1 |
< |
// This is the forcefield file for the Dipolar Unified-atom Force Field (DUFF). |
2 |
< |
// |
3 |
< |
// The sections are divided into AtomTypes, BondTypes, BendTypes, |
4 |
< |
// and TorsionTypes. |
5 |
< |
// |
6 |
< |
// Many parameters (but not all) are derived from the TRAPPE force field |
7 |
< |
// of Siepmann's group. |
8 |
< |
|
9 |
< |
begin AtomTypes |
10 |
< |
//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 |
< |
|
12 |
< |
CH4 0 0 16.05 0.279 3.73 |
13 |
< |
CH3 0 0 15.04 0.185 3.75 |
14 |
< |
CH2 0 0 14.03 0.0866 3.95 |
15 |
< |
CH 0 0 13.02 0.0189 4.68 |
16 |
< |
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 |
< |
HEAD 1 0 196 0.185 5.75 20.6 |
18 |
< |
TB1 0 0 14.03 0.0866 4.0 |
19 |
< |
TE1 0 0 15.04 0.185 4.0 |
20 |
< |
TB2 0 0 21.05 0.25 6.0 |
21 |
< |
TE2 0 0 22.56 0.5 6.0 |
22 |
< |
TB3 0 0 28.06 0.5 8.0 |
23 |
< |
TE3 0 0 30.08 0.75 8.0 |
24 |
< |
|
25 |
< |
end AtomTypes |
26 |
< |
|
27 |
< |
begin BondTypes |
28 |
< |
|
29 |
< |
//Atom1 Atom2 FixedBondType |
30 |
< |
//V_FixedBondType = 0 |
31 |
< |
|
32 |
< |
//Atom1 Atom2 HarmonicBondType b0 Kb (kcal/mol) |
33 |
< |
//V_HarmonicBondType = Kb(b- bo)^2 |
34 |
< |
//HarmonicBondType Examples |
35 |
< |
HEAD CH3 HarmonicBondType 2.75 260 |
36 |
< |
HEAD CH2 HarmonicBondType 2.75 260 |
37 |
< |
HEAD CH HarmonicBondType 2.75 260 |
38 |
< |
HEAD TB1 HarmonicBondType 2.76 260 |
39 |
< |
HEAD TB2 HarmonicBondType 3.20 260 |
40 |
< |
HEAD TB3 HarmonicBondType 3.63 260 |
41 |
< |
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 |
< |
TB2 TE2 HarmonicBondType 2.34 260 |
52 |
< |
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 |
< |
//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 |
< |
|
68 |
< |
begin BendTypes |
69 |
< |
|
70 |
< |
//HarmonicBendType |
71 |
< |
//Atom1 Atom2 Atom3 HarmonicBendType Ktheta Theta0 |
72 |
< |
//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 |
< |
HEAD CH2 CH2 HarmonicBendType 58.84 114.0 |
79 |
< |
HEAD TB1 TB1 HarmonicBendType 58.84 114.0 |
80 |
< |
HEAD TB2 TB2 HarmonicBendType 58.84 114.0 |
81 |
< |
HEAD TB3 TB3 HarmonicBendType 58.84 114.0 |
82 |
< |
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 |
< |
TB2 TB2 TB2 HarmonicBendType 58.84 114.0 |
100 |
< |
TB3 TB3 TB3 HarmonicBendType 58.84 114.0 |
101 |
< |
TE1 TB1 TB1 HarmonicBendType 58.84 114.0 |
102 |
< |
TE2 TB2 TB2 HarmonicBendType 58.84 114.0 |
103 |
< |
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 |
< |
TB2 HEAD GHOST GhostBendType 58.84 90.0 |
113 |
< |
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 |
> |
// |
4 |
> |
|
5 |
> |
// The sections are divided into AtomTypes, BondTypes, BendTypes, |
6 |
> |
|
7 |
> |
// and TorsionTypes. |
8 |
> |
|
9 |
> |
// |
10 |
> |
|
11 |
> |
// Many parameters (but not all) are derived from the TRAPPE force field |
12 |
> |
|
13 |
> |
// of Siepmann's group. |
14 |
> |
|
15 |
> |
|
16 |
> |
|
17 |
> |
begin AtomTypes |
18 |
> |
|
19 |
> |
//AtomTypeName isDirectional isLJ isCharge mass (amu) epsilon (kcal/mol) sigma (Ang) q (e) |
20 |
