1 |
< |
// This is the forcefield file for the Dipolar Unified-atom Force Field (DUFF). |
2 |
< |
|
1 |
> |
// This is the forcefield file for the Dipolar Unified-atom Force Field (DUFF) |
2 |
|
// |
3 |
< |
|
5 |
< |
// The sections are divided into AtomTypes, BondTypes, BendTypes, |
6 |
< |
|
7 |
< |
// and TorsionTypes. |
8 |
< |
|
3 |
> |
// The sections are divided into AtomTypes |
4 |
|
// |
5 |
< |
|
11 |
< |
// Many parameters (but not all) are derived from the TRAPPE force field |
12 |
< |
|
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 ElectrostaticAtomTypes |
73 |
+ |
end ElectrostaticAtomTypes |
74 |
|
|
75 |
< |
begin AtomTypes |
75 |
> |
begin StickyAtomTypes |
76 |
> |
end StickyAtomTypes |
77 |
|
|
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 |
78 |
|
|
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 |
– |
|
79 |
|
begin DirectionalAtomType |
80 |
|
//AtomTypeName isDipole isSticky I_xx (amu*Ang^2) I_yy I_zz dipole (Debye) w0 v0 (kcal/mol) v0p rl (Ang) ru rlp rup |
81 |
|
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 |
84 |
|
|
85 |
|
begin BondTypes |
86 |
|
|
87 |
+ |
//Atom1 Atom2 Fixed |
88 |
+ |
//V_Fixed = 0 |
89 |
|
|
90 |
+ |
//Atom1 Atom2 Harmonic b0 Kb (kcal/mol) |
91 |
+ |
//V_Harmonic = Kb(b- bo)^2 |
92 |
+ |
//Harmonic Examples |
93 |
+ |
HEAD CH3 Harmonic 2.75 260 |
94 |
+ |
HEAD CH2 Harmonic 2.75 260 |
95 |
+ |
HEAD CH Harmonic 2.75 260 |
96 |
+ |
HEAD TB1 Harmonic 2.76 260 |
97 |
+ |
HEAD TB2 Harmonic 3.20 260 |
98 |
+ |
HEAD TB3 Harmonic 3.63 260 |
99 |
+ |
CH3 CH3 Harmonic 1.526 260 |
100 |
+ |
CH3 CH2 Harmonic 1.526 260 |
101 |
+ |
CH3 CH Harmonic 1.526 260 |
102 |
+ |
CH2 CH2 Harmonic 1.526 260 |
103 |
+ |
CH2 CH Harmonic 1.526 260 |
104 |
+ |
CH CH Harmonic 1.526 260 |
105 |
+ |
TB1 TB1 Harmonic 1.526 260 |
106 |
+ |
TB2 TB2 Harmonic 2.34 260 |
107 |
+ |
TB3 TB3 Harmonic 3.12 260 |
108 |
+ |
TB1 TE1 Harmonic 1.526 260 |
109 |
+ |
TB2 TE2 Harmonic 2.34 260 |
110 |
+ |
TB3 TE3 Harmonic 3.12 260 |
111 |
|
|
112 |
< |
//Atom1 Atom2 FixedBondType |
112 |
> |
//Atom1 Atom2 Cubic b0 K3 K2 K1 K0 |
113 |
> |
//V_Cubic = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
114 |
|
|
58 |
– |
//V_FixedBondType = 0 |
115 |
|
|
116 |
+ |
//Atom1 Atom2 Quartic b0 K4 K3 K2 K1 K0 |
117 |
+ |
//V_Quartic = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
118 |
|
|
119 |
|
|
120 |
< |
//Atom1 Atom2 HarmonicBondType b0 Kb (kcal/mol) |
120 |
> |
//Atom1 Atom2 Polynomial b0 i Ki [j Kj] |
121 |
> |
//V_Quartic = Ki(b - b0)^i + Kj(b - b0)^j + ... |
122 |
|
|
64 |
– |
//V_HarmonicBondType = Kb(b- bo)^2 |
123 |
|
|
124 |
< |
//HarmonicBondType Examples |
124 |
> |
end s |
125 |
|
|
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 |
– |
|
126 |
|
begin BendTypes |
127 |
|
|
128 |
< |
|
129 |
< |
|
130 |
< |
//HarmonicBendType |
139 |
< |
|
140 |
< |
//Atom1 Atom2 Atom3 HarmonicBendType Ktheta Theta0 |
141 |
< |
|
142 |
< |
//V_HarmonicBendType = Ktheta(Theta - Theta0)^2 |
143 |
< |
|
128 |
> |
//Harmonic |
129 |
> |
//Atom1 Atom2 Atom3 Harmonic Ktheta Theta0 |
130 |
> |
//V_Harmonic = Ktheta(Theta - Theta0)^2 |
131 |
|
//Ktheta: kcal/mole/rad**2 |
145 |
– |
|
132 |
|
//Theta0: degrees |
133 |
< |
|
134 |
< |
//HarmonicBendType examples |
135 |
< |
|
136 |
< |
HEAD CH2 HEAD HarmonicBendType 58.84 114.0 |
137 |
< |
|
138 |
< |
HEAD CH2 CH3 HarmonicBendType 58.84 114.0 |
139 |
< |
|
140 |
< |
HEAD CH2 CH2 HarmonicBendType 58.84 114.0 |
141 |
< |
|
142 |
< |
HEAD TB1 TB1 HarmonicBendType 58.84 114.0 |
143 |
< |
|
144 |
< |
HEAD TB2 TB2 HarmonicBendType 58.84 114.0 |
145 |
< |
|
146 |
< |
HEAD TB3 TB3 HarmonicBendType 58.84 114.0 |
147 |
< |
|
148 |
< |
HEAD CH2 CH HarmonicBendType 58.84 114.0 |
149 |
< |
|
150 |
< |
HEAD CH CH3 HarmonicBendType 58.84 112.0 |
