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1 ; Table 2.5.2.1
2 ; GROMOS bond-stretching parameters
3 ;
4 ;
5 ; Bond type code
6 ; Force constant
7 ; Ideal bond length
8 ; Examples of usage in terms of non-bonded atom types
9 ;
10 ;
11 ; ICB(H)[N] CB[N] B0[N]
12 ;
13 #define gb_1 0.1000 1.5700e+07
14 ; H - OA 750
15 ;
16 #define gb_2 0.1000 1.8700e+07
17 ; H - N (all) 895
18 ;
19 #define gb_3 0.1090 1.2300e+07
20 ; HC - C 700
21 ;
22 #define gb_4 0.1230 1.6600e+07
23 ; C - O 1200
24 ;
25 #define gb_5 0.1250 1.3400e+07
26 ; C - OM 1000
27 ;
28 #define gb_6 0.1320 1.2000e+07
29 ; CR1 - NR (6-ring) 1000
30 ;
31 #define gb_7 0.1330 8.8700e+06
32 ; H - S 750
33 ;
34 #define gb_8 0.1330 1.0600e+07
35 ; C - NT, NL 900
36 ;
37 #define gb_9 0.1330 1.1800e+07
38 ; C, CR1 - N, NR, CR1, C (peptide, 5-ring) 1000
39 ;
40 #define gb_10 0.1340 1.0500e+07
41 ; C - N, NZ, NE 900
42 ;
43 #define gb_11 0.1340 1.1700e+07
44 ; C - NR (no H) (6-ring) 1000
45 ;
46 #define gb_12 0.1360 1.0200e+07
47 ; C - OA 900
48 ;
49 #define gb_13 0.1380 1.1000e+07
50 ; C - NR (heme) 1000
51 ;
52 #define gb_14 0.1390 8.6600e+06
53 ; CH2 - C, CR1 (6-ring) 800
54 ;
55 #define gb_15 0.1390 1.0800e+07
56 ; C, CR1 - CH2, C, CR1 (6-ring) 1000
57 ;
58 #define gb_16 0.1400 8.5400e+06
59 ; C, CR1, CH2 - NR (6-ring) 800
60 ;
61 #define gb_17 0.1430 8.1800e+06
62 ; CHn - OA 800
63 ;
64 #define gb_18 0.1430 9.2100e+06
65 ; CHn - OM 900
66 ;
67 #define gb_19 0.1435 6.1000e+06
68 ; CHn - OA (sugar) 600
69 ;
70 #define gb_20 0.1470 8.7100e+06
71 ; CHn - N, NT, NL, NZ, NE 900
72 ;
73 #define gb_21 0.1480 5.7300e+06
74 ; CHn - NR (5-ring) 600
75 ;
76 #define gb_22 0.1480 7.6400e+06
77 ; CHn - NR (6-ring) 800
78 ;
79 #define gb_23 0.1480 8.6000e+06
80 ; O, OM - P 900
81 ;
82 #define gb_24 0.1500 8.3700e+06
83 ; O - S 900
84 ;
85 #define gb_25 0.1520 5.4300e+06
86 ; CHn - CHn (sugar) 600
87 ;
88 #define gb_26 0.1530 7.1500e+06
89 ; C, CHn - C, CHn 800
90 ;
91 #define gb_27 0.1610 4.8400e+06
92 ; OA - P 600
93 ;
94 #define gb_28 0.1630 4.7200e+06
95 ; OA - SI 600
96 ;
97 #define gb_29 0.1780 5.9400e+06
98 ; CH3 - S 900
99 ;
100 #define gb_30 0.1830 5.6200e+06
101 ; CH2 - S 900
102 ;
103 #define gb_31 0.1870 3.5900e+06
104 ; CH1 - SI 600
105 ;
106 #define gb_32 0.1980 0.6400e+06
107 ; NR - FE 120
108 ;
109 #define gb_33 0.2040 5.0300e+06
110 ; S - S 1000
111 ;
112 #define gb_34 0.2000 0.6280e+06
113 ; NR (heme) - FE 120
114 ;
