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1 ; If you get a complaint about missing dummy types from pdb2gmx
2 ; is is straightforward to add it here.
3 ; First, determine the bonded atom type (for most forcefields except
4 ; opls it is probably identical to the nonbonded atomtype) for the
5 ; next atom bound to your N or C atom. Check the constrainttypes
6 ; section of the forcefield and determine which type of dummy mass
7 ; is used for an N (or C) bonded to that atomtype.
8 ; In the correct section below you can then add your atomtype
9 ; (not bonded atomtype!), the type of the bound heavy atom, and the
10 ; type of dummy mass to use in this case.
11 ;
12 ; If the dummy is a planar NH2 group you should just write planar
13 ; after the N atomtype name.
14 ; N.B: dummy masses must have names beginning with MNH2* , MNH3* , MCH3*.
16 [ CH3 ]
17 opls_135 opls_136 MCH3B
18 opls_135 opls_137 MCH3B
19 opls_135 opls_157 MCH3B
20 opls_135 opls_158 MCH3B
21 opls_135 opls_224B MCH3B
22 opls_135 opls_225B MCH3B
23 opls_135 opls_235 MCH3A
24 opls_135 opls_283 MCH3B
25 opls_135 opls_293B MCH3B
26 opls_135 opls_299 MCH3B
27 opls_135 opls_912B MCH3B
28 opls_209 opls_202 MCH3A
30 [ NH3 ]
31 opls_287 opls_283 MNH3
32 opls_287 opls_292 MNH3
33 opls_287 opls_292B MNH3
34 opls_287 opls_293 MNH3
35 opls_287 opls_293B MNH3
36 opls_287 opls_298 MNH3
37 opls_287 opls_299 MNH3
39 [ NH2 ]
40 opls_237 planar
41 opls_300 planar
42 opls_751 planar
43 opls_900 opls_906 MNH2
44 opls_900 opls_906B MNH2
45 opls_900 opls_912B MNH2
48 ; Data for generating dummy aromatic rings.
49 ; Actually we dont need all these bonds and angles,
50 ; but by specifying them here it is easier to improve
51 ; the dummy generation code later.
52 [ PHE ]
53 CG CD1 0.140
54 CG CD2 0.140
55 CD1 CE1 0.140
56 CD2 CE2 0.140
57 CE1 CZ 0.140
58 CE2 CZ 0.140
59 CD1 HD1 0.108
60 CD2 HD2 0.108
61 CE1 HE1 0.108
62 CE2 HE2 0.108
63 CZ HZ 0.108
64 CG CD1 CE1 120.0
65 CD1 CE1 CZ 120.0
66 CE1 CZ CE2 120.0
67 CZ CE2 CD2 120.0
68 CE2 CD2 CG 120.0
69 CD2 CG CD1 120.0
70 CG CD1 HD1 120.0
71 CG CD2 HD2 120.0
72 HD1 CD1 CE1 120.0
73 CD1 CE1 HE1 120.0
74 HE1 CE1 CZ 120.0
75 CE1 CZ HZ 120.0
76 HZ CZ CE2 120.0
77 CZ CE2 HE2 120.0
78 HE2 CE2 CD2 120.0
79 HD2 CD2 CG 120.0
81 [ TYR ]
82 CG CD1 0.140
83 CG CD2 0.140
84 CD1 CE1 0.140
85 CD2 CE2 0.140
86 CE1 CZ 0.140
87 CE2 CZ 0.140
88 CD1 HD1 0.108
89 CD2 HD2 0.108
90 CE1 HE1 0.108
91 CE2 HE2 0.108
92 CZ OH 0.1364
93 OH HH 0.0945
94 CG CD1 CE1 120.0
95 CD1 CE1 CZ 120.0
96 CE1 CZ CE2 120.0
97 CZ CE2 CD2 120.0
98 CE2 CD2 CG 120.0
99 CD2 CG CD1 120.0
100 CG CD1 HD1 120.0