> |
CH4 0 1 0 16.05 0.279 3.73 |
21 |
> |
CH3 0 1 0 15.04 0.185 3.75 |
22 |
> |
|
23 |
> |
CH2 0 1 0 14.03 0.0866 3.95 |
24 |
> |
|
25 |
> |
CH 0 1 0 13.02 0.0189 4.68 |
26 |
> |
|
27 |
> |
SSD 1 1 0 18.0153 0.152 3.035 |
28 |
> |
HEAD 1 1 0 196 0.185 5.75 |
29 |
> |
TB1 0 1 0 14.03 0.0866 4.0 |
30 |
> |
|
31 |
> |
TE1 0 1 0 15.04 0.185 4.0 |
32 |
> |
|
33 |
> |
TB2 0 1 0 21.05 0.25 6.0 |
34 |
> |
|
35 |
> |
TE2 0 1 0 22.56 0.5 6.0 |
36 |
> |
|
37 |
> |
TB3 0 1 0 28.06 0.5 8.0 |
38 |
> |
|
39 |
> |
TE3 0 1 0 30.08 0.75 8.0 |
40 |
> |
|
41 |
> |
|
42 |
> |
|
43 |
> |
end AtomTypes |
44 |
> |
|
45 |
> |
|
46 |
> |
begin DirectionalAtomType |
47 |
> |
//AtomTypeName isDipole isSticky I_xx (amu*Ang^2) I_yy I_zz dipole (Debye) w0 v0 (kcal/mol) v0p rl (Ang) ru rlp rup |
48 |
> |
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 |
49 |
> |
HEAD 1 0 1125 1125 250 20.6 |
50 |
> |
end DirectionalAtomType |
51 |
> |
|
52 |
> |
begin BondTypes |
53 |
> |
|
54 |
> |
|
55 |
> |
|
56 |
> |
//Atom1 Atom2 FixedBondType |
57 |
> |
|
58 |
> |
//V_FixedBondType = 0 |
59 |
> |
|
60 |
> |
|
61 |
> |
|
62 |
> |
//Atom1 Atom2 HarmonicBondType b0 Kb (kcal/mol) |
63 |
> |
|
64 |
> |
//V_HarmonicBondType = Kb(b- bo)^2 |
65 |
> |
|
66 |
> |
//HarmonicBondType Examples |
67 |
> |
|
68 |
> |
HEAD CH3 HarmonicBondType 2.75 260 |
69 |
> |
|
70 |
> |
HEAD CH2 HarmonicBondType 2.75 260 |
71 |
> |
|
72 |
> |
HEAD CH HarmonicBondType 2.75 260 |
73 |
> |
|
74 |
> |
HEAD TB1 HarmonicBondType 2.76 260 |
75 |
> |
|
76 |
> |
HEAD TB2 HarmonicBondType 3.20 260 |
77 |
> |
|
78 |
> |
HEAD TB3 HarmonicBondType 3.63 260 |
79 |
> |
|
80 |
> |
CH3 CH3 HarmonicBondType 1.526 260 |
81 |
> |
|
82 |
> |
CH3 CH2 HarmonicBondType 1.526 260 |
83 |
> |
|
84 |
> |
CH3 CH HarmonicBondType 1.526 260 |
85 |
> |
|
86 |
> |
CH2 CH2 HarmonicBondType 1.526 260 |
87 |
> |
|
88 |
> |
CH2 CH HarmonicBondType 1.526 260 |
89 |
> |
|
90 |
> |
CH CH HarmonicBondType 1.526 260 |
91 |
> |
|
92 |
> |
TB1 TB1 HarmonicBondType 1.526 260 |
93 |
> |
|
94 |
> |
TB2 TB2 HarmonicBondType 2.34 260 |
95 |
> |
|
96 |
> |
TB3 TB3 HarmonicBondType 3.12 260 |
97 |
> |
|
98 |
> |
TB1 TE1 HarmonicBondType 1.526 260 |
99 |
> |
|
100 |
> |
TB2 TE2 HarmonicBondType 2.34 260 |
101 |
> |
|
102 |
> |
TB3 TE3 HarmonicBondType 3.12 260 |
103 |
> |
|
104 |
> |
|
105 |
> |
|
106 |
> |
//Atom1 Atom2 CubicBondType b0 K3 K2 K1 K0 |
107 |
> |
|
108 |
> |
//V_CubicBondType = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
109 |
> |
|
110 |
> |
|
111 |
> |
|
112 |
> |
|
113 |
> |
|
114 |
> |
//Atom1 Atom2 QuadraticBondType b0 K4 K3 K2 K1 K0 |
115 |
> |
|
116 |
> |
//V_QuadraticBondType = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
117 |
> |
|
118 |
> |
|
119 |
> |
|
120 |
> |
|
121 |
> |
|
122 |
> |
//Atom1 Atom2 PolynomialBondType b0 i Ki [j Kj] |
123 |
> |
|
124 |
> |
//V_QuadraticBondType = Ki(b - b0)^i + Kj(b - b0)^j + ... |
125 |
> |
|
126 |
> |
|
127 |
> |
|
128 |
> |
|
129 |
> |
|
130 |
> |
end BondTypes |
131 |
> |
|
132 |
> |
|
133 |
> |
|
134 |
> |
begin BendTypes |
135 |
