-
Notifications
You must be signed in to change notification settings - Fork 0
/
cCMP-NMIA_GMX-proc.top
554 lines (537 loc) · 41 KB
/
cCMP-NMIA_GMX-proc.top
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
; CMP-NMIA_GMX.top created by acpype
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094
OS OS 0.00000 0.00000 A 3.00001e-01 7.11280e-01 ; 1.68 0.1700
OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104
HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000
H1 H1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157
P P 0.00000 0.00000 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000
O2 O2 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100
H2 H2 0.00000 0.00000 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157
N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
CM CM 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
H4 H4 0.00000 0.00000 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150
HA HA 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150
CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
N2 N2 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157
NC NC 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100
CB CB 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
K+ K+ 0.00000 0.00000 A 3.03796e-01 8.10369e-01 ; 1.70 0.1937
OW OW 0.00000 0.00000 A 3.15075e-01 6.35968e-01 ; 1.77 0.1520
HW HW 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000
[ moleculetype ]
;name nrexcl
CMP-NMIA 3
[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot bond_type
1 CT 1 CMP C1' 1 0.006600 12.01000 ; qtot 0.007
2 OS 1 CMP O4' 2 -0.354800 16.00000 ; qtot -0.348
3 CT 1 CMP C4' 3 0.106500 12.01000 ; qtot -0.242
4 CT 1 CMP C3' 4 0.202200 12.01000 ; qtot -0.040
5 CT 1 CMP C2' 5 0.067000 12.01000 ; qtot 0.028
6 OH 1 CMP O2' 6 -0.613901 16.00000 ; qtot -0.586
7 HO 1 CMP HO'2 7 0.418600 1.00800 ; qtot -0.168
8 H1 1 CMP H2'1 8 0.097200 1.00800 ; qtot -0.071
9 OS 1 CMP O3' 9 -0.524601 16.00000 ; qtot -0.595
10 P 1 CMP P 10 1.166200 30.97000 ; qtot 0.571
11 OS 1 CMP O5' 11 -0.498900 16.00000 ; qtot 0.072
12 CT 1 CMP C5' 12 0.055800 12.01000 ; qtot 0.128
13 H1 1 CMP H5'1 13 0.067900 1.00800 ; qtot 0.196
14 H1 1 CMP H5'2 14 0.067900 1.00800 ; qtot 0.264
15 O2 1 CMP O1P 15 -0.776001 16.00000 ; qtot -0.512
16 O2 1 CMP O2P 16 -0.776001 16.00000 ; qtot -1.288
17 H1 1 CMP H3' 17 0.061500 1.00800 ; qtot -1.227
18 H1 1 CMP H4' 18 0.117400 1.00800 ; qtot -1.109
19 H2 1 CMP H1' 19 0.202900 1.00800 ; qtot -0.907
20 N* 1 CMP N1 20 -0.048400 14.01000 ; qtot -0.955
21 CM 1 CMP C6 21 0.005300 12.01000 ; qtot -0.950
22 H4 1 CMP H6 22 0.195800 1.00800 ; qtot -0.754
23 CM 1 CMP C5 23 -0.521501 12.01000 ; qtot -1.275
24 HA 1 CMP H5 24 0.192800 1.00800 ; qtot -1.083
25 CA 1 CMP C4 25 0.818501 12.01000 ; qtot -0.264
26 N2 1 CMP N4 26 -0.953001 14.01000 ; qtot -1.217
27 H 1 CMP H41 27 0.423400 1.00800 ; qtot -0.794
28 H 1 CMP H42 28 0.423400 1.00800 ; qtot -0.370
29 NC 1 CMP N3 29 -0.758401 14.01000 ; qtot -1.129
30 C 1 CMP C2 30 0.753801 12.01000 ; qtot -0.375
31 O 1 CMP O2 31 -0.625201 16.00000 ; qtot -1.000
32 CA 2 NMI C1 32 -0.117555 12.01000 ; qtot -1.118
33 HA 2 NMI H1 33 0.159661 1.00800 ; qtot -0.958
