| 1 |
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// This is the forcefield file for the Dipolar Unified-atom Force Field (DUFF). |
| 2 |
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// |
| 3 |
< |
// The sections are divided into AtomTypes, BondTypes, BendTypes, |
| 4 |
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// and TorsionTypes. |
| 5 |
< |
// |
| 6 |
< |
// Many parameters (but not all) are derived from the TRAPPE force field |
| 7 |
< |
// of Siepmann's group. |
| 8 |
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|
| 9 |
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begin AtomTypes |
| 10 |
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//Atom isDipole isSSD mass LJ epsilon ( kcal/mol) LJ sigma (Angstroms) Dipole Moment (Debye) w0 v0 (kcal/mol) v0p (kcal/mol) rl (Angstroms) ru (Angstroms) rlp (Angstroms) rup (Angstroms) |
| 11 |
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|
| 12 |
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CH4 0 0 16.05 0.279 3.73 |
| 13 |
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CH3 0 0 15.04 0.185 3.75 |
| 14 |
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CH2 0 0 14.03 0.0866 3.95 |
| 15 |
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CH 0 0 13.02 0.0189 4.68 |
| 16 |
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SSD 1 1 18.0153 0.152 3.035 2.42 0.07715 3.9 3.9 2.4 3.8 2.75 3.35 |
| 17 |
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HEAD 1 0 196 0.185 5.75 20.6 |
| 18 |
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TB1 0 0 14.03 0.0866 4.0 |
| 19 |
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TE1 0 0 15.04 0.185 4.0 |
| 20 |
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TB2 0 0 21.05 0.25 6.0 |
| 21 |
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TE2 0 0 22.56 0.5 6.0 |
| 22 |
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TB3 0 0 28.06 0.5 8.0 |
| 23 |
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TE3 0 0 30.08 0.75 8.0 |
| 24 |
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|
| 25 |
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end AtomTypes |
| 26 |
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|
| 27 |
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begin BondTypes |
| 28 |
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|
| 29 |
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//Atom1 Atom2 FixedBondType |
| 30 |
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//V_FixedBondType = 0 |
| 31 |
< |
|
| 32 |
< |
//Atom1 Atom2 HarmonicBondType b0 Kb (kcal/mol) |
| 33 |
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//V_HarmonicBondType = Kb(b- bo)^2 |
| 34 |
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//HarmonicBondType Examples |
| 35 |
< |
HEAD CH3 HarmonicBondType 2.75 260 |
| 36 |
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HEAD CH2 HarmonicBondType 2.75 260 |
| 37 |
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HEAD CH HarmonicBondType 2.75 260 |
| 38 |
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HEAD TB1 HarmonicBondType 2.76 260 |
| 39 |
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HEAD TB2 HarmonicBondType 3.20 260 |
| 40 |
< |
HEAD TB3 HarmonicBondType 3.63 260 |
| 41 |
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CH3 CH3 HarmonicBondType 1.526 260 |
| 42 |
< |
CH3 CH2 HarmonicBondType 1.526 260 |
| 43 |
< |
CH3 CH HarmonicBondType 1.526 260 |