151 |
< |
|
152 |
< |
HEAD CH CH2 HarmonicBendType 58.84 112.0 |
153 |
< |
|
154 |
< |
HEAD CH CH HarmonicBendType 58.84 112.0 |
155 |
< |
|
156 |
< |
CH3 CH2 CH3 HarmonicBendType 58.84 114.0 |
157 |
< |
|
158 |
< |
CH3 CH2 CH2 HarmonicBendType 58.84 114.0 |
159 |
< |
|
160 |
< |
CH3 CH2 CH HarmonicBendType 58.84 114.0 |
161 |
< |
|
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 |
133 |
> |
//Harmonic examples |
134 |
> |
HEAD CH2 HEAD Harmonic 58.84 114.0 |
135 |
> |
HEAD CH2 CH3 Harmonic 58.84 114.0 |
136 |
> |
HEAD CH2 CH2 Harmonic 58.84 114.0 |
137 |
> |
HEAD TB1 TB1 Harmonic 58.84 114.0 |
138 |
> |
HEAD TB2 TB2 Harmonic 58.84 114.0 |
139 |
> |
HEAD TB3 TB3 Harmonic 58.84 114.0 |
140 |
> |
HEAD CH2 CH Harmonic 58.84 114.0 |
141 |
> |
HEAD CH CH3 Harmonic 58.84 112.0 |
142 |
> |
HEAD CH CH2 Harmonic 58.84 112.0 |
143 |
> |
HEAD CH CH Harmonic 58.84 112.0 |
144 |
> |
CH3 CH2 CH3 Harmonic 58.84 114.0 |
145 |
> |
CH3 CH2 CH2 Harmonic 58.84 114.0 |
146 |
> |
CH3 CH2 CH Harmonic 58.84 114.0 |
147 |
> |
CH3 CH CH3 Harmonic 58.84 112.0 |
148 |
> |
CH3 CH CH2 Harmonic 58.84 112.0 |
149 |
> |
CH3 CH CH Harmonic 58.84 112.0 |
150 |
> |
CH2 CH2 CH2 Harmonic 58.84 114.0 |
151 |
> |
CH2 CH2 CH Harmonic 58.84 114.0 |
152 |
> |
CH2 CH CH2 Harmonic 58.84 112.0 |
153 |
> |
CH2 CH CH Harmonic 58.84 112.0 |
154 |
> |
CH CH2 CH Harmonic 58.84 114.0 |
155 |
> |
CH CH CH Harmonic 58.84 112.0 |
156 |
> |
TB1 TB1 TB1 Harmonic 58.84 114.0 |
157 |
> |
TB2 TB2 TB2 Harmonic 58.84 114.0 |
158 |
> |
TB3 TB3 TB3 Harmonic 58.84 114.0 |
159 |
> |
TE1 TB1 TB1 Harmonic 58.84 114.0 |
160 |
> |
TE2 TB2 TB2 Harmonic 58.84 114.0 |
161 |
> |
TE3 TB3 TB3 Harmonic 58.84 114.0 |
162 |
|
|
163 |
+ |
//GhostBend |
164 |
+ |
//Atom1 Atom2 GHOST GhostBend Ktheta Theta0 |
165 |
|
//Atom2 must be directional atom |
166 |
+ |
//Ghost examples |
167 |
+ |
CH2 HEAD GHOST GhostBend 0.00176972 129.783 |
168 |
+ |
CH2 HEAD GHOST GhostBend 58.84 90.0 |
169 |
+ |
TB1 HEAD GHOST GhostBend 58.84 90.0 |
170 |
+ |
TB2 HEAD GHOST GhostBend 58.84 90.0 |
171 |
+ |
TB3 HEAD GHOST GhostBend 58.84 90.0 |
172 |
|
|
173 |
< |
//GhostBendType examples |
174 |
< |
|
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 |
< |
|
173 |
> |
//UreyBradley |
174 |
> |
//Atom1 Atom2 Atom3 UreyBradley Ktheta Theta0 Kub S0 |
175 |
|
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
233 |
– |
|
176 |
|
//Ktheta: kcal/mole/rad**2 |
235 |
– |
|
177 |
|
//Theta0: degrees |
237 |
– |
|
178 |
|
//Kub: kcal/mole/A**2 |
239 |
– |
|
179 |
|
//S0: A |
180 |
|
|
181 |
+ |
//Cubic |
182 |
+ |
//Atom1 Atom2 Atom3 Cubic Theta0 K3 K2 K1 K0 |
183 |
+ |
//V_Cubic = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
184 |
|
|
185 |
+ |
//Quartic |
186 |
+ |
//Atom1 Atom2 Atom3 Quartic Theta0 K4 K3 K2 K1 K0 |
187 |
+ |
//V_Quartic = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
188 |
|
|
189 |
< |
//CubicBendType |
189 |
> |
//Polynomial |
190 |
> |
//Atom1 Atom2 Atom3 Polynomial Theta0 i Ki [j Kj] |
191 |
> |
//V_Polynomial = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ... |
192 |
|
|
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 |
– |
|
193 |
|
end BendTypes |
194 |
|
|
270 |
– |
|
271 |
– |
|
195 |
|
begin TorsionTypes |
196 |
|
|
197 |
+ |
//Cubic |
198 |
+ |
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
199 |
+ |
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
200 |
+ |
//Cubic Examples |
201 |
+ |
HEAD CH2 CH2 HEAD Cubic 5.9602 -0.2568 -3.802 2.1586 |
202 |
+ |
HEAD CH2 CH HEAD Cubic 3.3254 -0.4215 -1.686 1.1661 |
203 |
+ |
HEAD CH CH HEAD Cubic 3.3254 -0.4215 -1.686 1.1661 |
204 |
+ |
HEAD CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
205 |
+ |
HEAD CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
206 |
+ |