115 #define gb_35 0.1000 2.3200e+07
116 ; HWat - OWat 1110
117 ;
118 #define gb_36 0.1100 1.2100e+07
119 ; HChl - CChl 700
120 ;
121 #define gb_37 0.1758 8.1200e+06
122 ; CChl - CLChl 1200
123 ;
124 #define gb_38 0.1530 8.0400e+06
125 ; ODmso - SDmso 900
126 ;
127 #define gb_39 0.1950 4.9500e+06
128 ; SDmso - CDmso 900
129 ;
130 #define gb_40 0.1760 8.1000e+06
131 ; CCl4 - CLCl4 1200
132 ;
133 #define gb_41 0.163299 8.7100e+06
134 ; HWat - HWat 1110
135 ;
136 #define gb_42 0.233839 2.6800e+06
137 ; HChl - CLChl 700
138 ;
139 #define gb_43 0.290283 2.9800e+06
140 ; CLChl - CLChl 1200
141 ;
142 #define gb_44 0.280412 2.3900e+06
143 ; ODmso - CDmso 900
144 ;
145 #define gb_45 0.292993 2.1900e+06
146 ; CDmso - CDmso 900
147 ;
148 #define gb_46 0.198842 3.9700e+06
149 ; HMet - CMet 750
150 ;
151 #define gb_47 0.287407 3.0400e+06
152 ; CLCl4 - CLCl4 1200
153 ;
154 ;---
155 ; Table 2.5.3.1.
156 ; GROMOS bond-angle bending parameters
157 ;
158 ;
159 ; Bond-angle type code
160 ; Force constant
161 ; Ideal bond angle
162 ; Example of usage in terms of non-bonded atom types
163 ;
164 ;
165 ; ICT(H)[N] CT[N] (T0[N])
166 ;
167 #define ga_1 90.00 420.00
168 ; NR(heme) - FE - NR(heme) 100
169 ;
170 #define ga_2 96.00 405.00
171 ; H - S - CH2 95
172 ;
173 #define ga_3 100.00 475.00
174 ; CH2 - S - CH3 110
175 ;
176 #define ga_4 103.00 420.00
177 ; OA - P - OA 95
178 ;
179 #define ga_5 104.00 490.00
180 ; CH2 - S - S 110
181 ;
182 #define ga_6 108.00 465.00
183 ; NR, C, CR1(5-ring) 100
184 ;
185 #define ga_7 109.50 285.00
186 ; CHn - CHn - CHn, NR(6-ring) (sugar) 60
187 ;
188 #define ga_8 109.50 320.00
189 ; CHn, OA - CHn - OA, NR(ring) (sugar) 68
190 ;
191 #define ga_9 109.50 380.00
192 ; H - NL, NT - H, CHn - OA - CHn(sugar) 80
193 ;
194 #define ga_10 109.50 425.00
195 ; H - NL - C, CHn H - NT - CHn 90
196 ;
197 #define ga_11 109.50 450.00
198 ; X - OA, SI - X 95
199 ;
200 #define ga_12 109.50 520.00
201 ; CHn,C - CHn - C, CHn, OA, OM, N, NE 110
202 ;
203 #define ga_13 109.60 450.00
204 ; OM - P - OA 95
205 ;
206 #define ga_14 111.00 530.00
207 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
208 ;
209 #define ga_15 113.00 545.00
210 ; CHn - CH2 - S 110
211 ;
212 #define ga_16 115.00 50.00
213 ; NR(heme) - FE - NR 10
214 ;
215 #define ga_17 115.00 460.00
216 ; H - N - CHn 90
217 ;
218 #define ga_18 115.00 610.00
219 ; CHn, C - C - OA, N, NT, NL 120
220 ;
221 #define ga_19 116.00 465.00
222 ; H - NE - CH2 90