| 44 |
< |
CH2 CH2 HarmonicBondType 1.526 260 |
| 45 |
< |
CH2 CH HarmonicBondType 1.526 260 |
| 46 |
< |
CH CH HarmonicBondType 1.526 260 |
| 47 |
< |
TB1 TB1 HarmonicBondType 1.526 260 |
| 48 |
< |
TB2 TB2 HarmonicBondType 2.34 260 |
| 49 |
< |
TB3 TB3 HarmonicBondType 3.12 260 |
| 50 |
< |
TB1 TE1 HarmonicBondType 1.526 260 |
| 51 |
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TB2 TE2 HarmonicBondType 2.34 260 |
| 52 |
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TB3 TE3 HarmonicBondType 3.12 260 |
| 53 |
< |
|
| 54 |
< |
//Atom1 Atom2 CubicBondType b0 K3 K2 K1 K0 |
| 55 |
< |
//V_CubicBondType = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
| 56 |
< |
|
| 57 |
< |
|
| 58 |
< |
//Atom1 Atom2 QuadraticBondType b0 K4 K3 K2 K1 K0 |
| 59 |
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//V_QuadraticBondType = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
| 60 |
< |
|
| 61 |
< |
|
| 62 |
< |
//Atom1 Atom2 PolynomialBondType b0 i Ki [j Kj] |
| 63 |
< |
//V_QuadraticBondType = Ki(b - b0)^i + Kj(b - b0)^j + ... |
| 64 |
< |
|
| 65 |
< |
|
| 66 |
< |
end BondTypes |
| 67 |
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|
| 68 |
< |
begin BendTypes |
| 69 |
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|
| 70 |
< |
//HarmonicBendType |
| 71 |
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//Atom1 Atom2 Atom3 HarmonicBendType Ktheta Theta0 |
| 72 |
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//V_HarmonicBendType = Ktheta(Theta - Theta0)^2 |
| 73 |
< |
//Ktheta: kcal/mole/rad**2 |
| 74 |
< |
//Theta0: degrees |
| 75 |
< |
//HarmonicBendType examples |
| 76 |
< |
HEAD CH2 HEAD HarmonicBendType 58.84 114.0 |
| 77 |
< |
HEAD CH2 CH3 HarmonicBendType 58.84 114.0 |
| 78 |
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HEAD CH2 CH2 HarmonicBendType 58.84 114.0 |
| 79 |
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HEAD TB1 TB1 HarmonicBendType 58.84 114.0 |
| 80 |
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HEAD TB2 TB2 HarmonicBendType 58.84 114.0 |
| 81 |
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HEAD TB3 TB3 HarmonicBendType 58.84 114.0 |
| 82 |
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HEAD CH2 CH HarmonicBendType 58.84 114.0 |
| 83 |
< |
HEAD CH CH3 HarmonicBendType 58.84 112.0 |
| 84 |
< |
HEAD CH CH2 HarmonicBendType 58.84 112.0 |
| 85 |
< |
HEAD CH CH HarmonicBendType 58.84 112.0 |
| 86 |
< |
CH3 CH2 CH3 HarmonicBendType 58.84 114.0 |
| 87 |
< |
CH3 CH2 CH2 HarmonicBendType 58.84 114.0 |
| 88 |
< |
CH3 CH2 CH HarmonicBendType 58.84 114.0 |
| 89 |
< |
CH3 CH CH3 HarmonicBendType 58.84 112.0 |
| 90 |
< |
CH3 CH CH2 HarmonicBendType 58.84 112.0 |
| 91 |
< |
CH3 CH CH HarmonicBendType 58.84 112.0 |
| 92 |
< |
CH2 CH2 CH2 HarmonicBendType 58.84 114.0 |
| 93 |
< |
CH2 CH2 CH HarmonicBendType 58.84 114.0 |
| 94 |
< |
CH2 CH CH2 HarmonicBendType 58.84 112.0 |
| 95 |
< |
CH2 CH CH HarmonicBendType 58.84 112.0 |
| 96 |
< |
CH CH2 CH HarmonicBendType 58.84 114.0 |
| 97 |
< |
CH CH CH HarmonicBendType 58.84 112.0 |
| 98 |
< |
TB1 TB1 TB1 HarmonicBendType 58.84 114.0 |
| 99 |
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TB2 TB2 TB2 HarmonicBendType 58.84 114.0 |
| 100 |
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TB3 TB3 TB3 HarmonicBendType 58.84 114.0 |
| 101 |
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TE1 TB1 TB1 HarmonicBendType 58.84 114.0 |
| 102 |
< |
TE2 TB2 TB2 HarmonicBendType 58.84 114.0 |
