| 1 |
begin AtomTypes |
| 2 |
//Name mass (amu) |
| 3 |
CH4 16.05 |
| 4 |
CH3 15.04 |
| 5 |
CH2 14.03 |
| 6 |
CH 13.02 |
| 7 |
CE 28.01 //C-O |
| 8 |
CK 28.01 //C=O |
| 9 |
HDP 14.03 //Head Dipole |
| 10 |
NC4 73.137 //CH2-N(CH3)3 |
| 11 |
PO4 108.995 //PO4-CH2 |
| 12 |
SSD 18.0153 |
| 13 |
SSD1 18.0153 |
| 14 |
SSD_E 18.0153 |
| 15 |
SSD_RF 18.0153 |
| 16 |
end AtomTypes |
| 17 |
|
| 18 |
|
| 19 |
|
| 20 |
begin DirectionalAtomTypes |
| 21 |
//Name I_xx I_yy I_zz (All moments in (amu*Ang^2) |
| 22 |
SSD 1.7696 0.6145 1.1550 |
| 23 |
SSD1 1.7696 0.6145 1.1550 |
| 24 |
SSD_E 1.7696 0.6145 1.1550 |
| 25 |
SSD_RF 1.7696 0.6145 1.1550 |
| 26 |
HDP 2.221 0.0 2.221 |
| 27 |
CE 13.643 13.643 0.0 |
| 28 |
CK 10.161 10.161 0.0 |
| 29 |
end DirectionalAtomTypes |
| 30 |
|
| 31 |
begin LennardJonesAtomTypes |
| 32 |
//Name epsilon sigma |
| 33 |
SSD 0.152 3.051 |
| 34 |
SSD1 0.152 3.016 |
| 35 |
SSD_E 0.152 3.035 |
| 36 |
SSD_RF 0.152 3.019 |
| 37 |
|
| 38 |
//CH3 3.75 98.0 |
| 39 |
//CH2 3.94 46.0 |
| 40 |
//CH 4.33 10.0 |
| 41 |
CH3 0.195 3.75 |
| 42 |
CH2 0.0914 3.95 |
| 43 |
CH 0.0199 4.68 |
| 44 |
CK 0.311 3.592 |
| 45 |
CE 0.294 3.427 |
| 46 |
PO4 0.543 4.55 |
| 47 |
NC4 1.1 4.11 |
| 48 |
HDP 0.0914 3.95 |
| 49 |
end LennardJonesAtomTypes |
| 50 |
|
| 51 |
begin ChargeAtomTypes |
| 52 |
// name charge |
| 53 |
end ChargeAtomTypes |
| 54 |
|
| 55 |
begin MultipoleAtomTypes |
| 56 |
//only support up tp quadrupole. |
| 57 |
//possible format: |
| 58 |
// name d theta phi psi dipole_moment |
| 59 |
// name s theta phi psi dipole_moment splitdipole_distance |
| 60 |
// name q theta phi psi Qxx Qyy Qzz |
| 61 |
// name dq theta phi psi dipole_moment Qxx Qyy Qzz |
| 62 |
// name sq theta phi psi dipole_moment splitdipole_distance Qxx Qyy Qzz |
| 63 |
// euler angles are given in units of degree |
| 64 |
// dipoles are given in units of Debye |
| 65 |
// split dipole distances are given in units of Angstrom |
| 66 |
// quadrupoles are given in units of |
| 67 |
// |
| 68 |
SSD_E d 0.0 0.0 0.0 2.42 |
| 69 |
SSD_RF d 0.0 0.0 0.0 2.48 |
| 70 |
SSD d 0.0 0.0 0.0 2.35 |
| 71 |
SSD1 d 0.0 0.0 0.0 2.35 |
| 72 |
CE d 0.0 0.0 0.0 1.693 |
| 73 |
CK d 0.0 0.0 0.0 2.478 |
| 74 |
HDP s 0.0 0.0 0.0 20.6 4.63 |
| 75 |
end MultipoleAtomTypes |
| 76 |
|
| 77 |
|
| 78 |
begin BondTypes |
| 79 |
|
| 80 |
//Atom1 Atom2 Fixed |
| 81 |
//V_Fixed = 0 |
| 82 |
|
| 83 |
//Atom1 Atom2 Harmonic b0 Kb (kcal/mol) |
| 84 |
//V_Harmonic = 0.5*Kb(b- bo)^2 |
| 85 |
//Harmonic Examples |
| 86 |
|
| 87 |
//CHx-CHy 1.54 |
| 88 |
CH3 CH3 Harmonic 1.54 260 |
| 89 |