34 CA 2 NMI C2 34 -0.173065 12.01000 ; qtot -1.131
35 HA 2 NMI H2 35 0.156711 1.00800 ; qtot -0.974
36 CB 2 NMI C3 36 0.000479 12.01000 ; qtot -0.974
37 N* 2 NMI N7 37 -0.062833 14.01000 ; qtot -1.037
38 C 2 NMI C8 38 0.743188 12.01000 ; qtot -0.293
39 OS 2 NMI O9 39 -0.437480 16.00000 ; qtot -0.731
40 C 2 NMI C10 40 0.758669 12.01000 ; qtot 0.028
41 O 2 NMI O10 41 -0.538154 16.00000 ; qtot -0.510
42 O 2 NMI O8 42 -0.558132 16.00000 ; qtot -1.069
43 CT 2 NMI C7 43 -0.222525 12.01000 ; qtot -1.291
44 H1 2 NMI H71 44 0.111079 1.00800 ; qtot -1.180
45 H1 2 NMI H72 45 0.111079 1.00800 ; qtot -1.069
46 H1 2 NMI H73 46 0.111079 1.00800 ; qtot -0.958
47 CB 2 NMI C4 47 -0.056779 12.01000 ; qtot -1.015
48 CA 2 NMI C5 48 -0.184941 12.01000 ; qtot -1.200
49 HA 2 NMI H5 49 0.181405 1.00800 ; qtot -1.018
50 CA 2 NMI C6 50 -0.131085 12.01000 ; qtot -1.149
51 HA 2 NMI H6 51 0.149200 1.00800 ; qtot -1.000
[ bonds ]
; ai aj funct r k
1 2 1 1.4100e-01 2.6778e+05 ; C1' - O4'
1 5 1 1.5260e-01 2.5941e+05 ; C1' - C2'
1 19 1 1.0900e-01 2.8451e+05 ; C1' - H1'
1 20 1 1.4750e-01 2.8200e+05 ; C1' - N1
2 3 1 1.4100e-01 2.6778e+05 ; O4' - C4'
3 4 1 1.5260e-01 2.5941e+05 ; C4' - C3'
3 12 1 1.5260e-01 2.5941e+05 ; C4' - C5'
3 18 1 1.0900e-01 2.8451e+05 ; C4' - H4'
4 5 1 1.5260e-01 2.5941e+05 ; C3' - C2'
4 9 1 1.4100e-01 2.6778e+05 ; C3' - O3'
4 17 1 1.0900e-01 2.8451e+05 ; C3' - H3'
5 6 1 1.4100e-01 2.6778e+05 ; C2' - O2'
5 8 1 1.0900e-01 2.8451e+05 ; C2' - H2'1
6 7 1 9.6000e-02 4.6275e+05 ; O2' - HO'2
9 10 1 1.6100e-01 1.9246e+05 ; O3' - P
10 11 1 1.6100e-01 1.9246e+05 ; P - O5'
10 15 1 1.4800e-01 4.3932e+05 ; P - O1P
10 16 1 1.4800e-01 4.3932e+05 ; P - O2P
11 12 1 1.4100e-01 2.6778e+05 ; O5' - C5'
12 13 1 1.0900e-01 2.8451e+05 ; C5' - H5'1
12 14 1 1.0900e-01 2.8451e+05 ; C5' - H5'2
20 21 1 1.3650e-01 3.7489e+05 ; N1 - C6
20 30 1 1.3830e-01 3.5480e+05 ; N1 - C2
21 22 1 1.0800e-01 3.0711e+05 ; C6 - H6
21 23 1 1.3500e-01 4.5940e+05 ; C6 - C5
23 24 1 1.0800e-01 3.0711e+05 ; C5 - H5
23 25 1 1.4330e-01 3.5731e+05 ; C5 - C4
25 26 1 1.3400e-01 4.0250e+05 ; C4 - N4
25 29 1 1.3390e-01 4.0417e+05 ; C4 - N3
26 27 1 1.0100e-01 3.6317e+05 ; N4 - H41
26 28 1 1.0100e-01 3.6317e+05 ; N4 - H42
29 30 1 1.3580e-01 3.8242e+05 ; N3 - C2
30 31 1 1.2290e-01 4.7698e+05 ; C2 - O2
32 33 1 1.0800e-01 3.0711e+05 ; C1 - H1
32 34 1 1.4000e-01 3.9246e+05 ; C1 - C2
32 50 1 1.4000e-01 3.9246e+05 ; C1 - C6
34 35 1 1.0800e-01 3.0711e+05 ; C2 - H2
34 36 1 1.4040e-01 3.9246e+05 ; C2 - C3
36 37 1 1.3740e-01 3.6484e+05 ; C3 - N7
36 47 1 1.3700e-01 4.3514e+05 ; C3 - C4
37 38 1 1.3830e-01 3.5480e+05 ; N7 - C8
37 43 1 1.4750e-01 2.8200e+05 ; N7 - C7
38 39 1 1.3230e-01 3.7656e+05 ; C8 - O9
38 42 1 1.2290e-01 4.7698e+05 ; C8 - O8
39 40 1 1.3230e-01 3.7656e+05 ; O9 - C10
40 41 1 1.2290e-01 4.7698e+05 ; C10 - O10
40 47 1 1.4190e-01 3.7405e+05 ; C10 - C4
43 44 1 1.0900e-01 2.8451e+05 ; C7 - H71
43 45 1 1.0900e-01 2.8451e+05 ; C7 - H72
43 46 1 1.0900e-01 2.8451e+05 ; C7 - H73
47 48 1 1.4040e-01 3.9246e+05 ; C4 - C5
48 49 1 1.0800e-01 3.0711e+05 ; C5 - H5
48 50 1 1.4000e-01 3.9246e+05 ; C5 - C6
50 51 1 1.0800e-01 3.0711e+05 ; C6 - H6
[ pairs ]
; ai aj funct
1 7 1 ; C1' - HO'2
