ! C8-N9-C1'-H1', jal
ND2R5D CD315A CD325B CD315B 0.500 3 0.00 ! N9-C1a-C2D-C3a
ND2R5F CD315A CD325B CD315B 0.500 3 0.00 ! N9-C1a-C2D-C3a, jal
ND2R5D CD315A OD305A CD315B 1.500 3 0.00 ! N9-C1a-O4a-C4a, jal
ND2R5F CD315A OD305A CD315B 0.500 3 180.00 ! N9-C1a-O4a-C4a, jal
ND2R6C CD315A CD315B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' !RNA
ND2R6D CD315A CD315B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' !RNA
HDA2R5 CD315B CD315A ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1
HDA1R5 CD315B CD315A ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1
HDA1R5 CD315B CD315A ND2R6D 0.000 3 0.00 ! H2'-C2'-C1'-N1
ND2R6C CD315A CD315B CD315B 0.000 3 0.00 ! N1-C1a-C2D-C3a !RNA
ND2R5D CD315A CD315B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' !RNA
ND2R5F CD315A CD315B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' !RNA
HDA2R5 CD315B CD315A ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9
HDA2R5 CD315B CD315A ND2R5F 0.000 3 0.00 ! H2'-C2'-C1'-N9
HDA1R5 CD315B CD315A ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9
HDA1R5 CD315B CD315A ND2R5F 0.000 3 0.00 ! H2'-C2'-C1'-N9
ND2R5D CD315A CD315B CD315B 0.000 3 0.00 ! N9-C1a-C2D-C3a !RNA
ND2R5F CD315A CD315B CD315B 0.000 3 0.00 ! N9-C1a-C2D-C3a !RNA
ND2R6D CD315A CD315B CD315B 0.000 3 0.00 ! N1-C1a-C2D-C3a !RNA
ND2R6D CD315A CD325B HDA2R5 0.000 3 0.00 ! N1-C1a-C2D-H2D
CD2O4A ND2R6D CD315A HDA1R5 0.000 3 0.00 ! C2-N1-C1a-H1a, from C27, jal
CD2R6H ND2R6D CD315A HDA1R5 0.195 3 0.00 ! C6-N1-C1a-H1a
ND2R6D CD315A OD305A CD315B 1.000 3 0.00 ! N1-C1a-O4a-C4a jal TESTING 05/16, was zero
ND2R6D CD315A CD325B CD315B 0.500 3 0.00 ! N1-C1a-C2D-C3a, jal TESTING 06/16, was zero
CD2R6J CD2R6H ND2R6D CD315A 11.000 2 180.00 ! C5-C6-N1-C1', from C27, jal
HDR6B CD2R6H ND2R6D CD315A 0.300 2 180.00 ! H6-C6-N1-C1', from C27
OD2C1B CD2O4A ND2R6D CD315A 11.000 2 180.00 ! O2-C2-N1-C1', from C27
ND2R6B CD2O4A ND2R6D CD315A 11.000 2 180.00 ! N3-C2-N1-C1', from C27
ND2R6D CD2O4A ND2R6D CD315A 11.000 2 180.00 ! N3-C2-N1-C1'
ND2R6C CD2O4A ND2R6D CD315A 11.000 2 180.00 ! N3-C2-N1-C1'
! Chi Adenine/Guanine
!O4'-C1'-N9-C4, ADE
! jal manual refinement
OD305A CD315A ND2R5D CD2R6F 0.350 1 0.00
OD305A CD315A ND2R5D CD2R6F 0.500 3 0.00
OD305A CD315A ND2R5D CD2R6F 0.021 6 0.00
!O4'-C1'-N9-C4, GUA
! jal manual refinement
OD305A CD315A ND2R5F CD2R6F 0.575 1 0.00
OD305A CD315A ND2R5F CD2R6F 0.536 2 0.00
OD305A CD315A ND2R5F CD2R6F 0.320 3 0.00 ! jal, manual refinement
OD305A CD315A ND2R5F CD2R6F 0.033 6 0.00
!O4'-C1'-N9-C8
CD2R5F ND2R5F CD315A OD305A 1.400 1 0.00 ! GUA, jal
CD2R5F ND2R5D CD315A OD305A 1.500 1 0.00 ! ADE, jal
!GUA C2'-C1'-N9-C4
CD2R6F ND2R5F CD315A CD325B 0.000 3 0.00 ! GUA, DNA
CD2R6F ND2R5F CD315A CD315B 0.000 3 0.00 ! GUA, RNA
!ADE C2'-C1'-N9-C4
CD2R6F ND2R5D CD315A CD325B 1.200 1 0.00 ! ADE, DNA
CD2R6F ND2R5D CD315A CD315B 1.200 1 0.00 ! ADE, RNA
!C2'-C1'-N9-C8
CD2R5F ND2R5F CD315A CD325B 0.000 3 180.00 ! GUA, jal
CD2R5F ND2R5F CD315A CD315B 0.000 3 180.00 ! GUA, jal
CD2R5F ND2R5D CD315A CD325B 0.000 3 180.00 ! ADE, jal
CD2R5F ND2R5D CD315A CD315B 0.000 3 180.00 ! ADE, jal
! Chi Cytosine/Thymine
!O4'-C1'-N1-C2, CYT
! jal manual refinement
CD2O4A ND2R6C CD315A OD305A 0.800 1 0.00
CD2O4A ND2R6C CD315A OD305A 0.700 2 0.00
!O4'-C1'-N1-C2, THY
! jal manual refinement
OD305A CD315A ND2R6D CD2O4A 1.779 1 0.00
OD305A CD315A ND2R6D CD2O4A 0.969 2 0.00
OD305A CD315A ND2R6D CD2O4A 0.500 3 180.00
!O4'-C1'-N1-C6
CD2R6H ND2R6C CD315A OD305A 0.350 1 0.00 ! CYT
CD2R6H ND2R6D CD315A OD305A 1.900 1 0.00 ! THY
!C2'-C1'-N1-C2
CD2O4A ND2R6C CD315A CD325B 0.000 3 0.00 ! CYT
CD2O4A ND2R6C CD315A CD315B 0.000 3 0.00 ! CYT
CD2O4A ND2R6D CD315A CD325B 0.750 3 0.00 ! THY, for agreement with nu0/nu4 surf
CD2O4A ND2R6D CD315A CD315B 0.750 3 0.00 ! URA, copied from THY - test!