223 ;
224 #define ga_20 116.00 620.00
225 ; CH2 - N - CH1 120
226 ;
227 #define ga_21 117.00 635.00
228 ; CH3 - N - C, CHn - C - OM 120
229 ;
230 #define ga_22 120.00 390.00
231 ; H - NT, NZ, NE - C 70
232 ;
233 #define ga_23 120.00 445.00
234 ; H - NT, NZ - H 80
235 ;
236 #define ga_24 120.00 505.00
237 ; H - N - CH3, H, HC - 6-ring, H - NT - CHn 90
238 ;
239 #define ga_25 120.00 530.00
240 ; P, SI - OA - CHn, P 95
241 ;
242 #define ga_26 120.00 560.00
243 ; N, C, CR1 (6-ring, no H) 100
244 ;
245 #define ga_27 120.00 670.00
246 ; NZ - C - NZ, NE 120
247 ;
248 #define ga_28 120.00 780.00
249 ; OM - P - OM 140
250 ;
251 #define ga_29 121.00 685.00
252 ; O - C - CHn, C CH3 - N - CHn 120
253 ;
254 #define ga_30 122.00 700.00
255 ; CH1, CH2 - N - C 120
256 ;
257 #define ga_31 123.00 415.00
258 ; H - N - C 70
259 ;
260 #define ga_32 124.00 730.00
261 ; O - C - OA, N, NT, NL C - NE - CH2 120
262 ;
263 #define ga_33 125.00 375.00
264 ; FE - NR - CR1 (5-ring) 60
265 ;
266 #define ga_34 125.00 750.00
267 ; - 120
268 ;
269 #define ga_35 126.00 575.00
270 ; H, HC - 5-ring 90
271 ;
272 #define ga_36 126.00 640.00
273 ; X(noH) - 5-ring 100
274 ;
275 #define ga_37 126.00 770.00
276 ; OM - C - OM 120
277 ;
278 #define ga_38 132.00 760.00
279 ; 5, 6 ring connnection 100
280 ;
281 #define ga_39 155.00 2215.00
282 ; SI - OA - SI 95
283 ;
284 #define ga_40 109.50 434.00
285 ; HWat - OWat - HWat 92
286 ;
287 #define ga_41 107.57 484.00
288 ; HChl - CChl - CLChl 105
289 ;
290 #define ga_42 111.30 632.00
291 ; CLChl - CChl - CLChl 131
292 ;
293 #define ga_43 97.40 469.00
294 ; CDmso - SDmso - CDmso 110
295 ;
296 #define ga_44 106.75 503.00
297 ; CDmso - SDmso - ODmso 110
298 ;
299 #define ga_45 108.53 443.00
300 ; HMet - OMet - CMet 95
301 ;
302 #define ga_46 109.50 618.00
303 ; CLCl4 - CCl4 - CLCl4 131
304 ;
305 ; Table 2.5.4.1
306 ; GROMOS improper (harmonic) dihedral angle parameters
307 ;
308 ;
309 ; Improper dihedral-angle type code
310 ; Force constant
311 ; Ideal improper dihedral angle
312 ; Example of usage
313 ;
314 ;
315 ; ICQ(H)[N] CQ[N] (Q0[N])
316 ;
317 #define gi_1 0.0 167.42309
318 ; planar groups 40
319 ;
320 #define gi_2 35.26439 334.84617
321 ; tetrahedral centres 80
322 ;
323 #define gi_3 0.0 669.69235
324 ; heme iron 160
325 ;
326 ; Table 2.5.5.1
327 ; GROMOS (trigonometric) dihedral torsional angle parameters
328 ;
329 ;
330 ; Dihedral-angle type code
331 ; Force constant