1 9 1 ; C1' - O3'
1 12 1 ; C1' - C5'
1 17 1 ; C1' - H3'
1 18 1 ; C1' - H4'
1 22 1 ; C1' - H6
1 23 1 ; C1' - C5
1 29 1 ; C1' - N3
1 31 1 ; C1' - O2
2 6 1 ; O4' - O2'
2 8 1 ; O4' - H2'1
2 9 1 ; O4' - O3'
2 11 1 ; O4' - O5'
2 13 1 ; O4' - H5'1
2 14 1 ; O4' - H5'2
2 17 1 ; O4' - H3'
2 21 1 ; O4' - C6
2 30 1 ; O4' - C2
3 6 1 ; C4' - O2'
3 8 1 ; C4' - H2'1
3 10 1 ; C4' - P
4 7 1 ; C3' - HO'2
4 11 1 ; C3' - O5'
4 13 1 ; C3' - H5'1
4 14 1 ; C3' - H5'2
4 15 1 ; C3' - O1P
4 16 1 ; C3' - O2P
5 10 1 ; C2' - P
5 12 1 ; C2' - C5'
5 18 1 ; C2' - H4'
5 21 1 ; C2' - C6
5 30 1 ; C2' - C2
6 9 1 ; O2' - O3'
6 17 1 ; O2' - H3'
7 8 1 ; HO'2 - H2'1
8 9 1 ; H2'1 - O3'
8 17 1 ; H2'1 - H3'
9 12 1 ; O3' - C5'
9 18 1 ; O3' - H4'
10 13 1 ; P - H5'1
10 14 1 ; P - H5'2
10 17 1 ; P - H3'
11 18 1 ; O5' - H4'
12 15 1 ; C5' - O1P
12 16 1 ; C5' - O2P
12 17 1 ; C5' - H3'
13 18 1 ; H5'1 - H4'
14 18 1 ; H5'2 - H4'
17 18 1 ; H3' - H4'
19 3 1 ; H1' - C4'
19 4 1 ; H1' - C3'
19 6 1 ; H1' - O2'
19 8 1 ; H1' - H2'1
19 21 1 ; H1' - C6
19 30 1 ; H1' - C2
20 3 1 ; N1 - C4'
20 4 1 ; N1 - C3'
20 6 1 ; N1 - O2'
20 8 1 ; N1 - H2'1
20 24 1 ; N1 - H5
20 25 1 ; N1 - C4
21 26 1 ; C6 - N4
21 29 1 ; C6 - N3
21 31 1 ; C6 - O2
22 24 1 ; H6 - H5
22 25 1 ; H6 - C4
22 30 1 ; H6 - C2
23 27 1 ; C5 - H41
23 28 1 ; C5 - H42
23 30 1 ; C5 - C2
24 26 1 ; H5 - N4
24 29 1 ; H5 - N3
25 31 1 ; C4 - O2
26 30 1 ; N4 - C2
27 29 1 ; H41 - N3
28 29 1 ; H42 - N3
32 37 1 ; C1 - N7
32 47 1 ; C1 - C4
32 49 1 ; C1 - H5
33 35 1 ; H1 - H2
33 36 1 ; H1 - C3
33 48 1 ; H1 - C5
33 51 1 ; H1 - H6
34 38 1 ; C2 - C8
34 40 1 ; C2 - C10
34 43 1 ; C2 - C7
34 48 1 ; C2 - C5
34 51 1 ; C2 - H6
35 37 1 ; H2 - N7
35 47 1 ; H2 - C4
35 50 1 ; H2 - C6
36 39 1 ; C3 - O9
36 41 1 ; C3 - O10
36 42 1 ; C3 - O8
36 44 1 ; C3 - H71
36 45 1 ; C3 - H72
36 46 1 ; C3 - H73
36 49 1 ; C3 - H5
36 50 1 ; C3 - C6
37 40 1 ; N7 - C10
37 48 1 ; N7 - C5
38 41 1 ; C8 - O10
38 44 1 ; C8 - H71
38 45 1 ; C8 - H72
38 46 1 ; C8 - H73
38 47 1 ; C8 - C4
39 43 1 ; O9 - C7
39 48 1 ; O9 - C5
40 42 1 ; C10 - O8
40 49 1 ; C10 - H5
40 50 1 ; C10 - C6
41 48 1 ; O10 - C5
42 43 1 ; O8 - C7
43 47 1 ; C7 - C4
47 51 1 ; C4 - H6
49 51 1 ; H5 - H6
[ angles ]
; ai aj ak funct theta cth
1 2 3 1 1.0950e+02 5.0208e+02 ; C1' - O4' - C4'
1 5 4 1 1.0950e+02 3.3472e+02 ; C1' - C2' - C3'
1 5 6 1 1.0950e+02 4.1840e+02 ; C1' - C2' - O2'
1 5 8 1 1.0950e+02 4.1840e+02 ; C1' - C2' - H2'1
1 20 21 1 1.2120e+02 5.8576e+02 ; C1' - N1 - C6
1 20 30 1 1.1760e+02 5.8576e+02 ; C1' - N1 - C2
2 1 5 1 1.0950e+02 4.1840e+02 ; O4' - C1' - C2'
2 1 19 1 1.0950e+02 4.1840e+02 ; O4' - C1' - H1'
2 1 20 1 1.0950e+02 4.1840e+02 ; O4' - C1' - N1
2 3 4 1 1.0950e+02 4.1840e+02 ; O4' - C4' - C3'
2 3 12 1 1.0950e+02 4.1840e+02 ; O4' - C4' - C5'
2 3 18 1 1.0950e+02 4.1840e+02 ; O4' - C4' - H4'
3 4 5 1 1.0950e+02 3.3472e+02 ; C4' - C3' - C2'
3 4 9 1 1.0950e+02 4.1840e+02 ; C4' - C3' - O3'
3 4 17 1 1.0950e+02 4.1840e+02 ; C4' - C3' - H3'
3 12 11 1 1.0950e+02 4.1840e+02 ; C4' - C5' - O5'
3 12 13 1 1.0950e+02 4.1840e+02 ; C4' - C5' - H5'1
3 12 14 1 1.0950e+02 4.1840e+02 ; C4' - C5' - H5'2
4 3 12 1 1.0950e+02 3.3472e+02 ; C3' - C4' - C5'
4 3 18 1 1.0950e+02 4.1840e+02 ; C3' - C4' - H4'
4 5 6 1 1.0950e+02 4.1840e+02 ; C3' - C2' - O2'