!C2'-C1'-N1-C6
CD2R6H ND2R6C CD315A CD325B 0.000 3 180.00 ! CYT
CD2R6H ND2R6D CD315A CD325B 0.000 3 180.00 ! THY
CD2R6H ND2R6C CD315A CD315B 0.000 3 180.00 ! CYT
CD2R6H ND2R6D CD315A CD315B 0.000 3 180.00 ! URA
! End of Chi's !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!dihedrals that include both base and sugar atoms (but not glycosidic linkage)
! Cyt
CD2R6J CD2R6H ND2R6C CD315A 11.000 2 180.00 ! C5-C6-N1-C1', from C27, jal
HDR6B CD2R6H ND2R6C CD315A 0.300 2 180.00 ! H6-C6-N1-C1', from C27
OD2C1B CD2O4A ND2R6C CD315A 11.000 2 180.00 ! O2-C2-N1-C1', from C27, jal
ND2R6B CD2O4A ND2R6C CD315A 11.000 2 180.00 ! N3-C2-N1-C1', from C27, jal
! Thy
ND2R6C CD2O4A ND2R6C CD315A 11.000 2 180.00 ! N3-C2-N1-C1', jal
! Ade/Gua
ND2R6B CD2R6F ND2R5D CD315A 11.000 2 180.00 ! N3-C4-N9-C1'
ND2R6B CD2R6F ND2R5F CD315A 11.000 2 180.00 ! N3-C4-N9-C1'
CD2R6F CD2R6F ND2R5D CD315A 11.000 2 180.00 ! C5-C4-N9-C1', from C27
CD2R6F CD2R6F ND2R5F CD315A 11.000 2 180.00 ! C5-C4-N9-C1', from C27
ND2R5E CD2R5F ND2R5D CD315A 11.000 2 180.00 ! N7-C8-N9-C1', from C27, jal
ND2R5E CD2R5F ND2R5F CD315A 11.000 2 180.00 ! N7-C8-N9-C1', from C27, jal
HDR5B CD2R5F ND2R5D CD315A 0.300 2 180.00 ! H8-C8-N9-C1', from C27, jal
HDR5B CD2R5F ND2R5F CD315A 0.300 2 180.00 ! H8-C8-N9-C1', from C27, jal
!Hydrogens
HDA1R5 CD325B CD315A OD305A 0.195 3 180.00 ! H3'-C3'-C4'-O4'
HDA1R5 CD325B CD315A HDA1R5 0.200 3 0.00 ! H3'-C3'-C4'-H4'
OD305A CD315A OD31A HDP1A 0.200 3 0.00 ! HO1-O1-C1-O4
HDA1R5 CD315A OD305A CD315B 0.000 3 0.00 ! H1'-C1'-O4'-C4'
HDA1R5 CD315A CD325B CD315B 0.195 3 0.00 ! H1'-C1'-C2'-C3'
HDA1R5 CD315A CD325B HDA2R5 0.195 3 0.00 ! TF2M, cmb
HDA1R5 CD315B CD315A OD305A 0.195 3 180.00 ! H3'-C3'-C4'-O4'
HDA1R5 CD315B CD315A HDA1R5 0.200 3 0.00 ! H3'-C3'-C4'-H4'
HDA1R5 CD315A CD315B CD315B 0.195 3 0.00 ! H1'-C1'-C2'-C3' !RNA
! Exocyclic groups
CD315A OD305A CD315B CD32C 0.300 3 0.00 ! C5'-C4'-O4'-C1'
CD315A CD325B CD315B OD30BN 0.200 3 0.00 ! C1'-C2'-C3'-O3'
CD315A OD305A CD315B CD32A 0.300 3 0.00 ! C5'-C4'-O4'-C1'
CD315A CD325B CD315B OD31A 0.200 3 0.00 ! C1'-C2'-C3'-O3'
CD315A CD325B CD315B OD31G 0.200 3 0.00 ! C1'-C2'-C3'-O3', DNA 3TER (jal)
CD315A CD315B CD315B OD30BN 0.200 3 0.00 ! C1'-C2'-C3'-O3'
CD315A CD315B CD315B OD31A 0.200 3 0.00 ! C1'-C2'-C3'-O3'
CD315A CD315B CD315B OD31G 0.200 3 0.00 ! C1'-C2'-C3'-O3', DNA 3TER (jal)
CD315B CD315B CD315A OD31A 0.200 3 0.00 ! C1'-C2'-C3'-O3', for BRIB
CD315B CD315B CD315B CD32C 0.200 3 0.00 ! C5'-C4'-C3'-C2'
CD315B CD315B CD315B CD32A 0.200 3 0.00 ! C5'-C4'-C3'-C2'
HDA1R5 CD315B OD305A CD315A 0.000 3 0.00 ! H4'-C4'-O4'-C1'
OD305A CD315A CD325B HDA2R5 0.200 3 0.00 ! TF2M, cmb
HDA1R5 CD315B CD325B CD315A 0.195 3 0.00 ! H3'-C3'-C2'-C1'
! Hydroxyl group in RNA
CD315B OD305A CD315A OD31A 0.000 3 180.00 ! O1-C1-O4-C4, for BRIB
!! jal for RNA
!conflict with DNA; used for 3TER in DNA. May need new atom type as this changes the
!DNA energy
! C1'-C2'-O2'-H2'
CD315A CD315B OD31A HDP1A 2.360 1 0.00 ! jal
CD315A CD315B OD31A HDP1A 0.830 2 0.00 ! jal
CD315A CD315B OD31A HDP1A 0.340 3 0.00 ! jal
! C3'-C2'-O2'-H2'
! jal: added new atom type (OD31G) to resolve DNA/RNA conflict
CD315B CD315B OD31A HDP1A 2.360 1 0.00
CD315B CD315B OD31G HDP1A 0.200 1 0.00
!