> |
|
136 |
> |
|
137 |
> |
|
138 |
> |
//HarmonicBendType |
139 |
> |
|
140 |
> |
//Atom1 Atom2 Atom3 HarmonicBendType Ktheta Theta0 |
141 |
> |
|
142 |
> |
//V_HarmonicBendType = Ktheta(Theta - Theta0)^2 |
143 |
> |
|
144 |
> |
//Ktheta: kcal/mole/rad**2 |
145 |
> |
|
146 |
> |
//Theta0: degrees |
147 |
> |
|
148 |
> |
//HarmonicBendType examples |
149 |
> |
|
150 |
> |
HEAD CH2 HEAD HarmonicBendType 58.84 114.0 |
151 |
> |
|
152 |
> |
HEAD CH2 CH3 HarmonicBendType 58.84 114.0 |
153 |
> |
|
154 |
> |
HEAD CH2 CH2 HarmonicBendType 58.84 114.0 |
155 |
> |
|
156 |
> |
HEAD TB1 TB1 HarmonicBendType 58.84 114.0 |
157 |
> |
|
158 |
> |
HEAD TB2 TB2 HarmonicBendType 58.84 114.0 |
159 |
> |
|
160 |
> |
HEAD TB3 TB3 HarmonicBendType 58.84 114.0 |
161 |
> |
|
162 |
> |
HEAD CH2 CH HarmonicBendType 58.84 114.0 |
163 |
> |
|
164 |
> |
HEAD CH CH3 HarmonicBendType 58.84 112.0 |
165 |
> |
|
166 |
> |
HEAD CH CH2 HarmonicBendType 58.84 112.0 |
167 |
> |
|
168 |
> |
HEAD CH CH HarmonicBendType 58.84 112.0 |
169 |
> |
|
170 |
> |
CH3 CH2 CH3 HarmonicBendType 58.84 114.0 |
171 |
> |
|
172 |
> |
CH3 CH2 CH2 HarmonicBendType 58.84 114.0 |
173 |
> |
|
174 |
> |
CH3 CH2 CH HarmonicBendType 58.84 114.0 |
175 |
> |
|
176 |
> |
CH3 CH CH3 HarmonicBendType 58.84 112.0 |
177 |
> |
|
178 |
> |
CH3 CH CH2 HarmonicBendType 58.84 112.0 |
179 |
> |
|
180 |
> |
CH3 CH CH HarmonicBendType 58.84 112.0 |
181 |
> |
|
182 |
> |
CH2 CH2 CH2 HarmonicBendType 58.84 114.0 |
183 |
> |
|
184 |
> |
CH2 CH2 CH HarmonicBendType 58.84 114.0 |
185 |
> |
|
186 |
> |
CH2 CH CH2 HarmonicBendType 58.84 112.0 |
187 |
> |
|
188 |
> |
CH2 CH CH HarmonicBendType 58.84 112.0 |
189 |
> |
|
190 |
> |
CH CH2 CH HarmonicBendType 58.84 114.0 |
191 |
> |
|
192 |
> |
CH CH CH HarmonicBendType 58.84 112.0 |
193 |
> |
|
194 |
> |
TB1 TB1 TB1 HarmonicBendType 58.84 114.0 |
195 |
> |
|
196 |
> |
TB2 TB2 TB2 HarmonicBendType 58.84 114.0 |
197 |
> |
|
198 |
> |
TB3 TB3 TB3 HarmonicBendType 58.84 114.0 |
199 |
> |
|
200 |
> |
TE1 TB1 TB1 HarmonicBendType 58.84 114.0 |
201 |
> |
|
202 |
> |
TE2 TB2 TB2 HarmonicBendType 58.84 114.0 |
203 |
> |
|
204 |
> |
TE3 TB3 TB3 HarmonicBendType 58.84 114.0 |
205 |
> |
|
206 |
> |
|
207 |
> |
|
208 |
> |
//GhostBend |
209 |
> |
|
210 |
> |
//Atom1 Atom2 GHOST GhostBendType Ktheta Theta0 |
211 |
> |
|
212 |
> |
//Atom2 must be directional atom |
213 |
> |
|
214 |
> |
//GhostBendType examples |
215 |
> |
|
216 |
> |
CH2 HEAD GHOST GhostBendType 0.00176972 129.783 |
217 |
> |
|
218 |
> |
CH2 HEAD GHOST GhostBendType 58.84 90.0 |
219 |
> |
|
220 |
> |
TB1 HEAD GHOST GhostBendType 58.84 90.0 |
221 |
> |
|
222 |
> |
TB2 HEAD GHOST GhostBendType 58.84 90.0 |
223 |
> |
|
224 |
> |
TB3 HEAD GHOST GhostBendType 58.84 90.0 |
225 |
> |
|
226 |
> |
|
227 |
> |
|
228 |
> |
//UreyBradleyBend |
229 |
> |
|
230 |
> |
//Atom1 Atom2 Atom3 UreyBradleyBend Ktheta Theta0 Kub S0 |
231 |
> |
|
232 |
> |
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
233 |
> |
|
234 |
> |
//Ktheta: kcal/mole/rad**2 |
235 |
> |
|
236 |
> |
//Theta0: degrees |
237 |