4 5 8 1 1.0950e+02 4.1840e+02 ; C3' - C2' - H2'1
4 9 10 1 1.2050e+02 8.3680e+02 ; C3' - O3' - P
5 1 19 1 1.0950e+02 4.1840e+02 ; C2' - C1' - H1'
5 1 20 1 1.0950e+02 4.1840e+02 ; C2' - C1' - N1
5 4 9 1 1.0950e+02 4.1840e+02 ; C2' - C3' - O3'
5 4 17 1 1.0950e+02 4.1840e+02 ; C2' - C3' - H3'
5 6 7 1 1.0850e+02 4.6024e+02 ; C2' - O2' - HO'2
6 5 8 1 1.0950e+02 4.1840e+02 ; O2' - C2' - H2'1
9 4 17 1 1.0950e+02 4.1840e+02 ; O3' - C3' - H3'
9 10 11 1 1.0260e+02 3.7656e+02 ; O3' - P - O5'
9 10 15 1 1.0823e+02 8.3680e+02 ; O3' - P - O1P
9 10 16 1 1.0823e+02 8.3680e+02 ; O3' - P - O2P
10 11 12 1 1.2050e+02 8.3680e+02 ; P - O5' - C5'
11 10 15 1 1.0823e+02 8.3680e+02 ; O5' - P - O1P
11 10 16 1 1.0823e+02 8.3680e+02 ; O5' - P - O2P
11 12 13 1 1.0950e+02 4.1840e+02 ; O5' - C5' - H5'1
11 12 14 1 1.0950e+02 4.1840e+02 ; O5' - C5' - H5'2
12 3 18 1 1.0950e+02 4.1840e+02 ; C5' - C4' - H4'
13 12 14 1 1.0950e+02 2.9288e+02 ; H5'1 - C5' - H5'2
15 10 16 1 1.1990e+02 1.1715e+03 ; O1P - P - O2P
19 1 20 1 1.0950e+02 4.1840e+02 ; H1' - C1' - N1
20 21 22 1 1.1910e+02 4.1840e+02 ; N1 - C6 - H6
20 21 23 1 1.2120e+02 5.8576e+02 ; N1 - C6 - C5
20 30 29 1 1.1860e+02 5.8576e+02 ; N1 - C2 - N3
20 30 31 1 1.2090e+02 6.6944e+02 ; N1 - C2 - O2
21 20 30 1 1.2160e+02 5.8576e+02 ; C6 - N1 - C2
21 23 24 1 1.1970e+02 4.1840e+02 ; C6 - C5 - H5
21 23 25 1 1.1700e+02 5.2718e+02 ; C6 - C5 - C4
22 21 23 1 1.1970e+02 4.1840e+02 ; H6 - C6 - C5
23 25 26 1 1.2010e+02 5.8576e+02 ; C5 - C4 - N4
23 25 29 1 1.2150e+02 5.8576e+02 ; C5 - C4 - N3
24 23 25 1 1.2330e+02 4.1840e+02 ; H5 - C5 - C4
25 26 27 1 1.2000e+02 4.1840e+02 ; C4 - N4 - H41
25 26 28 1 1.2000e+02 4.1840e+02 ; C4 - N4 - H42
25 29 30 1 1.2050e+02 5.8576e+02 ; C4 - N3 - C2
26 25 29 1 1.1930e+02 5.8576e+02 ; N4 - C4 - N3
27 26 28 1 1.2000e+02 2.9288e+02 ; H41 - N4 - H42
29 30 31 1 1.2250e+02 6.6944e+02 ; N3 - C2 - O2
32 34 35 1 1.2000e+02 4.1840e+02 ; C1 - C2 - H2
32 34 36 1 1.2000e+02 5.2718e+02 ; C1 - C2 - C3
32 50 48 1 1.2000e+02 5.2718e+02 ; C1 - C6 - C5
32 50 51 1 1.2000e+02 4.1840e+02 ; C1 - C6 - H6
33 32 34 1 1.2000e+02 4.1840e+02 ; H1 - C1 - C2
33 32 50 1 1.2000e+02 4.1840e+02 ; H1 - C1 - C6
34 32 50 1 1.2000e+02 5.2718e+02 ; C2 - C1 - C6
34 36 37 1 1.0620e+02 5.8576e+02 ; C2 - C3 - N7
34 36 47 1 1.1730e+02 5.2718e+02 ; C2 - C3 - C4
35 34 36 1 1.2000e+02 4.1840e+02 ; H2 - C2 - C3
36 37 38 1 1.2160e+02 5.8576e+02 ; C3 - N7 - C8
36 37 43 1 1.2580e+02 5.8576e+02 ; C3 - N7 - C7
36 47 40 1 1.1920e+02 5.2718e+02 ; C3 - C4 - C10
36 47 48 1 1.1730e+02 5.2718e+02 ; C3 - C4 - C5
37 36 47 1 1.0620e+02 5.8576e+02 ; N7 - C3 - C4
37 38 39 1 1.2090e+02 6.6944e+02 ; N7 - C8 - O9
37 38 42 1 1.2090e+02 6.6944e+02 ; N7 - C8 - O8
37 43 44 1 1.0950e+02 4.1840e+02 ; N7 - C7 - H71
37 43 45 1 1.0950e+02 4.1840e+02 ; N7 - C7 - H72
37 43 46 1 1.0950e+02 4.1840e+02 ; N7 - C7 - H73
38 37 43 1 1.1760e+02 5.8576e+02 ; C8 - N7 - C7
38 39 40 1 1.1700e+02 5.0208e+02 ; C8 - O9 - C10
39 38 42 1 1.2500e+02 6.6944e+02 ; O9 - C8 - O8
39 40 41 1 1.2500e+02 6.6944e+02 ; O9 - C10 - O10
39 40 47 1 1.1500e+02 6.6944e+02 ; O9 - C10 - C4
40 47 48 1 1.3000e+02 5.8576e+02 ; C10 - C4 - C5
41 40 47 1 1.2880e+02 6.6944e+02 ; O10 - C10 - C4