CH3 CH2 Harmonic 1.54 260 |
| 90 |
CH3 CH Harmonic 1.54 260 |
| 91 |
CH2 CH2 Harmonic 1.54 260 |
| 92 |
CH2 CH Harmonic 1.54 260 |
| 93 |
CH CH Harmonic 1.54 260 |
| 94 |
|
| 95 |
PO4 CH2 Harmonic 2.67 260 |
| 96 |
CH2 CE Harmonic 1.54 260 |
| 97 |
CE CE Harmonic 2.27 260 |
| 98 |
CE CK Harmonic 2.08 317 |
| 99 |
|
| 100 |
//CHx-C aldehyde/ketone 1.52 |
| 101 |
CH3 CK Harmonic 1.52 317 |
| 102 |
CH2 CK Harmonic 1.52 317 |
| 103 |
CH CK Harmonic 1.52 317 |
| 104 |
|
| 105 |
end BondTypes |
| 106 |
|
| 107 |
begin BendTypes |
| 108 |
|
| 109 |
//Harmonic |
| 110 |
//Atom1 Atom2 Atom3 Harmonic Theta0 Ktheta |
| 111 |
//V_Harmonic = 0.5*Ktheta(Theta - Theta0)^2 |
| 112 |
//Ktheta: kcal/mole/rad**2 |
| 113 |
//Theta0: degrees |
| 114 |
//Harmonic examples |
| 115 |
|
| 116 |
//CHx-CH2-CHy 114 62500 (ktheta/kb) |
| 117 |
CH3 CH2 CH3 Harmonic 114.0 124.15 |
| 118 |
CH3 CH2 CH2 Harmonic 114.0 124.15 |
| 119 |
CH3 CH2 CH Harmonic 114.0 124.15 |
| 120 |
CH2 CH2 CH2 Harmonic 114.0 124.15 |
| 121 |
CH2 CH2 CH Harmonic 114.0 124.15 |
| 122 |
CH CH2 CH Harmonic 114.0 124.15 |
| 123 |
|
| 124 |
//CHx-CH-CHy 112 62500 (ktheta/kb) |
| 125 |
CH3 CH CH3 Harmonic 112.0 124.15 |
| 126 |
CH3 CH CH2 Harmonic 112.0 124.15 |
| 127 |
CH3 CH CH Harmonic 112.0 124.15 |
| 128 |
CH2 CH CH3 Harmonic 112.0 124.15 |
| 129 |
CH2 CH CH2 Harmonic 112.0 124.15 |
| 130 |
CH2 CH CH Harmonic 112.0 124.15 |
| 131 |
CH CH CH3 Harmonic 112.0 124.15 |
| 132 |
CH CH CH2 Harmonic 112.0 124.15 |
| 133 |
CH CH CH Harmonic 112.0 124.15 |
| 134 |
|
| 135 |
//CHx-C(=O)-CHy 117.2 62500 |
| 136 |
CH3 CK CH3 Harmonic 117.2 124.15 |
| 137 |
CH3 CK CH2 Harmonic 117.2 124.15 |
| 138 |
CH3 CK CH Harmonic 117.2 124.15 |
| 139 |
CH2 CK CH2 Harmonic 117.2 124.15 |
| 140 |
CH2 CK CH Harmonic 117.2 124.15 |
| 141 |
CH CK CH Harmonic 117.2 124.15 |
| 142 |
CE CK CH3 Harmonic 117.2 124.15 |
| 143 |
CE CK CH2 Harmonic 117.2 124.15 |
| 144 |
CE CK CH Harmonic 117.2 124.15 |
| 145 |
|
| 146 |
CH2 CH2 CK Harmonic 114 124.15 |
| 147 |
CE CE CK Harmonic 114 124.15 |
| 148 |
CH2 CE CE Harmonic 117.2 124.15 |
| 149 |
CH2 CE CK Harmonic 114 124.15 |
| 150 |
|
| 151 |
PO4 CH2 CE Harmonic 180.0 124.15 |
| 152 |
//GhostBend |
| 153 |
//Atom1 Atom2 GHOST GhostBend Theta0 Ktheta |
| 154 |
//Atom2 must be directional atom |
| 155 |
//Ghost examples |
| 156 |
CH2 HDP GHOST GhostBend 129.783 0.00354 |
| 157 |
NC4 PO4 CH2 Harmonic 98.03 20.00 |
| 158 |
//CHx-C=O 121.4 62500 |
| 159 |
//since the dipole direction is from Oxygen to carbon in CK |
| 160 |
//The equilibrium angle becomes its supplementary angle |
