1 |
tim |
2106 |
begin AtomTypes |
2 |
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//Name mass (amu) |
3 |
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CH4 16.05 |
4 |
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CH3 15.04 |
5 |
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CH2 14.03 |
6 |
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CH 13.02 |
7 |
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CE 28.01 //C-O |
8 |
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CK 28.01 //C=O |
9 |
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HDP 14.03 //Head Dipole |
10 |
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NC4 73.137 //CH2-N(CH3)3 |
11 |
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PO4 108.995 //PO4-CH2 |
12 |
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SSD 18.0153 |
13 |
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SSD1 18.0153 |
14 |
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SSD_E 18.0153 |
15 |
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SSD_RF 18.0153 |
16 |
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end AtomTypes |
17 |
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18 |
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19 |
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20 |
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begin DirectionalAtomTypes |
21 |
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//Name I_xx I_yy I_zz (All moments in (amu*Ang^2) |
22 |
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SSD 1.7696 0.6145 1.1550 |
23 |
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SSD1 1.7696 0.6145 1.1550 |
24 |
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SSD_E 1.7696 0.6145 1.1550 |
25 |
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SSD_RF 1.7696 0.6145 1.1550 |
26 |
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HDP 2.221 0.0 2.221 |
27 |
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CE 13.643 13.643 0.0 |
28 |
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CK 10.161 10.161 0.0 |
29 |
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end DirectionalAtomTypes |
30 |
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31 |
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begin LennardJonesAtomTypes |
32 |
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//Name epsilon sigma |
33 |
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SSD 0.152 3.051 |
34 |
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SSD1 0.152 3.016 |
35 |
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SSD_E 0.152 3.035 |
36 |
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SSD_RF 0.152 3.019 |
37 |
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38 |
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//CH3 3.75 98.0 |
39 |
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//CH2 3.94 46.0 |
40 |
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//CH 4.33 10.0 |
41 |
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CH3 0.195 3.75 |
42 |
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CH2 0.0914 3.95 |
43 |
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CH 0.0199 4.68 |
44 |
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CK 0.311 3.592 |
45 |
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CE 0.294 3.427 |
46 |
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PO4 0.543 4.55 |
47 |
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NC4 1.1 4.11 |
48 |
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HDP 0.0914 3.95 |
49 |
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end LennardJonesAtomTypes |
50 |
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51 |
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begin ChargeAtomTypes |
52 |
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// name charge |
53 |
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end ChargeAtomTypes |
54 |
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55 |
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begin MultipoleAtomTypes |
56 |
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//only support up tp quadrupole. |
57 |
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//possible format: |
58 |
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// name d theta phi psi dipole_moment |
59 |
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// name s theta phi psi dipole_moment splitdipole_distance |
60 |
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// name q theta phi psi Qxx Qyy Qzz |
61 |
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// name dq theta phi psi dipole_moment Qxx Qyy Qzz |
62 |
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// name sq theta phi psi dipole_moment splitdipole_distance Qxx Qyy Qzz |
63 |
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// euler angles are given in units of degree |
64 |
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// dipoles are given in units of Debye |
65 |
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// split dipole distances are given in units of Angstrom |
66 |
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// quadrupoles are given in units of |
67 |
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// |
68 |
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SSD_E d 0.0 0.0 0.0 2.42 |
69 |
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SSD_RF d 0.0 0.0 0.0 2.48 |
70 |
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SSD d 0.0 0.0 0.0 2.35 |
71 |
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SSD1 d 0.0 0.0 0.0 2.35 |
72 |
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CE d 0.0 0.0 0.0 1.693 |
73 |
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CK d 0.0 0.0 0.0 2.478 |
74 |
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HDP s 0.0 0.0 0.0 20.6 4.63 |
75 |
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end MultipoleAtomTypes |
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77 |
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78 |
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begin BondTypes |
79 |
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80 |
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//Atom1 Atom2 Fixed |
81 |
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//V_Fixed = 0 |
82 |
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83 |
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//Atom1 Atom2 Harmonic b0 Kb (kcal/mol) |
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//V_Harmonic = 0.5*Kb(b- bo)^2 |
85 |
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//Harmonic Examples |
86 |
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87 |
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//CHx-CHy 1.54 |
88 |
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CH3 CH3 Harmonic 1.54 260 |
89 |
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CH3 CH2 Harmonic 1.54 260 |
90 |
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CH3 CH Harmonic 1.54 260 |
91 |
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CH2 CH2 Harmonic 1.54 260 |
92 |
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CH2 CH Harmonic 1.54 260 |
93 |
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CH CH Harmonic 1.54 260 |
94 |
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95 |
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PO4 CH2 Harmonic 2.67 260 |
96 |
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CH2 CE Harmonic 1.54 260 |
97 |
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CE CE Harmonic 2.27 260 |
98 |
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CE CK Harmonic 2.08 317 |
99 |
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100 |
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//CHx-C aldehyde/ketone 1.52 |
101 |
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CH3 CK Harmonic 1.52 317 |
102 |
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CH2 CK Harmonic 1.52 317 |
103 |
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CH CK Harmonic 1.52 317 |
104 |
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105 |
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end BondTypes |
106 |
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107 |
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begin BendTypes |
108 |
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109 |
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//Harmonic |
110 |
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//Atom1 Atom2 Atom3 Harmonic Theta0 Ktheta |
111 |
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//V_Harmonic = 0.5*Ktheta(Theta - Theta0)^2 |
112 |
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//Ktheta: kcal/mole/rad**2 |
113 |
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//Theta0: degrees |
114 |
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//Harmonic examples |
115 |
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116 |