44 43 45 1 1.0950e+02 2.9288e+02 ; H71 - C7 - H72
44 43 46 1 1.0950e+02 2.9288e+02 ; H71 - C7 - H73
45 43 46 1 1.0950e+02 2.9288e+02 ; H72 - C7 - H73
47 48 49 1 1.2000e+02 4.1840e+02 ; C4 - C5 - H5
47 48 50 1 1.2000e+02 5.2718e+02 ; C4 - C5 - C6
48 50 51 1 1.2000e+02 4.1840e+02 ; C5 - C6 - H6
49 48 50 1 1.2000e+02 4.1840e+02 ; H5 - C5 - C6
[ dihedrals ] ; propers
; treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet
; i j k l func C0 C1 C2 C3 C4 C5
1 2 3 4 3 2.43927 4.80742 -0.83680 -6.40989 0.00000 0.00000 ; C1'- O4'- C4'- C3'
1 2 3 12 3 2.43927 4.80742 -0.83680 -6.40989 0.00000 0.00000 ; C1'- O4'- C4'- C5'
1 2 3 18 3 1.60387 4.81160 0.00000 -6.41547 0.00000 0.00000 ; C1'- O4'- C4'- H4'
1 5 4 3 3 3.68192 3.09616 -2.09200 -3.01248 0.00000 0.00000 ; C1'- C2'- C3'- C4'
1 5 4 9 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C1'- C2'- C3'- O3'
1 5 4 17 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C1'- C2'- C3'- H3'
1 5 6 7 3 1.71544 0.96232 0.00000 -2.67776 0.00000 0.00000 ; C1'- C2'- O2'- HO'2
1 20 21 22 3 15.48080 0.00000 -15.48080 0.00000 0.00000 0.00000 ; C1'- N1- C6- H6
1 20 21 23 3 15.48080 0.00000 -15.48080 0.00000 0.00000 0.00000 ; C1'- N1- C6- C5
1 20 30 29 3 12.13360 0.00000 -12.13360 0.00000 0.00000 0.00000 ; C1'- N1- C2- N3
1 20 30 31 3 12.13360 0.00000 -12.13360 0.00000 0.00000 0.00000 ; C1'- N1- C2- O2
2 1 5 4 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; O4'- C1'- C2'- C3'
2 1 5 6 3 0.60250 1.80749 9.83240 -2.40998 0.00000 0.00000 ; O4'- C1'- C2'- O2'
2 1 5 8 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; O4'- C1'- C2'- H2'1
2 1 20 30 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; O4'- C1'- N1- C2
2 3 4 5 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; O4'- C4'- C3'- C2'
2 3 4 9 3 0.60250 1.80749 9.83240 -2.40998 0.00000 0.00000 ; O4'- C4'- C3'- O3'
2 3 4 17 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; O4'- C4'- C3'- H3'
2 3 12 11 3 0.60250 1.80749 9.83240 -2.40998 0.00000 0.00000 ; O4'- C4'- C5'- O5'
2 3 12 13 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; O4'- C4'- C5'- H5'1
2 3 12 14 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; O4'- C4'- C5'- H5'2
3 4 5 6 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C4'- C3'- C2'- O2'
3 4 5 8 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C4'- C3'- C2'- H2'1
3 4 9 10 3 1.60387 4.81160 0.00000 -6.41547 0.00000 0.00000 ; C4'- C3'- O3'- P
3 12 11 10 3 1.60387 4.81160 0.00000 -6.41547 0.00000 0.00000 ; C4'- C5'- O5'- P
4 3 12 11 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C3'- C4'- C5'- O5'
4 3 12 13 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C3'- C4'- C5'- H5'1
4 3 12 14 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C3'- C4'- C5'- H5'2
4 5 6 7 3 1.71544 0.96232 0.00000 -2.67776 0.00000 0.00000 ; C3'- C2'- O2'- HO'2
4 9 10 11 3 1.04600 3.13800 10.04160 -4.18400 0.00000 0.00000 ; C3'- O3'- P- O5'
4 9 10 15 3 1.04600 3.13800 0.00000 -4.18400 0.00000 0.00000 ; C3'- O3'- P- O1P
4 9 10 16 3 1.04600 3.13800 0.00000 -4.18400 0.00000 0.00000 ; C3'- O3'- P- O2P
5 1 2 3 3 2.43927 4.80742 -0.83680 -6.40989 0.00000 0.00000 ; C2'- C1'- O4'- C4'
