| blob | 6356c97fb6c09c68691057abe6d1c7373c46db23 |
1 [ bondedtypes ]
2 ; Column 1 : default bondtype
3 ; Column 2 : default angletype
4 ; Column 3 : default proper dihedraltype
5 ; Column 4 : default improper dihedraltype
6 ; Column 5 : This controls the generation of dihedrals from the bonding.
7 ; All possible dihedrals are generated automatically. A value of
8 ; 1 here means that all these are retained. A value of
9 ; 0 here requires generated dihedrals be removed if
10 ; * there are any dihedrals on the same central atoms
11 ; specified in the residue topology, or
12 ; * there are other identical generated dihedrals
13 ; sharing the same central atoms, or
14 ; * there are other generated dihedrals sharing the
15 ; same central bond that have fewer hydrogen atoms
16 ; Column 6 : number of neighbors to exclude from non-bonded interactions
17 ; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
18 ; 0 = do not generate such
19 ; Column 8 : 1 = remove proper dihedrals if found centered on the same
20 ; bond as an improper dihedral
21 ; 0 = do not generate such
22 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
23 1 5 9 2 1 3 1 0
25 ; =====================================================================
26 ; RNA
28 ;-----------------------------------------------------------------------
29 [ RA ]
30 ; H61 H62;
31 ; \ /
32 ; N6
33 ; |
34 ; C6
35 ; // \
36 ; N1 C5--N7\\
37 ; | || C8-H8
38 ; C2 C4--N9/
39 ; / \\ / \
40 ; H2 N3 \
41 ; \
42 ; \
43 ; \
44 ; O1P H5'1 H4' O4' \
45 ; | | \ / \ \
46 ; -P-O5'-C5'---C4' C1'
47 ; | | \ / \
48 ; O2P H5'2 C3'--C2' H1'
49 ; / \ / \
50 ; O3' H3' O2' H2'2
51 ; | |
52 ; H2'1
53 ;
54 [ atoms ]
55 P P 1.50 0
56 O1P ON3 -0.78 1
57 O2P ON3 -0.78 2
58 O5' ON2 -0.57 3
59 C5' CN8B -0.08 4
60 H5'1 HN8 0.09 5
61 H5'2 HN8 0.09 6
62 C4' CN7 0.16 7
63 H4' HN7 0.09 8
64 O4' ON6B -0.50 9
65 C1' CN7B 0.16 10
66 H1' HN7 0.09 11
67 N9 NN2 -0.05 12
68 C5 CN5 0.28 13
69 N7 NN4 -0.71 14
70 C8 CN4 0.34 15
71 H8 HN3 0.12 16
72 N1 NN3A -0.74 17
73 C2 CN4 0.50 18
74 H2 HN3 0.13 19
75 N3 NN3A -0.75 20
76 C4 CN5 0.43 21
77 C6 CN2 0.46 22
78 N6 NN1 -0.77 23
79 H61 HN1 0.38 24
80 H62 HN1 0.38 25
81 C2' CN7B 0.14 26
82 H2'2 HN7 0.09 27
83 O2' ON5 -0.66 28
84 H2'1 HN5 0.43 29
85 C3' CN7 0.01 30
86 H3' HN7 0.09 31
87 O3' ON2 -0.57 32
88 [ bonds ]
89 -O3' P
90 P O1P
91 P O2P
92 P O5'
93 O5' C5'
94 C5' C4'
95 C4' O4'
96 C4' C3'
97 O4' C1'
98 C1' N9
99 C1' C2'
100 N9 C4