!
CD315B CD315B CD315B OD31A 0.000 3 0.00 ! O2'-C2'-C3'-C4' !RNA
HDA1R5 CD315A CD315B OD31A 0.000 3 0.00 ! H1'-C1'-C2'-O2' !RNA
OD305A CD315A CD315B OD31A 0.000 3 0.00 ! O2'-C2'-C1'-O4' !RNA
HDA1R5 CD315B CD315B CD315A 0.195 3 0.00 ! H3'-C3'-C2'-C1' !RNA
OD31A CD315B CD315B OD31A 0.000 3 180.00 ! O2-C2-C1-O1, for BRIB
OD31A CD315B CD315B OD31G 0.000 3 180.00 ! O2'-C2'-C3'-O3', for RNA, jal
OD31A CD315B CD315A OD31A 0.000 3 180.00 ! O2'-C2'-C1'-O1, for BRIB
!! End of C1' is CD315A!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! Repeating torsions for GUA
CD2R6F ND2R5E CD2R5F ND2R5F 14.000 2 180.00 ! ADE
CD2R6F ND2R5F CD2R5F ND2R5E 6.000 2 180.00 ! ADE
CD2R6F ND2R5F CD2R5F HDR5B 3.500 2 180.00 ! ADE
CD33A ND2R5F CD2R5F ND2R5E 1.000 2 180.00 ! ADE
CD33A ND2R5F CD2R5F HDR5B 1.000 2 180.00 ! ADE
HDP1A ND2R5F CD2R5F ND2R5B 1.000 2 180.00 ! IMID
HDP1A ND2R5F CD2R5F ND2R5E 1.000 2 180.00 ! ADE
HDP1A ND2R5F CD2R5F HDR5B 1.000 2 180.00 ! ADE
CD2R5F ND2R5F CD2R6F ND2R6B 2.000 2 180.00 ! ADE
CD2R5F ND2R5F CD2R6F CD2R6F 6.000 2 180.00 ! ADE
CD33A ND2R5F CD2R6F ND2R6B 1.000 2 180.00 ! ADE, cmb
CD33A ND2R5F CD2R6F CD2R6F 1.000 2 180.00 ! ADE, cmb
HDP1A ND2R5F CD2R6F ND2R6B 1.500 2 180.00 ! ADE, cmb 04/10
HDP1A ND2R5F CD2R6F CD2R6F 1.200 2 180.00 ! ADE, cmb 04/10
CD2R5F ND2R5F CD33A HDA3A 0.000 3 0.00 ! ADE, jal
CD2R6F ND2R5F CD33A HDA3A 0.000 3 0.00 ! ADE, cmb
CD2R6C ND2R6B CD2R6F ND2R5F 2.500 2 180.00 ! ADE, butterfly motion, jal
ND2R5E CD2R6F CD2R6F ND2R5F 14.000 2 180.00 ! ADE, cmb 04/10
ND2R5F CD2R6F CD2R6F CD2O4A 0.000 2 180.00 ! GUA, jal
ND2R5F CD2R6F CD2R6F CD2R6C 3.000 2 180.00 ! ADE, va A; butterfly motion, cmb 04/10
CD32A ND2R5F CD2R6F ND2R6B 1.000 2 180.00 ! va; Et-Gua
CD32A ND2R5F CD2R6F CD2R6F 1.000 2 180.00 ! va; Et-Gua
CD32A ND2R5F CD2R5F ND2R5E 1.000 2 180.00 ! va; Et-Gua, jal
CD32A ND2R5F CD2R5F HDR5B 1.000 2 180.00 ! va; Et-Gua, jal
CD33A CD32A ND2R5F CD2R6F 1.000 3 0.00 ! va; Et-Gua
HDA2A CD32A ND2R5F CD2R6F 0.000 3 0.00 ! va; Et-Gua
HDA2A CD32A ND2R5F CD2R5F 0.000 3 0.00 ! va; Et-Gua, jal
CD33A CD32A ND2R5F CD2R5F 1.000 3 0.00 ! va; Et-Gua, jal
ND2R5F CD32A CD33A HDA3A 0.160 3 0.00 ! va; Et-Gua
ND2R6B CD2R6F ND2R5F CD315B 11.000 2 180.00 ! N3-C4-N9-C1'
CD2R6F CD2R6F ND2R5F CD315B 11.000 2 180.00 ! C5-C4-N9-C1', from C27
ND2R5F CD315B CD315B HDA1R5 0.000 3 0.00 ! N9-C1'-C2'-H2''
ND2R5F CD315B CD315B OD31A 0.000 3 0.00 ! N9-C1'-C2'-O2'
ND2R5F CD315B CD325B OD31A 0.000 3 0.00 ! N9-C1'-C2'-O2' ! RNA
ND2R5F CD315B CD315B CD315B 0.000 3 0.00 ! N9-C1'-C2'-C3'
ND2R5E CD2R5F ND2R5F CD315B 11.000 2 180.00 ! N7-C8-N9-C1', from C27, jal
HDR5B CD2R5F ND2R5F CD315B 0.300 2 180.00 ! H8-C8-N9-C1', from C27, jal