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//CHx-CH2-CHy 114 62500 (ktheta/kb) |
117 |
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CH3 CH2 CH3 Harmonic 114.0 124.15 |
118 |
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CH3 CH2 CH2 Harmonic 114.0 124.15 |
119 |
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CH3 CH2 CH Harmonic 114.0 124.15 |
120 |
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CH2 CH2 CH2 Harmonic 114.0 124.15 |
121 |
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CH2 CH2 CH Harmonic 114.0 124.15 |
122 |
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CH CH2 CH Harmonic 114.0 124.15 |
123 |
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124 |
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//CHx-CH-CHy 112 62500 (ktheta/kb) |
125 |
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CH3 CH CH3 Harmonic 112.0 124.15 |
126 |
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CH3 CH CH2 Harmonic 112.0 124.15 |
127 |
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CH3 CH CH Harmonic 112.0 124.15 |
128 |
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CH2 CH CH3 Harmonic 112.0 124.15 |
129 |
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CH2 CH CH2 Harmonic 112.0 124.15 |
130 |
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CH2 CH CH Harmonic 112.0 124.15 |
131 |
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CH CH CH3 Harmonic 112.0 124.15 |
132 |
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CH CH CH2 Harmonic 112.0 124.15 |
133 |
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CH CH CH Harmonic 112.0 124.15 |
134 |
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135 |
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//CHx-C(=O)-CHy 117.2 62500 |
136 |
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CH3 CK CH3 Harmonic 117.2 124.15 |
137 |
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CH3 CK CH2 Harmonic 117.2 124.15 |
138 |
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CH3 CK CH Harmonic 117.2 124.15 |
139 |
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CH2 CK CH2 Harmonic 117.2 124.15 |
140 |
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CH2 CK CH Harmonic 117.2 124.15 |
141 |
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CH CK CH Harmonic 117.2 124.15 |
142 |
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CE CK CH3 Harmonic 117.2 124.15 |
143 |
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CE CK CH2 Harmonic 117.2 124.15 |
144 |
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CE CK CH Harmonic 117.2 124.15 |
145 |
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146 |
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CH2 CH2 CK Harmonic 114 124.15 |
147 |
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CE CE CK Harmonic 114 124.15 |
148 |
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CH2 CE CE Harmonic 117.2 124.15 |
149 |
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CH2 CE CK Harmonic 114 124.15 |
150 |
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151 |
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PO4 CH2 CE Harmonic 180.0 124.15 |
152 |
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//GhostBend |
153 |
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//Atom1 Atom2 GHOST GhostBend Theta0 Ktheta |
154 |
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//Atom2 must be directional atom |
155 |
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//Ghost examples |
156 |
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CH2 HDP GHOST GhostBend 129.783 0.00354 |
157 |
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NC4 PO4 CH2 Harmonic 98.03 20.00 |
158 |
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//CHx-C=O 121.4 62500 |
159 |
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//since the dipole direction is from Oxygen to carbon in CK |
160 |
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//The equilibrium angle becomes its supplementary angle |
161 |
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CH3 CK GHOST GhostBend 58.6 124.15 |
162 |
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CH2 CK GHOST GhostBend 58.6 124.15 |
163 |
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CH CK GHOST GhostBend 58.6 124.15 |
164 |
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CH2 CE GHOST GhostBend 68.0 119.98 |
165 |
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end BendTypes |
166 |
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167 |
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begin TorsionTypes |
168 |
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169 |
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//Cubic |
170 |
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//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
171 |
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//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
172 |
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//Cubic Examples |
173 |
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//CHx-CH2-CH2-CHy 0 335.05 -68.19 791.32 |
174 |
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CH3 CH2 CH2 CH3 Cubic 6.287 0.2709 -4.050 2.237 |
175 |
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CH3 CH2 CH CH3 Cubic 6.287 0.2709 -4.050 2.237 |
176 |
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CH3 CH CH CH3 Cubic 6.287 0.2709 -4.050 2.237 |
177 |
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CH3 CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
178 |
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CH3 CH2 CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
179 |
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CH3 CH CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
180 |
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CH3 CH CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
181 |
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CH3 CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
182 |
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CH3 CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237 |
183 |
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CH3 CH CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
184 |
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CH3 CH CH CH Cubic 6.287 0.2709 -4.050 2.237 |
185 |
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CH2 CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
186 |
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CH2 CH2 CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
187 |
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CH2 CH CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
188 |
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CH2 CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
189 |
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CH2 CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237 |
190 |
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CH2 CH CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
191 |
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CH2 CH CH CH Cubic 6.287 0.2709 -4.050 2.237 |
192 |
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CH CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
193 |
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CH CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237 |
194 |
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CH CH CH CH Cubic 6.287 0.2709 -4.050 2.237 |
195 |
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CK CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
196 |
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197 |
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//CHx-CH2-CH2-O 0 176.62 -53.34 769.93 |
198 |
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CE CK CH2 CH2 Cubic 6.118 0.212 -4.237 1.668 |
199 |
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CH2 CE CE GHOST GhostTorsion 6.118 0.212 -4.237 1.668 |
200 |
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CH2 CE CK GHOST GhostTorsion 6.118 0.212 -4.237 1.668 |
201 |
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202 |
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//CHx-CHy-C=O 2035.58 -736.90 57.84 -293.23 |
203 |
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CH3 CH2 CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
204 |
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CH3 CH CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
205 |
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CH2 CH2 CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
206 |
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CH CH CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
207 |
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208 |
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end TorsionTypes |
209 |
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210 |
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