101 N9 C8
102 C4 N3
103 C2 N1
104 C6 N6
105 N6 H61
106 N6 H62
107 C6 C5
108 C5 N7
109 C2' C3'
110 C2' O2'
111 O2' H2'1
112 C3' O3'
113 C1' H1'
114 C2' H2'2
115 C3' H3'
116 C4' H4'
117 C5' H5'1
118 C5' H5'2
119 C8 H8
120 C2 H2
121 N1 C6
122 C2 N3
123 C4 C5
124 N7 C8
125 [ impropers ]
126 N6 C6 H61 H62
127 C6 N1 C5 N6
129 ;--------------------------------------------------------------------------
130 [ RC ]
131 ;
132 ; H42 H41
133 ; \ /
134 ; N4
135 ; |
136 ; C4
137 ; / \\
138 ; H5-C5 N3
139 ; || |
140 ; H6-C6 C2
141 ; \ / \\
142 ; N1 O2
143 ; \
144 ; \
145 ; \
146 ; O1P H5'1H4' O4' \
147 ; | | \ / \ \
148 ; -P-O5'-C5'---C4' C1'
149 ; | | \ / \
150 ; O2P H5'2 C3'--C2' H1'
151 ; / \ / \
152 ; O3' H3' O2' H2'2
153 ; | |
154 ; H2'1
155 [ atoms ]
156 P P 1.50 0
157 O1P ON3 -0.78 1
158 O2P ON3 -0.78 2
159 O5' ON2 -0.57 3
160 C5' CN8B -0.08 4
161 H5'1 HN8 0.09 5
162 H5'2 HN8 0.09 6
163 C4' CN7 0.16 7
164 H4' HN7 0.09 8
165 O4' ON6B -0.50 9
166 C1' CN7B 0.16 10
167 H1' HN7 0.09 11
168 N1 NN2 -0.13 12
169 C6 CN3 0.05 13
170 H6 HN3 0.17 14
171 C5 CN3 -0.13 15
172 H5 HN3 0.07 16
173 C2 CN1 0.52 17
174 O2 ON1C -0.49 18
175 N3 NN3 -0.66 19
176 C4 CN2 0.65 20
177 N4 NN1 -0.75 21
178 H41 HN1 0.37 22
179 H42 HN1 0.33 23
180 C2' CN7B 0.14 24
181 H2'2 HN7 0.09 25
182 O2' ON5 -0.66 26
183 H2'1 HN5 0.43 27
184 C3' CN7 0.01 28
185 H3' HN7 0.09 29
186 O3' ON2 -0.57 30
187 [ bonds ]
188 -O3' P
189 P O1P
190 P O2P
191 P O5'
192 O5' C5'
193 C5' C4'
194 C4' O4'
195 C4' C3'
196 O4' C1'
197 C1' N1
198 C1' C2'
199 N1 C2
200 N1 C6
201 C2 N3
202 C4 N4
203 N4 H41
204 N4 H42
205 C4 C5
206 C2' C3'
207 C3' O3'
208 C2' O2'
209 O2' H2'1
210 C1' H1'
211 C2' H2'2
212 C3' H3'
213 C4' H4'
214 C5' H5'1
215 C5' H5'2
216 C5 H5
217 C6 H6
218 C2 O2
219 C5 C6
220 N3 C4
221 [ impropers ]
222 C2 N1 N3 O2
223 C4 N3 C5 N4
224 N4 C4 H41 H42
226 ; --------------------------------------------------------------------
227 [ RG ]
228 ; O6
229 ; ||
230 ; C6
231 ; / \
232 ; H1-N1 C5--N7\\
233 ; | || C8-H8
234 ; C2 C4--N9/
235 ; / \\ / \
236 ; H21-N2 N3 \
237 ; | \
238 ; H22 \
239 ; \
240 ; O1P H5'1 H4' O4' \
241 ; | | \ / \ \
242 ; -P-O5'-C5'---C4' C1'
243 ; | | \ / \
244 ; O2P H5'2 C3'--C2' H1'
245 ; / \ / \
246 ; O3' H3' O2' H2'2
247 ; | |
248 ; H2'1
249 [ atoms ]
250 P P 1.50 0
251 O1P ON3 -0.78 1
252 O2P ON3 -0.78 2
253 O5' ON2 -0.57 3
254 C5' CN8B -0.08 4
255 H5'1 HN8 0.09 5
256 H5'2 HN8 0.09 6
257 C4' CN7 0.16 7
258 H4' HN7 0.09 8