! Repeating torsions for THY
ND2R6D CD315B CD325B HDA2R5 0.000 3 0.00 ! N1-C1a-C2D-H2D
CD2O4A ND2R6D CD315B HDA1R5 0.000 3 0.00 ! C2-N1-C1a-H1a, from C27, jal
CD2R6H ND2R6D CD315B HDA1R5 0.195 3 0.00 ! C6-N1-C1a-H1a
HDP1A ND2B1 CD2R6C ND2R6D 1.400 2 180.00 ! GUA, cmb 04/10
CD2R6B ND2R6B CD2O4A ND2R6D 0.600 2 180.00 ! CYT, cmb 04/10
CD2R6H ND2R6D CD2O4A ND2R6B 0.600 2 180.00 ! CYT, cmb 04/10
CD2R6H ND2R6B CD2O4A ND2R6D 1.500 2 180.00 ! THY, cmb
CD2R6H ND2R6D CD2O4A ND2R6D 1.500 2 180.00 ! THY, cmb 04/10
CD2R6H ND2R6D CD2O4A OD2C1B 1.600 2 180.00 ! CYT, cmb 04/10
CD33A ND2R6D CD2O4A ND2R6B 0.900 2 180.00 ! CYT, cmb 04/10
CD33A ND2R6D CD2O4A ND2R6D 0.700 2 180.00 ! THY, cmb 04/10
CD33A ND2R6D CD2O4A OD2C1B 0.900 2 180.00 ! CYT, cmb 04/10
HDP1A ND2R6B CD2O4A ND2R6D 1.600 2 180.00 ! THY, cmb 04/10
CD2R6F ND2R6B CD2R6C ND2R6D 2.000 2 180.00 ! GUA, cmb 04/10
CD2O4A ND2R6D CD2R6H CD2R6J 0.600 2 180.00 ! CYT, jal
CD2O4A ND2R6D CD2R6H HDR6B 3.600 2 180.00 ! CYT, jal
CD33A ND2R6D CD2R6H CD2R6J 1.000 2 180.00 ! CYT, jal
CD33A ND2R6D CD2R6H HDR6B 1.000 2 180.00 ! CYT, cmb 04/10
HDP1A ND2R6D CD2R6H CD2R6J 1.600 2 180.00 ! CYT, jal
HDP1A ND2R6D CD2R6H HDR6B 1.500 2 180.00 ! CYT, cmb 04/10
CD2O1A ND2R6D CD33A HDA3A 0.000 3 0.00 ! CYT, cmb 04/10
CD2O4A ND2R6D CD33A HDA3A 0.000 3 0.00 ! CYT, jal
CD2R6H ND2R6D CD33A HDA3A 0.000 3 0.00 ! CYT, cmb 04/10
CD2O4A ND2R6D CD2O4A ND2R6B 1.500 2 180.00 ! THY, jal
CD2O4A ND2R6D CD2O4A ND2R6D 1.500 2 180.00 ! THY, jal
CD2O4A ND2R6D CD2O4A OD2C1B 0.900 2 180.00 ! THY, jal
CD2O4A ND2R6D CD2O4A CD2R6J 0.900 2 180.00 ! THY, jal
CD2R6C ND2R6D CD2O4A OD2C1B 8.000 2 180.00 ! GUA, jal
CD2R6C ND2R6D CD2O4A CD2R6F 0.200 2 180.00 ! GUA, jal
HDP1A ND2R6D CD2O4A ND2R6B 3.800 2 180.00 ! THY, jal
HDP1A ND2R6D CD2O4A ND2R6D 3.800 2 180.00 ! THY, jal
HDP1A ND2R6D CD2O4A OD2C1B 0.000 2 180.00 ! THY, jal
HDP1A ND2R6D CD2O4A CD2R6J 4.800 2 180.00 ! THY, jal
HDP1A ND2R6D CD2O4A CD2R6F 3.600 2 180.00 ! GUA, jal
CD2O4A ND2R6D CD2R6C ND2B1 4.000 2 180.00 ! GUA, jal
CD2O4A ND2R6D CD2R6C ND2R6B 0.200 2 180.00 ! GUA, jal
HDP1A ND2R6D CD2R6C ND2B1 0.000 2 180.00 ! GUA, cmb 04/10
HDP1A ND2R6D CD2R6C ND2R6B 3.600 2 180.00 ! GUA, cmb 04/10
ND2R6D CD2O4A CD2R6J CD2R6H 1.800 2 180.00 ! THY, jal
ND2R6D CD2O4A CD2R6J CD33A 1.000 2 180.00 ! THY, jal
ND2R6D CD2O4A CD2R6J HDR6A 1.000 2 180.00 ! URA, jal
ND2R6D CD2O4A CD2R6F ND2R5E 2.000 2 180.00 ! GUA, jal
ND2R6D CD2O4A CD2R6F CD2R6F 0.200 2 180.00 ! GUA, jal
CD2O4A CD2R6J CD2R6H ND2R6D 3.000 2 180.00 ! THY, jal
CD2R6B CD2R6J CD2R6H ND2R6D 0.800 2 180.00 ! CYT, jal
CD33A CD2R6J CD2R6H ND2R6D 5.600 2 180.00 ! THY, jal
HDR6A CD2R6J CD2R6H ND2R6D 2.800 2 180.00 ! CYT, jal
ND2R6D CD315B OD305A CD315B 0.000 3 0.00 ! N1-C1a-O4a-C4a