| 103 |
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TE3 TB3 TB3 HarmonicBendType 58.84 114.0 |
| 104 |
< |
|
| 105 |
< |
//GhostBend |
| 106 |
< |
//Atom1 Atom2 GHOST GhostBendType Ktheta Theta0 |
| 107 |
< |
//Atom2 must be directional atom |
| 108 |
< |
//GhostBendType examples |
| 109 |
< |
CH2 HEAD GHOST GhostBendType 0.00176972 129.783 |
| 110 |
< |
CH2 HEAD GHOST GhostBendType 58.84 90.0 |
| 111 |
< |
TB1 HEAD GHOST GhostBendType 58.84 90.0 |
| 112 |
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TB2 HEAD GHOST GhostBendType 58.84 90.0 |
| 113 |
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TB3 HEAD GHOST GhostBendType 58.84 90.0 |
| 114 |
< |
|
| 115 |
< |
//UreyBradleyBend |
| 116 |
< |
//Atom1 Atom2 Atom3 UreyBradleyBend Ktheta Theta0 Kub S0 |
| 117 |
< |
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
| 118 |
< |
//Ktheta: kcal/mole/rad**2 |
| 119 |
< |
//Theta0: degrees |
| 120 |
< |
//Kub: kcal/mole/A**2 |
| 121 |
< |
//S0: A |
| 122 |
< |
|
| 123 |
< |
//CubicBendType |
| 124 |
< |
//Atom1 Atom2 Atom3 CubicBendType Theta0 K3 K2 K1 K0 |
| 125 |
< |
//V_CubicBendType = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
| 126 |
< |
|
| 127 |
< |
//QuadraticBendType |
| 128 |
< |
//Atom1 Atom2 Atom3 QuadraticBendType Theta0 K4 K3 K2 K1 K0 |
| 129 |
< |
//V_QuadraticBendType = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
| 130 |
< |
|
| 131 |
< |
//PolynomialBendType |
| 132 |
< |
//Atom1 Atom2 Atom3 PolynomialBendType Theta0 i Ki [j Kj] |
| 133 |
< |
//V_PolynomialBendType = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ... |
| 134 |
< |
|
| 135 |
< |
end BendTypes |
| 136 |
< |
|
| 137 |
< |
begin TorsionTypes |
| 138 |
< |
|
| 139 |
< |
//CubicTorsionType |
| 140 |
< |
//Atom1 Atom2 Atom3 Atom4 CubicTorsionType k3 k2 k1 k0 ( all are kcal/mol ) |
| 141 |
< |
//V_CubicTorsionType = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 142 |
< |
//CubicTorsionType Examples |
| 143 |
< |
HEAD CH2 CH2 HEAD CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 144 |
< |
HEAD CH2 CH HEAD CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 145 |
< |
HEAD CH CH HEAD CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 146 |
< |
HEAD CH2 CH2 CH3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 147 |
< |
HEAD CH2 CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 148 |
< |
HEAD CH CH2 CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 149 |
< |
HEAD CH CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 150 |
< |
HEAD CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 151 |
< |
HEAD CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 152 |
< |
HEAD CH CH2 CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 153 |
< |
HEAD CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 154 |
< |
HEAD CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 155 |
< |
HEAD CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 156 |
< |
HEAD CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 157 |
< |
HEAD CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 158 |
< |
HEAD TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 159 |
< |
HEAD TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 160 |
< |
HEAD TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 161 |
< |
CH3 CH2 CH2 CH3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 162 |
< |
CH3 CH2 CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 163 |
< |