101 CG CD2 HD2 120.0
102 HD1 CD1 CE1 120.0
103 CD1 CE1 HE1 120.0
104 HE1 CE1 CZ 120.0
105 CE1 CZ OH 120.0
106 CZ OH HH 113.0
107 OH CZ CE2 120.0
108 CZ CE2 HE2 120.0
109 HE2 CE2 CD2 120.0
110 HD2 CD2 CG 120.0
112 [ TRP ] ; angles from MD sim, corrected to be perfectly planar
113 CB CG 0.1495
114 CG CD1 0.1352
115 CD1 NE1 0.1381
116 NE1 CE2 0.138
117 CE2 CD2 0.1419
118 CD2 CG 0.1459
119 CE2 CZ2 0.140
120 CZ2 CH2 0.140
121 CH2 CZ3 0.140
122 CZ3 CE3 0.140
123 CE3 CD2 0.1404
124 CD1 HD1 0.108
125 NE1 HE1 0.101
126 CE3 HE3 0.108
127 CZ2 HZ2 0.108
128 CZ3 HZ3 0.108
129 CH2 HH2 0.108
130 CB CG CD1 125.6
131 CB CG CD2 128.7
132 CG CD1 NE1 109.7
133 CD1 NE1 CE2 111.7
134 NE1 CE2 CD2 104.3
135 CE2 CD2 CG 108.5
136 CD2 CG CD1 105.7
137 NE1 CE2 CZ2 135.7
138 CE2 CZ2 CH2 120.0
139 CZ2 CH2 CZ3 120.0
140 CH2 CZ3 CE3 120.0
141 CZ3 CE3 CD2 120.0
142 CE2 CD2 CE3 120.0
143 CD2 CE2 CZ2 120.0
144 CE3 CD2 CG 131.5
145 CG CD1 HD1 124.6
146 HD1 CD1 NE1 125.7
147 CD1 NE1 HE1 122.7
148 HE1 NE1 CE2 125.6
149 CZ3 CE3 HE3 120.0
150 HE3 CE3 CD2 120.0
151 CE2 CZ2 HZ2 120.0
152 HZ2 CZ2 CH2 120.0
153 CH2 CZ3 HZ3 120.0
154 HZ3 CZ3 CE3 120.0
155 CZ2 CH2 HH2 120.0
156 HH2 CH2 CZ3 120.0
158 [ HISA ] ; angles from MD sim, corrected to be perfectly planar
159 CG ND1 0.1381
160 ND1 CE1 0.1343
161 CE1 NE2 0.1335
162 NE2 CD2 0.1394
163 CD2 CG 0.137
164 ND1 HD1 0.101
165 CE1 HE1 0.108
166 CD2 HD2 0.108
167 CG ND1 CE1 107.4
168 ND1 CE1 NE2 113.1
169 CE1 NE2 CD2 104.5
170 NE2 CD2 CG 109.3
171 CD2 CG ND1 105.7
172 CG ND1 HD1 127.7
173 HD1 ND1 CE1 124.9
174 ND1 CE1 HE1 122.9
175 HE1 CE1 NE2 124.0
176 CG CD2 HD2 129.0
177 HD2 CD2 NE2 121.7
179 [ HISB ] ; angles from MD sim, corrected to be perfectly planar
180 CG ND1 0.1394
181 ND1 CE1 0.1335
182 CE1 NE2 0.1343
183 NE2 CD2 0.1381
184 CD2 CG 0.137
185 CD2 HD2 0.108
186 CE1 HE1 0.108
187 NE2 HE2 0.101
188 CG ND1 CE1 104.9
189 ND1 CE1 NE2 112.9
190 CE1 NE2 CD2 107.3
191 NE2 CD2 CG 106.4
192 CD2 CG ND1 108.5
193 NE2 CD2 HD2 122.4
194 HD2 CD2 CG 131.2
195 ND1 CE1 HE1 123.8
196 HE1 CE1 NE2 123.3
197 CE1 NE2 HE2 125.9
198 HE2 NE2 CD2 126.8
200 [ HISH ] ; angles from MD sim, corrected to be perfectly planar
201 CG ND1 0.1381
202 ND1 CE1 0.1343
203 CE1 NE2 0.1343
204 NE2 CD2 0.1381
205 CD2 CG 0.137
206 ND1 HD1 0.101
207 CE1 HE1 0.108
208 CD2 HD2 0.108
209 NE2 HE2 0.101
210 CG ND1 CE1 107.4
211 ND1 CE1 NE2 111.4
212 CE1 NE2 CD2 107.2
213 NE2 CD2 CG 107.4
214 CD2 CG ND1 106.6
215 CG ND1 HD1 127.4
216 HD1 ND1 CE1 125.2
217 ND1 CE1 HE1 124.3
218 HE1 CE1 NE2 124.3
219 CE1 NE2 HE2 126.4
220 HE2 NE2 CD2 126.4
221 NE2 CD2 HD2 120.8
222 HD2 CD2 CG 131.8