> |
|
238 |
> |
//Kub: kcal/mole/A**2 |
239 |
> |
|
240 |
> |
//S0: A |
241 |
> |
|
242 |
> |
|
243 |
> |
|
244 |
> |
//CubicBendType |
245 |
> |
|
246 |
> |
//Atom1 Atom2 Atom3 CubicBendType Theta0 K3 K2 K1 K0 |
247 |
> |
|
248 |
> |
//V_CubicBendType = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
249 |
> |
|
250 |
> |
|
251 |
> |
|
252 |
> |
//QuadraticBendType |
253 |
> |
|
254 |
> |
//Atom1 Atom2 Atom3 QuadraticBendType Theta0 K4 K3 K2 K1 K0 |
255 |
> |
|
256 |
> |
//V_QuadraticBendType = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
257 |
> |
|
258 |
> |
|
259 |
> |
|
260 |
> |
//PolynomialBendType |
261 |
> |
|
262 |
> |
//Atom1 Atom2 Atom3 PolynomialBendType Theta0 i Ki [j Kj] |
263 |
> |
|
264 |
> |
//V_PolynomialBendType = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ... |
265 |
> |
|
266 |
> |
|
267 |
> |
|
268 |
> |
end BendTypes |
269 |
> |
|
270 |
> |
|
271 |
> |
|
272 |
> |
begin TorsionTypes |
273 |
> |
|
274 |
> |
|
275 |
> |
|
276 |
> |
//CubicTorsionType |
277 |
> |
|
278 |
> |
//Atom1 Atom2 Atom3 Atom4 CubicTorsionType k3 k2 k1 k0 ( all are kcal/mol ) |
279 |
> |
|
280 |
> |
//V_CubicTorsionType = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
281 |
> |
|
282 |
> |
//CubicTorsionType Examples |
283 |
> |
|
284 |
> |
HEAD CH2 CH2 HEAD CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
285 |
> |
|
286 |
> |
HEAD CH2 CH HEAD CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
287 |
> |
|
288 |
> |
HEAD CH CH HEAD CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
289 |
> |
|
290 |
> |
HEAD CH2 CH2 CH3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
291 |
> |
|
292 |
> |
HEAD CH2 CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
293 |
> |
|
294 |
> |
HEAD CH CH2 CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
295 |
> |
|
296 |
> |
HEAD CH CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
297 |
> |
|
298 |
> |
HEAD CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
299 |
> |
|
300 |
> |
HEAD CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
301 |
> |
|
302 |
> |
HEAD CH CH2 CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
303 |
> |
|
304 |
> |
HEAD CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
305 |
> |
|
306 |
> |
HEAD CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
307 |
> |
|
308 |
> |
HEAD CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
309 |
> |
|
310 |
> |
HEAD CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
311 |
> |
|
312 |
> |
HEAD CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
313 |
> |
|
314 |
> |
HEAD TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
315 |
> |
|
316 |
> |
HEAD TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
317 |
> |
|
318 |
> |
HEAD TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
319 |
> |
|
320 |
> |
CH3 CH2 CH2 CH3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
321 |
> |
|
322 |
> |
CH3 CH2 CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
323 |
> |
|
324 |
> |
CH3 CH CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