CH3 CH CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 164 |
< |
CH3 CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 165 |
< |
CH3 CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 166 |
< |
CH3 CH CH2 CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 167 |
< |
CH3 CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 168 |
< |
CH3 CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 169 |
< |
CH3 CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 170 |
< |
CH3 CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 171 |
< |
CH3 CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 172 |
< |
CH2 CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 173 |
< |
CH2 CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 174 |
< |
CH2 CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 175 |
< |
CH2 CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 176 |
< |
CH2 CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 177 |
< |
CH2 CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 178 |
< |
CH2 CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 179 |
< |
CH CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 180 |
< |
CH CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 181 |
< |
CH CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
| 182 |
< |
TB1 TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 183 |
< |
TB2 TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 184 |
< |
TB3 TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 185 |
< |
TE1 TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 186 |
< |
TE2 TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 187 |
< |
TE3 TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
| 188 |
< |
|
| 189 |
< |
//CharmmTorsionType |
| 190 |
< |
//Atom1 Atom2 Atom3 Atom4 CharmmTorsionType Kchi n delta [Kchi n delta] |
| 191 |
< |
//V_CharmmTorsionType = Kchi(1 + cos(n(chi) - delta)) |
| 192 |
< |
//Kchi: kcal/mole |
| 193 |
< |
//n: multiplicity |
| 194 |
< |
//delta: degrees |
| 195 |
< |
//in some cases, a CharmmTorsionType may have two or three terms. If n is equal to 0, it falls back to harmonic form |
| 196 |
< |
|
| 197 |
< |
//QuadraticTorsionType |
| 198 |
< |
//Atom1 Atom2 Atom3 Atom4 QuadraticTorsionType k4 k3 k2 k1 k0 ( all are kcal/mol ) |
| 199 |
< |
//V_QuadraticTorsionType = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 200 |
< |
|
| 201 |
< |
//PolynomialTorsionType |
| 202 |
< |
//Atom1 Atom2 Atom3 Atom4 PolynomialTorsionType i Ki [j Kj] |
| 203 |
< |
//VPolynomialTorsionType = Ki (cos phi)^i + ... + Kj (cos phi)^j |
| 204 |
< |
|
| 1 |
> |
// This is the forcefield file for the Dipolar Unified-atom Force Field (DUFF) |
| 2 |
> |
// |
| 3 |
> |
// The sections are divided into AtomTypes |
| 4 |
> |
// |
| 5 |
> |
//any parameters (but not all) are derived from the TRAPPE force field |
| 6 |
> |
// of Siepmann's group. |
| 7 |
> |
begin AtomTypes |
| 8 |
> |
//Name mass (amu) |
| 9 |
> |
CH4 16.05 |
| 10 |
> |
CH3 15.04 |
| 11 |
> |
CH2 14.03 |
| 12 |
> |
CH 13.02 |
| 13 |
> |
SSD 18.0153 |
| 14 |
> |
HEAD 196 |
| 15 |
> |
TB1 14.03 |
| 16 |
> |
TE1 15.04 |
| 17 |
> |
TB2 21.05 |
| 18 |
> |
TE2 22.56 |
| 19 |
> |
TB3 28.06 |
| 20 |
> |
TE3 30.08 |
| 21 |
> |
H 1.00794 |
| 22 |
> |
He 4.002602 |
| 23 |
> |
C 12.0107 |
| 24 |
> |
N 14.00674 |
| 25 |
> |
O 15.9994 |
| 26 |
> |
F 18.9984032 |
| 27 |
> |
Ne 20.1797 |
| 28 |
> |
S 32.066 |
| 29 |
> |
Cl 35.4527 |
| 30 |
> |
Ar 39.948 |
| 31 |
> |