5 1 20 21 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; C2'- C1'- N1- C6
5 1 20 30 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; C2'- C1'- N1- C2
5 4 3 12 3 3.68192 3.09616 -2.09200 -3.01248 0.00000 0.00000 ; C2'- C3'- C4'- C5'
5 4 3 18 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C2'- C3'- C4'- H4'
5 4 9 10 3 1.60387 4.81160 0.00000 -6.41547 0.00000 0.00000 ; C2'- C3'- O3'- P
6 5 4 9 3 0.60250 1.80749 9.83240 -2.40998 0.00000 0.00000 ; O2'- C2'- C3'- O3'
6 5 4 17 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; O2'- C2'- C3'- H3'
7 6 5 8 3 0.69733 2.09200 0.00000 -2.78933 0.00000 0.00000 ; HO'2- O2'- C2'- H2'1
8 5 4 9 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; H2'1- C2'- C3'- O3'
8 5 4 17 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H2'1- C2'- C3'- H3'
9 4 3 12 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; O3'- C3'- C4'- C5'
9 4 3 18 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; O3'- C3'- C4'- H4'
9 10 11 12 3 1.04600 3.13800 10.04160 -4.18400 0.00000 0.00000 ; O3'- P- O5'- C5'
10 9 4 17 3 1.60387 4.81160 0.00000 -6.41547 0.00000 0.00000 ; P- O3'- C3'- H3'
10 11 12 13 3 1.60387 4.81160 0.00000 -6.41547 0.00000 0.00000 ; P- O5'- C5'- H5'1
10 11 12 14 3 1.60387 4.81160 0.00000 -6.41547 0.00000 0.00000 ; P- O5'- C5'- H5'2
11 12 3 18 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; O5'- C5'- C4'- H4'
12 3 4 17 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C5'- C4'- C3'- H3'
12 11 10 15 3 1.04600 3.13800 0.00000 -4.18400 0.00000 0.00000 ; C5'- O5'- P- O1P
12 11 10 16 3 1.04600 3.13800 0.00000 -4.18400 0.00000 0.00000 ; C5'- O5'- P- O2P
13 12 3 18 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H5'1- C5'- C4'- H4'
14 12 3 18 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H5'2- C5'- C4'- H4'
17 4 3 18 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H3'- C3'- C4'- H4'
19 1 2 3 3 1.60387 4.81160 0.00000 -6.41547 0.00000 0.00000 ; H1'- C1'- O4'- C4'
19 1 5 4 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H1'- C1'- C2'- C3'
19 1 5 6 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H1'- C1'- C2'- O2'
19 1 5 8 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H1'- C1'- C2'- H2'1
19 1 20 21 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; H1'- C1'- N1- C6
19 1 20 30 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; H1'- C1'- N1- C2
20 1 2 3 3 1.60247 4.80742 5.43920 -6.40989 0.00000 0.00000 ; N1- C1'- O4'- C4'
20 1 5 4 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; N1- C1'- C2'- C3'
20 1 5 6 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; N1- C1'- C2'- O2'
20 1 5 8 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; N1- C1'- C2'- H2'1
20 21 23 24 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; N1- C6- C5- H5
20 21 23 25 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; N1- C6- C5- C4
20 30 29 25 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; N1- C2- N3- C4
21 20 30 29 3 12.13360 0.00000 -12.13360 0.00000 0.00000 0.00000 ; C6- N1- C2- N3
21 20 30 31 3 12.13360 0.00000 -12.13360 0.00000 0.00000 0.00000 ; C6- N1- C2- O2
21 23 25 26 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ; C6- C5- C4- N4