| 161 |
CH3 CK GHOST GhostBend 58.6 124.15 |
| 162 |
CH2 CK GHOST GhostBend 58.6 124.15 |
| 163 |
CH CK GHOST GhostBend 58.6 124.15 |
| 164 |
CH2 CE GHOST GhostBend 68.0 119.98 |
| 165 |
end BendTypes |
| 166 |
|
| 167 |
begin TorsionTypes |
| 168 |
|
| 169 |
//Cubic |
| 170 |
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
| 171 |
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 172 |
//Cubic Examples |
| 173 |
//CHx-CH2-CH2-CHy 0 335.05 -68.19 791.32 |
| 174 |
CH3 CH2 CH2 CH3 Cubic 6.287 0.2709 -4.050 2.237 |
| 175 |
CH3 CH2 CH CH3 Cubic 6.287 0.2709 -4.050 2.237 |
| 176 |
CH3 CH CH CH3 Cubic 6.287 0.2709 -4.050 2.237 |
| 177 |
CH3 CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
| 178 |
CH3 CH2 CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
| 179 |
CH3 CH CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
| 180 |
CH3 CH CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
| 181 |
CH3 CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
| 182 |
CH3 CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237 |
| 183 |
CH3 CH CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
| 184 |
CH3 CH CH CH Cubic 6.287 0.2709 -4.050 2.237 |
| 185 |
CH2 CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
| 186 |
CH2 CH2 CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
| 187 |
CH2 CH CH CH2 Cubic 6.287 0.2709 -4.050 2.237 |
| 188 |
CH2 CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
| 189 |
CH2 CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237 |
| 190 |
CH2 CH CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
| 191 |
CH2 CH CH CH Cubic 6.287 0.2709 -4.050 2.237 |
| 192 |
CH CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237 |
| 193 |
CH CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237 |
| 194 |
CH CH CH CH Cubic 6.287 0.2709 -4.050 2.237 |
| 195 |
CK CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237 |
| 196 |
|
| 197 |
//CHx-CH2-CH2-O 0 176.62 -53.34 769.93 |
| 198 |
CE CK CH2 CH2 Cubic 6.118 0.212 -4.237 1.668 |
| 199 |
CH2 CE CE GHOST GhostTorsion 6.118 0.212 -4.237 1.668 |
| 200 |
CH2 CE CK GHOST GhostTorsion 6.118 0.212 -4.237 1.668 |
| 201 |
|
| 202 |
//CHx-CHy-C=O 2035.58 -736.90 57.84 -293.23 |
| 203 |
CH3 CH2 CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
| 204 |
CH3 CH CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
| 205 |
CH2 CH2 CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
| 206 |
CH CH CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227 |
| 207 |
|
| 208 |
end TorsionTypes |
| 209 |
|
| 210 |
|