Br 79.904 |
| 32 |
> |
Kr 83.80 |
| 33 |
> |
end AtomTypes |
| 34 |
> |
|
| 35 |
> |
begin DirectionalAtomTypes |
| 36 |
> |
//Name I_xx I_yy I_zz (All moments in (amu*Ang^2) |
| 37 |
> |
SSD 1.7696 0.6145 1.1550 |
| 38 |
> |
SSD1 1.7696 0.6145 1.1550 |
| 39 |
> |
SSD_E 1.7696 0.6145 1.1550 |
| 40 |
> |
SSD_RF 1.7696 0.6145 1.1550 |
| 41 |
> |
HEAD 1125 1125 250 |
| 42 |
> |
end DirectionalAtomTypes |
| 43 |
> |
|
| 44 |
> |
begin LennardJonesAtomTypes |
| 45 |
> |
//Name epsilon sigma |
| 46 |
> |
CH4 0.279 3.73 |
| 47 |
> |
CH3 0.185 3.75 |
| 48 |
> |
CH2 0.0866 3.95 |
| 49 |
> |
CH 0.0189 4.68 |
| 50 |
> |
SSD 0.152 3.035 |
| 51 |
> |
HEAD 0.185 .75 |
| 52 |
> |
TB1 0.0866 4.0 |
| 53 |
> |
TE1 0.185 4.0 |
| 54 |
> |
TB2 0.25 6.0 |
| 55 |
> |
TE2 0.5 6.0 |
| 56 |
> |
TB3 0.5 8.0 |
| 57 |
> |
TE3 0.75 8.0 |
| 58 |
> |
H 0.017090056482 2.81 |
| 59 |
> |
He 0.020269601874 2.28 |
| 60 |
> |
C 0.101745452544 3.35 |
| 61 |
> |
N 0.074123151951 3.31 |
| 62 |
> |
O 0.122412497592 2.95 |
| 63 |
> |
F 0.104924997936 2.83 |
| 64 |
> |
Ne 0.09339914589 2.72 |
| 65 |
> |
S 0.36366050421 3.52 |
| 66 |
> |
Cl 0.344781953445 3.35 |
| 67 |
> |
Ar 0.238068461226 3.41 |
| 68 |
> |
Br 0.511111921764 3.54 |
| 69 |
> |
Kr 0.32590340268 3.83 |
| 70 |
> |
end LennardJonesAtomTypes |
| 71 |
> |
|
| 72 |
> |
begin ChargeAtomTypes |
| 73 |
> |
end ChargeAtomTypes |
| 74 |
> |
|
| 75 |
> |
begin DipoleAtomTypes |
| 76 |
> |
end DipoleAtomTypes |
| 77 |
> |
|
| 78 |
> |
begin StickyAtomTypes |
| 79 |
> |
end StickyAtomTypes |
| 80 |
> |
|
| 81 |
> |
|
| 82 |
> |
begin DirectionalAtomType |
| 83 |
> |
//AtomTypeName isDipole isSticky I_xx (amu*Ang^2) I_yy I_zz dipole (Debye) w0 v0 (kcal/mol) v0p rl (Ang) ru rlp rup |
| 84 |
> |
SSD 1 1 1.7696 0.6145 1.1550 2.35 0.07715 3.7284 3.7284 2.75 3.35 2.75 4.0 |
| 85 |
> |
HEAD 1 0 1125 1125 250 20.6 |
| 86 |
> |
end DirectionalAtomType |
| 87 |
> |
|
| 88 |
> |
begin BondTypes |
| 89 |
> |
|
| 90 |
> |
//Atom1 Atom2 Fixed |
| 91 |
> |
//V_Fixed = 0 |
| 92 |
> |
|
| 93 |
> |
//Atom1 Atom2 Harmonic b0 Kb (kcal/mol) |
| 94 |
> |
//V_Harmonic = Kb(b- bo)^2 |
| 95 |
> |
//Harmonic Examples |
| 96 |
> |
HEAD CH3 Harmonic 2.75 260 |
| 97 |
> |
HEAD CH2 Harmonic 2.75 260 |
| 98 |
> |
HEAD CH Harmonic 2.75 260 |
| 99 |
> |
HEAD TB1 Harmonic 2.76 260 |
| 100 |
> |
HEAD TB2 Harmonic 3.20 260 |
| 101 |
> |
HEAD TB3 Harmonic 3.63 260 |
| 102 |
> |
CH3 CH3 Harmonic 1.526 260 |
| 103 |
> |
CH3 CH2 Harmonic 1.526 260 |
| 104 |
> |
CH3 CH Harmonic 1.526 260 |
| 105 |
> |
CH2 CH2 Harmonic 1.526 260 |
| 106 |
> |
CH2 CH Harmonic 1.526 260 |
| 107 |
> |
CH CH Harmonic 1.526 260 |
| 108 |
> |
TB1 TB1 Harmonic 1.526 260 |
| 109 |
> |
TB2 TB2 Harmonic 2.34 260 |
| 110 |
> |
TB3 TB3 Harmonic 3.12 260 |
| 111 |
> |
TB1 TE1 Harmonic 1.526 260 |
| 112 |
> |
TB2 TE2 Harmonic 2.34 260 |
| 113 |
> |
TB3 TE3 Harmonic 3.12 260 |
| 114 |
> |
|
| 115 |
> |
//Atom1 Atom2 Cubic b0 K3 K2 K1 K0 |
| 116 |
> |
//V_Cubic = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
| 117 |
> |
|
| 118 |
> |
|
| 119 |
> |
//Atom1 Atom2 Quartic b0 K4 K3 K2 K1 K0 |
| 120 |
> |
//V_Quartic = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
| 121 |
> |
|
| 122 |
> |
|
| 123 |
> |
//Atom1 Atom2 Polynomial b0 i Ki [j Kj] |
| 124 |
> |
//V_Quartic = Ki(b - b0)^i + Kj(b - b0)^j + ... |
| 125 |
> |
|
| 126 |
> |
|
| 127 |
> |
end s |
| 128 |
> |
|
| 129 |
> |
begin BendTypes |
| 130 |
> |
|
| 131 |
> |
//Harmonic |
| 132 |
> |
//Atom1 Atom2 Atom3 Harmonic Ktheta Theta0 |