21 23 25 29 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ; C6- C5- C4- N3
22 21 20 30 3 15.48080 0.00000 -15.48080 0.00000 0.00000 0.00000 ; H6- C6- N1- C2
22 21 23 24 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; H6- C6- C5- H5
22 21 23 25 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; H6- C6- C5- C4
23 21 20 30 3 15.48080 0.00000 -15.48080 0.00000 0.00000 0.00000 ; C5- C6- N1- C2
23 25 26 27 3 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; C5- C4- N4- H41
23 25 26 28 3 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; C5- C4- N4- H42
23 25 29 30 3 40.16640 0.00000 -40.16640 0.00000 0.00000 0.00000 ; C5- C4- N3- C2
24 23 25 26 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ; H5- C5- C4- N4
24 23 25 29 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ; H5- C5- C4- N3
25 29 30 31 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C4- N3- C2- O2
26 25 29 30 3 40.16640 0.00000 -40.16640 0.00000 0.00000 0.00000 ; N4- C4- N3- C2
27 26 25 29 3 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; H41- N4- C4- N3
28 26 25 29 3 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; H42- N4- C4- N3
32 34 36 37 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; C1- C2- C3- N7
32 34 36 47 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; C1- C2- C3- C4
32 50 48 47 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C1- C6- C5- C4
32 50 48 49 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C1- C6- C5- H5
33 32 34 35 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H1- C1- C2- H2
33 32 34 36 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H1- C1- C2- C3
33 32 50 48 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H1- C1- C6- C5
33 32 50 51 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H1- C1- C6- H6
34 32 50 48 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C2- C1- C6- C5
34 32 50 51 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C2- C1- C6- H6
34 36 37 38 3 13.80720 0.00000 -13.80720 0.00000 0.00000 0.00000 ; C2- C3- N7- C8
34 36 37 43 3 13.80720 0.00000 -13.80720 0.00000 0.00000 0.00000 ; C2- C3- N7- C7
34 36 47 40 3 45.60560 0.00000 -45.60560 0.00000 0.00000 0.00000 ; C2- C3- C4- C10
34 36 47 48 3 45.60560 0.00000 -45.60560 0.00000 0.00000 0.00000 ; C2- C3- C4- C5
35 34 32 50 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H2- C2- C1- C6
35 34 36 37 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; H2- C2- C3- N7
35 34 36 47 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; H2- C2- C3- C4
36 34 32 50 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C3- C2- C1- C6
36 37 38 39 3 12.13360 0.00000 -12.13360 0.00000 0.00000 0.00000 ; C3- N7- C8- O9
36 37 38 42 3 12.13360 0.00000 -12.13360 0.00000 0.00000 0.00000 ; C3- N7- C8- O8
36 37 43 44 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; C3- N7- C7- H71
36 37 43 45 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; C3- N7- C7- H72
36 37 43 46 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; C3- N7- C7- H73
36 47 40 39 3 25.10400 0.00000 -25.10400 0.00000 0.00000 0.00000 ; C3- C4- C10- O9
36 47 40 41 3 25.10400 0.00000 -25.10400 0.00000 0.00000 0.00000 ; C3- C4- C10- O10