ND2R6D CD315B CD325B CD315B 0.000 3 0.00 ! N1-C1a-C2D-C3a
CD2R6J CD2R6H ND2R6D CD315B 11.000 2 180.00 ! C5-C6-N1-C1', from C27, jal
HDR6B CD2R6H ND2R6D CD315B 0.300 2 180.00 ! H6-C6-N1-C1', from C27
ND2R6D CD315B CD315B HDA1R5 0.000 3 0.00 ! N1-C1'-C2'-H2''
ND2R6D CD315B CD315B OD31A 0.000 3 0.00 ! N1-C1'-C2'-O2'
ND2R6D CD315B CD325B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' ! RNA
ND2R6C CD315B CD325B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' ! RNA
ND2R5D CD315B CD325B OD31A 0.000 3 0.00 ! N1/N9-C1'-C2'-O2' ! RNA
ND2R6D CD315B CD315B CD315B 0.000 3 0.00 ! N1-C1'-C2'-C3'
OD2C1B CD2O4A ND2R6D CD315B 11.000 2 180.00 ! O2-C2-N1-C1', from C27
ND2R6B CD2O4A ND2R6D CD315B 11.000 2 180.00 ! N3-C2-N1-C1', from C27
ND2R6D CD2O4A ND2R6D CD315B 11.000 2 180.00 ! N3-C2-N1-C1'
CD2O4A ND2R6C CD2O4A ND2R6D 1.500 2 180.00 ! THY, cmb 04/10
HDP1A ND2R6C CD2O4A ND2R6D 3.800 2 180.00 ! THY, cmb 04/10
CD2R6H ND2R6D CD2O4A ND2R6C 1.500 2 180.00 ! THY, cmb 04/10
ND2R6C CD2O4A ND2R6D CD315B 11.000 2 180.00 ! N3-C2-N1-C1'
! Torsions involving Hydrogens
HDA2R5 CD325B CD315B OD30BN 0.195 3 0.00 ! H2'-C2'-C3'-O3'
HDA1R5 CD325B CD315B OD30BN 0.195 3 0.00 ! H2'-C2'-C3'-O3'
HDA2R5 CD325B CD315B OD31G 0.195 3 0.00 ! H2'-C2'-C3'-O3T, DNA 3TER (jal)
HDA2R5 CD325B CD315A OD31A 0.195 3 0.00 ! H2'-C2'-C3'-O3T, for BDEO
HDA2R5 CD325B CD315B CD315B 0.195 3 0.00 ! H2'-C2'-C3'-C4'
HDA2R5 CD325B CD315B ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9
HDA2R5 CD325B CD315B ND2R5F 0.000 3 0.00 ! H2'-C2'-C1'-N9
HDA1R5 CD325B CD315B ND2R5D 0.000 3 0.00 ! H2'-C2'-C1'-N9
HDA1R5 CD325B CD315B ND2R5F 0.000 3 0.00 ! H2'-C2'-C1'-N9
HDA2R5 CD325B CD315B ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1
HDA1R5 CD325B CD315B ND2R6C 0.000 3 0.00 ! H2'-C2'-C1'-N1
HDA1R5 CD315B OD305A CD315B 0.000 3 0.00 ! H1'-C1'-O4'-C4'
HDA1R5 CD315B CD325B CD315B 0.195 3 0.00 ! H1'-C1'-C2'-C3'
CD2R6F ND2R5D CD315B HDA1R5 0.000 3 0.00 ! C4-N9-C1'-H1'
CD2R6F ND2R5F CD315B HDA1R5 0.000 3 0.00 ! C4-N9-C1'-H1'
CD2R5F ND2R5D CD315B HDA1R5 0.195 3 0.00 ! C8-N9-C1'-H1', jal
CD2R5F ND2R5F CD315B HDA1R5 0.195 3 0.00 ! C8-N9-C1'-H1', jal
CD2O4A ND2R6C CD315B HDA1R5 0.000 3 0.00 ! C2-N1-C1'-H1', jal
CD2R6H ND2R6C CD315B HDA1R5 0.195 3 0.00 ! C6-N1-C1'-H1'
HDA1R5 CD315B CD315B CD32C 0.195 3 0.00 ! H3'-C3'-C4'-C5'
HDA1R5 CD315B CD315B OD305A 0.195 3 180.00 ! H3'-C3'-C4'-O4'
HDA1R5 CD315B CD315B HDA1R5 0.195 3 0.00 ! H3'-C3'-C4'-H4'
HDA1R5 CD315B CD315B OD30BN 0.195 3 0.00 ! H4'-C4'-C3'-O3'
CD325B CD315B CD315B HDA1R5 0.000 3 0.00 ! H4'-C4'-C3'-C2'
HDA1R5 CD315B CD315B HDA2R5 0.200 3 0.00 ! TF2M, cmb
HDA2R5 CD315B CD315B OD30BN 0.200 3 0.00 ! H2D-C2D-C3a-O3a, from TF2M