325 |
> |
|
326 |
> |
CH3 CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
327 |
> |
|
328 |
> |
CH3 CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
329 |
> |
|
330 |
> |
CH3 CH CH2 CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
331 |
> |
|
332 |
> |
CH3 CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
333 |
> |
|
334 |
> |
CH3 CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
335 |
> |
|
336 |
> |
CH3 CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
337 |
> |
|
338 |
> |
CH3 CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
339 |
> |
|
340 |
> |
CH3 CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
341 |
> |
|
342 |
> |
CH2 CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
343 |
> |
|
344 |
> |
CH2 CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
345 |
> |
|
346 |
> |
CH2 CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
347 |
> |
|
348 |
> |
CH2 CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
349 |
> |
|
350 |
> |
CH2 CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
351 |
> |
|
352 |
> |
CH2 CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
353 |
> |
|
354 |
> |
CH2 CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
355 |
> |
|
356 |
> |
CH CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
357 |
> |
|
358 |
> |
CH CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
359 |
> |
|
360 |
> |
CH CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
361 |
> |
|
362 |
> |
TB1 TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
363 |
> |
|
364 |
> |
TB2 TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
365 |
> |
|
366 |
> |
TB3 TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
367 |
> |
|
368 |
> |
TE1 TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
369 |
> |
|
370 |
> |
TE2 TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
371 |
> |
|
372 |
> |
TE3 TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
373 |
> |
|
374 |
> |
|
375 |
> |
|
376 |
> |
//CharmmTorsionType |
377 |
> |
|
378 |
> |
//Atom1 Atom2 Atom3 Atom4 CharmmTorsionType Kchi n delta [Kchi n delta] |
379 |
> |
|
380 |
> |
//V_CharmmTorsionType = Kchi(1 + cos(n(chi) - delta)) |
381 |
> |
|
382 |
> |
//Kchi: kcal/mole |
383 |
> |
|
384 |
> |
//n: multiplicity |
385 |
> |
|
386 |
> |
//delta: degrees |
387 |
> |
|
388 |
> |
//in some cases, a CharmmTorsionType may have two or three terms. If n is equal to 0, it falls back to harmonic form |
389 |
> |
|
390 |
> |
|
391 |
> |
|
392 |
> |
//QuadraticTorsionType |
393 |
> |
|
394 |
> |
//Atom1 Atom2 Atom3 Atom4 QuadraticTorsionType k4 k3 k2 k1 k0 ( all are kcal/mol ) |
395 |
> |
|
396 |
> |
//V_QuadraticTorsionType = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
397 |
> |
|
398 |
> |
|
399 |
> |
|
400 |
> |
//PolynomialTorsionType |
401 |
> |
|
402 |
> |
//Atom1 Atom2 Atom3 Atom4 PolynomialTorsionType i Ki [j Kj] |
403 |
> |
|
404 |
> |
//VPolynomialTorsionType = Ki (cos phi)^i + ... + Kj (cos phi)^j |
405 |
> |
|
406 |
> |
|
407 |
> |
|
408 |
|
end TorsionTypes |