36 47 48 49 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; C3- C4- C5- H5
36 47 48 50 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; C3- C4- C5- C6
37 36 47 40 3 45.60560 0.00000 -45.60560 0.00000 0.00000 0.00000 ; N7- C3- C4- C10
37 36 47 48 3 45.60560 0.00000 -45.60560 0.00000 0.00000 0.00000 ; N7- C3- C4- C5
37 38 39 40 3 22.59360 0.00000 -22.59360 0.00000 0.00000 0.00000 ; N7- C8- O9- C10
38 37 36 47 3 13.80720 0.00000 -13.80720 0.00000 0.00000 0.00000 ; C8- N7- C3- C4
38 37 43 44 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; C8- N7- C7- H71
38 37 43 45 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; C8- N7- C7- H72
38 37 43 46 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; C8- N7- C7- H73
38 39 40 41 3 22.59360 0.00000 -22.59360 0.00000 0.00000 0.00000 ; C8- O9- C10- O10
38 39 40 47 3 22.59360 0.00000 -22.59360 0.00000 0.00000 0.00000 ; C8- O9- C10- C4
39 38 37 43 3 12.13360 0.00000 -12.13360 0.00000 0.00000 0.00000 ; O9- C8- N7- C7
39 40 47 48 3 25.10400 0.00000 -25.10400 0.00000 0.00000 0.00000 ; O9- C10- C4- C5
40 39 38 42 3 22.59360 0.00000 -22.59360 0.00000 0.00000 0.00000 ; C10- O9- C8- O8
40 47 48 49 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; C10- C4- C5- H5
40 47 48 50 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; C10- C4- C5- C6
41 40 47 48 3 25.10400 0.00000 -25.10400 0.00000 0.00000 0.00000 ; O10- C10- C4- C5
42 38 37 43 3 12.13360 0.00000 -12.13360 0.00000 0.00000 0.00000 ; O8- C8- N7- C7
43 37 36 47 3 13.80720 0.00000 -13.80720 0.00000 0.00000 0.00000 ; C7- N7- C3- C4
47 48 50 51 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C4- C5- C6- H6
49 48 50 51 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H5- C5- C6- H6
; treated as usual propers in GROMACS since Phase angle diff from 0 or 180 degrees
; i j k l func phase kd pn
2 1 20 21 1 16.00 1.47059 4 ; O4'- C1'- N1- C6
2 1 20 21 1 16.76 7.31681 2 ; O4'- C1'- N1- C6
2 1 20 21 1 149.86 4.28919 1 ; O4'- C1'- N1- C6
2 1 20 21 1 179.35 2.43300 3 ; O4'- C1'- N1- C6
[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
; i j k l func phase kd pn
1 20 21 30 1 180.00 4.18400 2 ; C1'- N1- C6- C2
20 23 21 22 1 180.00 4.60240 2 ; N1- C5- C6- H6
20 29 30 31 1 180.00 43.93200 2 ; N1- N3- C2- O2
21 25 23 24 1 180.00 4.60240 2 ; C6- C4- C5- H5
23 26 25 29 1 180.00 4.60240 2 ; C5- N4- C4- N3
25 27 26 28 1 180.00 4.18400 2 ; C4- H41- N4- H42
32 36 34 35 1 180.00 4.60240 2 ; C1- C3- C2- H2
32 48 50 51 1 180.00 4.60240 2 ; C1- C5- C6- H6
34 50 32 33 1 180.00 4.60240 2 ; C2- C6- C1- H1
37 39 38 42 1 180.00 43.93200 2 ; N7- O9- C8- O8
39 47 40 41 1 180.00 43.93200 2 ; O9- C4- C10- O10
47 50 48 49 1 180.00 4.60240 2 ; C4- C6- C5- H5
[ moleculetype ]
; molname nrexcl
K+ 1
[ atoms ]
; id at type res nr residu name at name cg nr charge mass
1 K+ 1 K+ K+ 1 1 39.100
[ moleculetype ]
; molname nrexcl ; TIP3P model
WAT 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OW 1 WAT O 1 -0.834 16.00000
2 HW 1 WAT H1 1 0.417 1.00800
3 HW 1 WAT H2 1 0.417 1.00800
[ settles ]
; i j funct length
1 1 0.09572 0.15139
[ exclusions ]
1 2 3
2 1 3
3 1 2
[ system ]
CMP-NMIA in water
[ molecules ]
; Compound nmols
CMP-NMIA 1
K+ 1
WAT 9303