CD325B CD315B CD315B HDA2R5 0.200 3 0.00 ! TF2M, cmb
CD315B OD305A CD315B HDA2R5 0.300 3 0.00 ! TF2M, cmb
OD305A CD315B CD315B HDA2R5 0.200 3 0.00 ! TF2M, cmb
CD315B CD325B CD315B HDA2R5 0.190 3 0.00 ! TF2M, cmb
HDA2R5 CD315B CD325B HDA2R5 0.190 3 0.00 ! THF, viv
HDA2R5 CD325B CD315B CD32C 0.200 3 0.00 ! H3'-C3'-C4'-C5', from TF2M
HDA2R5 CD315B CD315B CD32C 0.200 3 0.00 ! H3'-C3'-C4'-C5', from TF2M
CD32A CD315B CD315B HDA1R5 0.200 3 0.00 ! C5T-C4a-C3a-H3a, from TF2M
CD315B CD315B CD315B HDA1R5 0.200 3 0.00 ! C2a-C3a-C4a-H4a, from THF
HDA1R5 CD315B CD315B OD31A 0.200 3 0.00 ! H1a-C1a-C2a-O2a, from TF2M
HDA1R5 CD315B CD315B OD31G 0.200 3 0.00 ! H1a-C1a-C2a-O2a, from TF2M, DNA 3TER (jal)
HDA1R5 CD315B CD315A OD31A 0.200 3 0.00 ! H1a-C1a-C2a-O2a, from TF2M, fro BRIB
OD31A CD32A CD315B HDA1R5 0.270 1 0.00 ! O5T-C5T-C4a-H4a, from PRO1
HDA2A CD32A CD315B HDA1R5 0.200 3 0.00 ! H5T1-C5T-C4a-H4a, from TF2M
HDA2A CD32A CD315B OD305A 0.200 3 0.00 ! H5T1-C5T-C4a-O4a, from TF2M
HDP1A ND2B1 CD2R6B ND2R6B 1.300 2 180.00 ! CYT, cmb 04/10
HDP1A ND2B1 CD2R6B CD2R6J 1.300 2 180.00 ! CYT, jal
HDP1A ND2B1 CD2R6C ND2R6B 4.000 2 180.00 ! jal
HDP1A ND2B1 CD2R6C CD2R6F 4.000 2 180.00 ! jal
!
ND2R5D CD315B CD325B CD315B 0.000 3 0.00 ! N9-C1a-C2D-C3a
ND2R5F CD315B CD325B CD315B 0.000 3 0.00 ! N9-C1a-C2D-C3a
ND2R5D CD315B OD305A CD315B 0.000 3 0.00 ! N9-C1a-O4a-C4a
ND2R5F CD315B OD305A CD315B 0.000 3 0.00 ! N9-C1a-O4a-C4a
ND2R6C CD315B OD305A CD315B 0.000 3 0.00 ! N1-C1a-O4a-C4a
ND2R6C CD315B CD325B CD315B 0.000 3 0.00 ! N1-C1a-C2D-C3a
HDA2A CD32C OD30BN PD1AN 0.000 3 0.00
CD315B CD315B CD32C HDA2A 0.200 3 0.00
CD325B CD315B CD32C HDA2A 0.200 3 0.00
HDA1R5 CD315B CD32C HDA2A 0.200 3 0.00
HDA1R5 CD315B CD32C OD30BN 0.200 3 0.00
OD305A CD315B CD32C HDA2A 0.195 1 0.00
HDA1R5 CD315B OD30BN PD1AN 0.000 3 0.00
!Sugar
CD315B OD305A CD315A CD325B 0.250 3 0.00 ! C2'-C1'-O4'-C4' ! nu_0
CD315B CD325B CD315A OD305A 0.250 6 0.00 ! C3'-C2'-C1'-O4' ! nu_1
CD315A CD325B CD315B CD315B 0.250 3 0.00 ! C1'-C2'-C3'-C4' ! nu_2
CD325B CD315B CD315B OD305A 0.200 4 0.00 ! C2'-C3'-C4'-O4' ! nu_3
CD325B CD315B CD315B OD305A 0.060 5 180.00 ! C2'-C3'-C4'-O4' ! nu_3
CD325B CD315B CD315B OD305A 0.060 6 180.00 ! C2'-C3'-C4'-O4' ! nu_3
CD315A OD305A CD315B CD315B 0.400 6 180.00 ! C1'-O4'-C4'-C3' ! nu_4, was 0.2
CD315B OD305A CD315A CD315B 0.250 3 0.00 ! C2'-C1'-O4'-C4' ! nu_0 !RNA
CD315B CD315B CD315A OD305A 0.250 6 0.00 ! C3'-C2'-C1'-O4' ! nu_1 !RNA
CD315A CD315B CD315B CD315B 0.250 3 0.00 ! C1'-C2'-C3'-C4' ! nu_2 !RNA
CD315B CD315B CD315B OD305A 0.200 4 0.00 ! C2'-C3'-C4'-O4' ! nu_3 !RNA
CD315B CD315B CD315B OD305A 0.060 5 180.00 ! C2'-C3'-C4'-O4' ! nu_3 !RNA