| 133 |
> |
//V_Harmonic = Ktheta(Theta - Theta0)^2 |
| 134 |
> |
//Ktheta: kcal/mole/rad**2 |
| 135 |
> |
//Theta0: degrees |
| 136 |
> |
//Harmonic examples |
| 137 |
> |
HEAD CH2 HEAD Harmonic 58.84 114.0 |
| 138 |
> |
HEAD CH2 CH3 Harmonic 58.84 114.0 |
| 139 |
> |
HEAD CH2 CH2 Harmonic 58.84 114.0 |
| 140 |
> |
HEAD TB1 TB1 Harmonic 58.84 114.0 |
| 141 |
> |
HEAD TB2 TB2 Harmonic 58.84 114.0 |
| 142 |
> |
HEAD TB3 TB3 Harmonic 58.84 114.0 |
| 143 |
> |
HEAD CH2 CH Harmonic 58.84 114.0 |
| 144 |
> |
HEAD CH CH3 Harmonic 58.84 112.0 |
| 145 |
> |
HEAD CH CH2 Harmonic 58.84 112.0 |
| 146 |
> |
HEAD CH CH Harmonic 58.84 112.0 |
| 147 |
> |
CH3 CH2 CH3 Harmonic 58.84 114.0 |
| 148 |
> |
CH3 CH2 CH2 Harmonic 58.84 114.0 |
| 149 |
> |
CH3 CH2 CH Harmonic 58.84 114.0 |
| 150 |
> |
CH3 CH CH3 Harmonic 58.84 112.0 |
| 151 |
> |
CH3 CH CH2 Harmonic 58.84 112.0 |
| 152 |
> |
CH3 CH CH Harmonic 58.84 112.0 |
| 153 |
> |
CH2 CH2 CH2 Harmonic 58.84 114.0 |
| 154 |
> |
CH2 CH2 CH Harmonic 58.84 114.0 |
| 155 |
> |
CH2 CH CH2 Harmonic 58.84 112.0 |
| 156 |
> |
CH2 CH CH Harmonic 58.84 112.0 |
| 157 |
> |
CH CH2 CH Harmonic 58.84 114.0 |
| 158 |
> |
CH CH CH Harmonic 58.84 112.0 |
| 159 |
> |
TB1 TB1 TB1 Harmonic 58.84 114.0 |
| 160 |
> |
TB2 TB2 TB2 Harmonic 58.84 114.0 |
| 161 |
> |
TB3 TB3 TB3 Harmonic 58.84 114.0 |
| 162 |
> |
TE1 TB1 TB1 Harmonic 58.84 114.0 |
| 163 |
> |
TE2 TB2 TB2 Harmonic 58.84 114.0 |
| 164 |
> |
TE3 TB3 TB3 Harmonic 58.84 114.0 |
| 165 |
> |
|
| 166 |
> |
//GhostBend |
| 167 |
> |
//Atom1 Atom2 GHOST GhostBend Ktheta Theta0 |
| 168 |
> |
//Atom2 must be directional atom |
| 169 |
> |
//Ghost examples |
| 170 |
> |
CH2 HEAD GHOST GhostBend 0.00176972 129.783 |
| 171 |
> |
CH2 HEAD GHOST GhostBend 58.84 90.0 |
| 172 |
> |
TB1 HEAD GHOST GhostBend 58.84 90.0 |
| 173 |
> |
TB2 HEAD GHOST GhostBend 58.84 90.0 |
| 174 |
> |
TB3 HEAD GHOST GhostBend 58.84 90.0 |
| 175 |
> |
|
| 176 |
> |
//UreyBradley |
| 177 |
> |
//Atom1 Atom2 Atom3 UreyBradley Ktheta Theta0 Kub S0 |
| 178 |
> |
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
| 179 |
> |
//Ktheta: kcal/mole/rad**2 |
| 180 |
> |
//Theta0: degrees |
| 181 |
> |
//Kub: kcal/mole/A**2 |
| 182 |
> |
//S0: A |
| 183 |
> |
|
| 184 |
> |
//Cubic |
| 185 |
> |
//Atom1 Atom2 Atom3 Cubic Theta0 K3 K2 K1 K0 |
| 186 |
> |
//V_Cubic = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
| 187 |
> |
|
| 188 |
> |
//Quartic |
| 189 |
> |
//Atom1 Atom2 Atom3 Quartic Theta0 K4 K3 K2 K1 K0 |
| 190 |
> |
//V_Quartic = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
| 191 |
> |
|
| 192 |
> |
//Polynomial |
| 193 |
> |
//Atom1 Atom2 Atom3 Polynomial Theta0 i Ki [j Kj] |
| 194 |
> |
//V_Polynomial = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ... |
| 195 |
> |
|
| 196 |
> |
end BendTypes |
| 197 |
> |
|
| 198 |
> |
begin TorsionTypes |
| 199 |
> |
|
| 200 |
> |
//Cubic |
| 201 |
> |
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
| 202 |
> |
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 203 |
> |
//Cubic Examples |
| 204 |
> |
HEAD CH2 CH2 HEAD Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 205 |
> |
HEAD CH2 CH HEAD Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 206 |
> |
HEAD CH CH HEAD Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 207 |
> |
HEAD CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 208 |
> |
HEAD CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 209 |
> |