259 O4' ON6B -0.50 9
260 C1' CN7B 0.16 10
261 H1' HN7 0.09 11
262 N9 NN2B -0.02 12
263 C4 CN5 0.26 13
264 N2 NN1 -0.68 14
265 H21 HN1 0.32 15
266 H22 HN1 0.35 16
267 N3 NN3G -0.74 17
268 C2 CN2 0.75 18
269 N1 NN2G -0.34 19
270 H1 HN2 0.26 20
271 C6 CN1 0.54 21
272 O6 ON1 -0.51 22
273 C5 CN5G 0.00 23
274 N7 NN4 -0.60 24
275 C8 CN4 0.25 25
276 H8 HN3 0.16 26
277 C2' CN7B 0.14 27
278 H2'2 HN7 0.09 28
279 O2' ON5 -0.66 29
280 H2'1 HN5 0.43 30
281 C3' CN7 0.01 31
282 H3' HN7 0.09 32
283 O3' ON2 -0.57 33
284 [ bonds ]
285 -O3' P
286 P O1P
287 P O2P
288 P O5'
289 O5' C5'
290 C5' C4'
291 C4' O4'
292 C4' C3'
293 O4' C1'
294 C1' N9
295 C1' C2'
296 N9 C4
297 N9 C8
298 C4 N3
299 C2 N2
300 C2 N1
301 N2 H21
302 N2 H22
303 N1 H1
304 N1 C6
305 C6 C5
306 C5 N7
307 C2' C3'
308 C3' O3'
309 C2' O2'
310 O2' H2'1
311 C1' H1'
312 C2' H2'2
313 C3' H3'
314 C4' H4'
315 C5' H5'1
316 C5' H5'2
317 C8 H8
318 C2 N3
319 C4 C5
320 N7 C8
321 C6 O6
322 [ impropers ]
323 C2 N3 N1 N2
324 C6 N1 C5 O6
325 N2 H21 C2 H22
327 ;---------------------------------------------------------------------------
328 [ RU ]
329 ; O4
330 ; ||
331 ; C4 H3
332 ; / \ /
333 ; H5-C5 N3
334 ; || |
335 ; H6-C6 C2
336 ; \ / \\
337 ; N1 O2
338 ; \
339 ; \
340 ; \
341 ; O1P H5'1H4' O4' \
342 ; | | \ / \ \
343 ; -P-O5'-C5'---C4' C1'
344 ; | | \ / \
345 ; O2P H5'2 C3'--C2' H1'
346 ; / \ / \
347 ; O3' H3' O2' H2'2
348 ; | |
349 ; H2'1
350 ;
351 [ atoms ]
352 P P 1.50 0
353 O1P ON3 -0.78 1
354 O2P ON3 -0.78 2
355 O5' ON2 -0.57 3
356 C5' CN8B -0.08 4
357 H5'1 HN8 0.09 5
358 H5'2 HN8 0.09 6
359 C4' CN7 0.16 7
360 H4' HN7 0.09 8
361 O4' ON6B -0.50 9
362 C1' CN7B 0.16 10
363 H1' HN7 0.09 11
364 N1 NN2B -0.34 12
365 C6 CN3 0.20 13
366 H6 HN3 0.14 14
367 C2 CN1T 0.55 15
368 O2 ON1 -0.45 16
369 N3 NN2U -0.46 17
370 H3 HN2 0.36 18
371 C4 CN1 0.53 19
372 O4 ON1 -0.48 20
373 C5 CN3 -0.15 21
374 H5 HN3 0.10 22
375 C2' CN7B 0.14 23
376 H2'2 HN7 0.09 24
377 O2' ON5 -0.66 25
378 H2'1 HN5 0.43 26
379 C3' CN7 0.01 27
380 H3' HN7 0.09 28
381 O3' ON2 -0.57 29
382 [ bonds ]
383 -O3' P
384 P O1P
385 P O2P
386 P O5'
387 O5' C5'
388 C5' C4'
389 C4' O4'
390 C4' C3'
391 O4' C1'
392 C1' N1
393 C1' C2'
394 N1 C2
395 N1 C6
396 C2 N3
397 N3 H3
398 N3 C4
399 C4 C5
400 C2' C3'
401 C3' O3'
402 C2' O2'
403 O2' H2'1
404 C1' H1'
405 C2' H2'2
406 C3' H3'
407 C4' H4'
408 C5' H5'1
409 C5' H5'2
410 C5 H5
411 C6 H6
412 C2 O2
413 C4 O4
414 C5 C6
415 [ impropers ]
416 C2 N1 N3 O2
417 C4 N3 C5 O4