CD315B CD315B CD315B OD305A 0.060 6 180.00 ! C2'-C3'-C4'-O4' ! nu_3 !RNA
!Sugar torsions
! Exocyclic torsions
CD315B OD305A CD315B CD32C 0.300 3 0.00 ! C5'-C4'-O4'-C1'
CD325B CD315B CD315B CD32C 0.200 3 0.00 ! C5'-C4'-C3'-C2'
CD315B CD325B CD315B OD30BN 0.200 3 0.00 ! C1'-C2'-C3'-O3'
OD30BN CD315B CD315B OD305A 0.200 3 0.00 ! O4'-C4'-C3'-O3'
CD315B OD305A CD315B CD32A 0.300 3 0.00 ! C5'-C4'-O4'-C1'
CD325B CD315B CD315B CD32A 0.200 3 0.00 ! C5'-C4'-C3'-C2'
CD315B CD325B CD315B OD31A 0.200 3 0.00 ! C1'-C2'-C3'-O3'
CD315B CD325B CD315B OD31G 0.200 3 0.00 ! C1'-C2'-C3'-O3' DNA 3TER (jal)
OD31A CD315B CD315B OD305A 0.200 3 0.00 ! O4'-C4'-C3'-O3' !RNA
OD31G CD315B CD315B OD305A 0.200 3 0.00 ! O4'-C4'-C3'-O3' !DNA 3TER (jal)
CD315B CD325B CD315A OD31A 0.200 3 0.00 ! C1'-C2'-C3'-O3', for BDEO
!! DNA Backbone parameters !!
!DMPN specific, differs from lipid DMP
CD33C OD30BN PD1AN OD2C2C 1.090 1 180.00 ! DMP
CD33C OD30BN PD1AN OD2C2C 1.730 2 0.00 ! DMP
CD33C OD30BN PD1AN OD2C2C 0.610 3 180.00 ! DMP
CD33C OD30BN PD1AN OD30BN 2.140 1 180.00 ! DMP
CD33C OD30BN PD1AN OD30BN 3.000 2 0.00 ! DMP
CD33C OD30BN PD1AN OD30BN 1.760 3 0.00 ! DMP
PD1AN OD30BN CD33C HDA3A 0.000 3 0.00 ! DMP, nucleic acids
! Alpha
!! do not add 4-fold; over-stabilizes g+ in BII
CD32C OD30BN PD1AN OD30BN 1.200 2 0.00 !! k >= 0.6 necessary (BI ok w/o, BII terrible)
!Alpha_2: O1P-P-O5'-C5'
CD32C OD30BN PD1AN OD2C2C 0.300 3 0.00
!Beta
CD315B CD32C OD30BN PD1AN 0.800 1 220.00
!! jal - new 5'-OH beta
HDP1A OD31A CD32A CD315B 0.800 1 0.00 !TER
HDP1A OD31A CD32A CD315B 0.600 2 0.00 !TER
HDP1A OD31A CD32A CD315B 0.200 3 0.00 !TER
!! jal - apply to next two?
HDP1A OD31A CD315A CD315B 0.800 1 220.00 !TER, for BRIB
HDP1A OD31A CD315A CD325B 0.800 1 220.00 !TER, for BDEON
! Gamma
! jal - new from combined T3PS/R3PS fit
CD315B CD315B CD32C OD30BN 1.708 1 180.00
CD315B CD315B CD32C OD30BN 0.305 2 0.00
CD315B CD315B CD32C OD30BN 0.344 3 0.00
!Gamma 5TER
! jal - from gamma
OD31A CD32A CD315B CD315B 1.708 1 180.00
OD31A CD32A CD315B CD315B 0.305 2 0.00
OD31A CD32A CD315B CD315B 0.344 3 0.00
!Gamma_2: O4'-C4'-C5'-O5'
OD305A CD315B CD32C OD30BN 1.631 1 180.00
OD31A CD32A CD315B OD305A 1.631 1 180.00
!Delta
OD30BN CD315B CD315B CD32C 0.200 3 0.00
OD31A CD315B CD315B CD32C 0.200 3 0.00
OD31G CD315B CD315B CD32C 0.200 3 0.00 ! DNA 3TER (jal)
OD30BN CD315B CD315B CD32A 0.200 3 0.00
OD31A CD315B CD315B CD32A 0.200 3 0.00 !RNA
OD31G CD315B CD315B CD32A 0.200 3 0.00 ! DNA 3TER (jal)
!Epsilon
CD315B CD315B OD30BN PD1AN 1.600 1 0.00 !RNA; note the conflict of the P-O3'-C3'-C4'
CD315B CD315B OD30BN PD1AN 0.500 2 0.00 ! and P-O3'-C3'-C2' terms in RNA
CD315B CD315B OD30BN PD1AN 0.100 3 0.00 !