HEAD CH CH2 CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
207 |
+ |
HEAD CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
208 |
+ |
HEAD CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
209 |
+ |
HEAD CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
210 |
+ |
HEAD CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
211 |
+ |
HEAD CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
212 |
+ |
HEAD CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
213 |
+ |
HEAD CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
214 |
+ |
HEAD CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
215 |
+ |
HEAD CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
216 |
+ |
HEAD TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
217 |
+ |
HEAD TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
218 |
+ |
HEAD TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
219 |
+ |
CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
220 |
+ |
CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
221 |
+ |
CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
222 |
+ |
CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
223 |
+ |
CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
224 |
+ |
CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
225 |
+ |
CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
226 |
+ |
CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
227 |
+ |
CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
228 |
+ |
CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
229 |
+ |
CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
230 |
+ |
CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
231 |
+ |
CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
232 |
+ |
CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
233 |
+ |
CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
234 |
+ |
CH2 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
235 |
+ |
CH2 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
236 |
+ |
CH2 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
237 |
+ |
CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
238 |
+ |
CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
239 |
+ |
CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
240 |
+ |
TB1 TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
241 |
+ |
TB2 TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
242 |
+ |
TB3 TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
243 |
+ |
TE1 TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
244 |
+ |
TE2 TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
245 |
+ |
TE3 TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
246 |
|
|
247 |
< |
|
248 |
< |
//CubicTorsionType |
249 |
< |
|
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 |
< |
|
247 |
> |
//Charmm |
248 |
> |
//Atom1 Atom2 Atom3 Atom4 Charmm Kchi n delta [Kchi n delta] |
249 |
> |
//V_Charmm = Kchi(1 + cos(n(chi) - delta)) |
250 |
|
//Kchi: kcal/mole |
383 |
– |
|
251 |
|
//n: multiplicity |
385 |
– |
|
252 |
|
//delta: degrees |
253 |
+ |
//in some cases, a Charmm may have two or three terms. If n is equal to 0, it falls back to harmonic form |
254 |
|
|
255 |
< |
//in some cases, a CharmmTorsionType may have two or three terms. If n is equal to 0, it falls back to harmonic form |
255 |
> |
//Quartic |
256 |
> |
//Atom1 Atom2 Atom3 Atom4 Quartic k4 k3 k2 k1 k0 ( all are kcal/mol ) |
257 |
> |
//V_Quartic = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
258 |
|
|
259 |
+ |
//Polynomial |
260 |
+ |
//Atom1 Atom2 Atom3 Atom4 Polynomial i Ki [j Kj] |
261 |
+ |
//VPolynomial = Ki (cos phi)^i + ... + Kj (cos phi)^j |
262 |
|
|
263 |
< |
|
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 |
263 |
> |
end TorsionTypes |