HEAD CH CH2 CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 210 |
> |
HEAD CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 211 |
> |
HEAD CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 212 |
> |
HEAD CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 213 |
> |
HEAD CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 214 |
> |
HEAD CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 215 |
> |
HEAD CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 216 |
> |
HEAD CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 217 |
> |
HEAD CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 218 |
> |
HEAD CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 219 |
> |
HEAD TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 220 |
> |
HEAD TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 221 |
> |
HEAD TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 222 |
> |
CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 223 |
> |
CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 224 |
> |
CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 225 |
> |
CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 226 |
> |
CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 227 |
> |
CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 228 |
> |
CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 229 |
> |
CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 230 |
> |
CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 231 |
> |
CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 232 |
> |
CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 233 |
> |
CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 234 |
> |
CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 235 |
> |
CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 236 |
> |
CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 237 |
> |
CH2 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 238 |
> |
CH2 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 239 |
> |
CH2 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 240 |
> |
CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 241 |
> |
CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 242 |
> |
CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
| 243 |
> |
TB1 TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 244 |
> |
TB2 TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 245 |
> |
TB3 TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 246 |
> |
TE1 TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 247 |
> |
TE2 TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 248 |
> |
TE3 TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
| 249 |
> |
|
| 250 |
> |
//Charmm |
| 251 |
> |
//Atom1 Atom2 Atom3 Atom4 Charmm Kchi n delta [Kchi n delta] |
| 252 |
> |
//V_Charmm = Kchi(1 + cos(n(chi) - delta)) |
| 253 |
> |
//Kchi: kcal/mole |
| 254 |
> |
//n: multiplicity |
| 255 |
> |
//delta: degrees |
| 256 |
> |
//in some cases, a Charmm may have two or three terms. If n is equal to 0, it falls back to harmonic form |
| 257 |
> |
|
| 258 |
> |
//Quartic |
| 259 |
> |
//Atom1 Atom2 Atom3 Atom4 Quartic k4 k3 k2 k1 k0 ( all are kcal/mol ) |
| 260 |
> |
//V_Quartic = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
| 261 |
> |
|
| 262 |
> |
//Polynomial |
| 263 |
> |
//Atom1 Atom2 Atom3 Atom4 Polynomial i Ki [j Kj] |
| 264 |
> |
//VPolynomial = Ki (cos phi)^i + ... + Kj (cos phi)^j |
| 265 |
> |
|
| 266 |
|
end TorsionTypes |