!Epsilon_2: C2'-C3'-O3'-P/H3T
CD325B CD315B OD30BN PD1AN 0.250 1 180.00 ! jal
CD325B CD315B OD31G HDP1A 0.620 1 0.00 ! jal, for DNA nucleosides (fit4, opt 13)
CD325B CD315B OD31G HDP1A 0.673 3 0.00 ! jal, for DNA nucleosides (fit4, opt 13)
HDA1R5 CD315B OD31A HDP1A 0.000 1 0.00 !RNA
HDA1R5 CD315B OD31G HDP1A 0.000 1 0.00 !DNA 3TER (jal)
!Zeta
! 1-fold on zeta counteracts 2-fold to flatten @ 180
! 2-fold on zeta and zeta2 increase energy @ 180, so if one
! is increased, decrease the other to compensate
CD315B OD30BN PD1AN OD30BN 1.000 1 0.00
CD315B OD30BN PD1AN OD30BN 0.700 2 0.00 ! 1.407 too strong unless balanced out by 1-fold, k = 1.0 OK
CD315B OD30BN PD1AN OD2C2C 0.600 2 180.00 ! Zeta_2: C3'-O3'-P-O1P
CD315B OD30BN PD1AN OD2C2C 0.100 3 0.00 ! Zeta_2: C3'-O3'-P-O1P
!! End of DNA backbone torsions !!
!
CD315B CD315B CD315B OD30BN 0.300 3 0.00 ! C1'-C2'-C3'-O3', from TF2M
OD31A CD315B CD315B OD30BN 0.200 3 0.00 ! O2'-C2'-C3'-O3', from THF
HDA1R5 CD315B CD325B OD305A 0.200 3 0.00 ! H3'-C3'-C4'-O4', from THF
!dihedrals that include both base and sugar atoms (but not glycosidic linkage)
!! Cyt
CD2R6J CD2R6H ND2R6C CD315B 11.000 2 180.00 ! C5-C6-N1-C1', from C27, jal
HDR6B CD2R6H ND2R6C CD315B 0.300 2 180.00 ! H6-C6-N1-C1', from C27
ND2R6C CD315B CD315B HDA1R5 0.000 3 0.00 ! N1-C1'-C2'-H2''
ND2R6C CD315B CD315B OD31A 0.000 3 0.00 ! N1-C1'-C2'-O2' !RNA
ND2R6C CD315B CD315B CD315B 0.000 3 0.00 ! N1-C1'-C2'-C3'
OD2C1B CD2O4A ND2R6C CD315B 11.000 2 180.00 ! O2-C2-N1-C1', from C27, jal
ND2R6B CD2O4A ND2R6C CD315B 11.000 2 180.00 ! N3-C2-N1-C1', from C27, jal
!! Thy
ND2R6C CD2O4A ND2R6C CD315B 11.000 2 180.00 ! N3-C2-N1-C1', jal
!! Gua
ND2R6B CD2R6F ND2R5D CD315B 11.000 2 180.00 ! N3-C4-N9-C1'
CD2R6F CD2R6F ND2R5D CD315B 11.000 2 180.00 ! C5-C4-N9-C1', from C27
CD2R6F ND2R5D CD315B CD315B 0.000 3 0.00 ! C4-N9-C1'-C2'
ND2R5D CD315B CD315B HDA1R5 0.000 3 0.00 ! N9-C1'-C2'-H2''
ND2R5D CD315B CD315B OD31A 0.000 3 0.00 ! N9-C1'-C2'-O2' !RNA
ND2R5D CD315B CD315B CD315B 0.000 3 0.00 ! N9-C1'-C2'-C3'
ND2R5E CD2R5F ND2R5D CD315B 11.000 2 180.00 ! N7-C8-N9-C1', from C27
HDR5B CD2R5F ND2R5D CD315B 0.300 2 180.00 ! H8-C8-N9-C1', from C27
CD2R5F ND2R5D CD315B CD315B 0.000 3 180.00 ! C8-N9-C1'-C2'
!! 5TER
HDA2A CD32A CD315B CD315B 0.200 3 0.00 ! H5T1-C5T-C4'-C3', from TF2M
!! jal for R3PS, copied from T3PS for analogous types
HDA2R5 CD315A CD315B HDA1R5 0.190 3 0.00 ! jal
CD315B CD315B CD315A HDA2R5 0.190 3 0.00 ! jal
CD315A CD315B CD315B HDA2R5 0.190 3 0.00 ! jal
HDA2R5 CD315A CD315B OD31A 0.000 3 0.00 ! jal
HDA2R5 CD315A CD315B OD31G 0.000 3 0.00 ! jal
HDA2R5 CD315B CD315B OD31A 0.000 3 0.00 ! jal
HDA2R5 CD315B CD315B OD31G 0.000 3 0.00 ! jal
CD315B CD315B CD315B HDA2R5 0.200 3 0.00 ! jal
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
CD2O4A ND2R6D ND2R6C OD2C1B 80.000 0 0.00 ! CYT, jal
ND2B1 CD2R6B HDP1A HDP1A 12.000 0 0.00 ! CYT, cmb 04/10
ND2B1 CD2R6C HDP1A HDP1A 12.000 0 0.00 ! ADE/GUA, cmb 04/10
CD2R6C ND2R6B CD2R6F ND2B1 60.000 0 0.00 ! ADE, cmb 04/10
NONBONDED nbxmod 5 atom vatom cdiel vdistance switch vswitch -
cutnb 16.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
END
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