332 ; Phase shift
333 ; Multiplicity
334 ; Example of usage in terms of non-bonded atom types
335 ;
336 ;
337 ; ICP(H)[N] CP[N] PD[N] NP[N]
338 ;
339 #define gd_1 180.000 5.86 2
340 ; -C-C- 1.4
341 ;
342 #define gd_2 180.000 7.11 2
343 ; -C-OA- (at ring) 1.7
344 ;
345 #define gd_3 180.000 16.7 2
346 ; -C-OA- (carboxyl) 4.0
347 ;
348 #define gd_4 180.000 33.5 2
349 ; -C-N, NT, NE, NZ,NR- 8.0
350 ;
351 #define gd_5 180.000 41.8 2
352 ; -C-CR1- (6-ring) 10.0
353 ;
354 #define gd_6 0.000 0.0 2
355 ; -CH1 (sugar)-NR(base)- 0.0
356 ;
357 #define gd_7 0.000 0.418 2
358 ; O-CH1-CHn-no O 0.1
359 ;
360 #define gd_8 0.000 2.09 2
361 ; O-CH1-CHn-O 0.5
362 ;
363 #define gd_9 0.000 3.14 2
364 ; -OA-P- 0.75
365 ;
366 #define gd_10 0.000 16.7 2
367 ; -S-S- 4.0
368 ;
369 #define gd_11 0.000 1.05 3
370 ; -OA-P- 0.25
371 ;
372 #define gd_12 0.000 1.26 3
373 ; -CHn-OA(no sugar)- 0.3
374 ;
375 #define gd_13 0.000 2.93 3
376 ; -CH2-S- 0.7
377 ;
378 #define gd_14 0.000 3.77 3
379 ; -C,CHn,SI-NT,NL,OA(sugar)- 0.9
380 ;
381 #define gd_15 0.000 4.18 3
382 ; HC-C-S- 1.0
383 ;
384 #define gd_16 0.000 5.44 3
385 ; HC-C-C- 1.3
386 ;
387 #define gd_17 0.000 5.92 3 ;ref 1 et 43A2
388 ; -CHn,SI-CHn- 1.4
389 ;
390 #define gd_18 0.000 0.0 4
391 ; -NR-FE- 0.0
392 ;
393 #define gd_19 180.000 1.0 6
394 ; -CHn-N,NE- 0.24
395 ;
396 #define gd_20 0.000 1.0 6
397 ; -CHn-C,NR (ring), CR1- 0.24
398 ;
399 #define gd_21 0.000 3.77 6
400 ; -CHn-NT- 0.9
401 ;
403 ; get the constraint distances for dummy atom constructions
404 #include "ff_dum.itp"
406 [ constrainttypes ]
407 ; now the constraints for the rigid NH3 groups
408 MNH3 C 2 DC_MNC1
409 MNH3 CH1 2 DC_MNC2
410 MNH3 CH2 2 DC_MNC2
411 MNH3 MNH3 2 DC_MNMN
412 ; and the angle-constraints for OH and SH groups in proteins:
413 CH2 H 2 DC_CO
414 CH1 H 2 DC_CO
415 C H 2 DC_CO
416 P H 2 DC_PO
418 ; bond-, angle- and dihedraltypes for specbonds:
419 [ bondtypes ]
420 S S 2 gb_33
421 NR FE 2 gb_32
422 ; cystine - heme link (is CR1-S, use CH2-S):
423 S CR1 2 gb_30
425 [ angletypes ]
426 CH1 CH2 S 2 ga_15
427 CH2 S S 2 ga_5
428 CR1 NR FE 2 ga_33
429 NR FE NR 2 ga_16
430 ; cystine - heme link (is CH2-S-CR1, use CH2-S-CH2):
431 CH2 S CR1 2 ga_3
432 ; cystine - heme link (is S-CR1-C/CH2, use CHn-CH2-S):
433 S CR1 C 2 ga_15
434 S CR1 CH2 2 ga_15
436 [ dihedraltypes ]
437 S S 1 gd_10
438 NR FE 1 gd_18
439 CH2 S 1 gd_13
440 ; cystine - heme link (is CH2-S-CR1-C, use -CH2-S-):
441 CR1 S 1 gd_13