| blob | 36bcf15933eba4ae6ae60c6cfd22f706a30d94f1 |
1 ; New format introduced in Gromacs 3.1.4.
2 ; Dont use this forcefield with earlier versions.
4 ; This residue database includes new reparameterized sidechain dihedrals
5 ; from Kaminski et al (JPCB, 2001) that override the default atomtype-based
6 ; dihedrals. We use set 2 for SER and THR, set 2 for ASP, and the better
7 ; separate dihedrals for LEU and VAL instead of the combined ones, since we
8 ; can specify them here without using introducing extra atom types.
9 ; (That was the reason they were combined in the paper).
11 ; NB: OPLS chargegroups are not strictly neutral, since we mainly
12 ; use them to optimize the neighborsearching. For accurate simulations
13 ; you should use PME.
15 [ bondedtypes ]
16 ; Column 1 : default bondtype
17 ; Column 2 : default angletype
18 ; Column 3 : default proper dihedraltype
19 ; Column 4 : default improper dihedraltype
20 ; Column 5 : This controls the generation of dihedrals from the bonding.
21 ; All possible dihedrals are generated automatically. A value of
22 ; 1 here means that all these are retained. A value of
23 ; 0 here requires generated dihedrals be removed if
24 ; * there are any dihedrals on the same central atoms
25 ; specified in the residue topology, or
26 ; * there are other identical generated dihedrals
27 ; sharing the same central atoms, or
28 ; * there are other generated dihedrals sharing the
29 ; same central bond that have fewer hydrogen atoms
30 ; Column 6 : number of neighbors to exclude from non-bonded interactions
31 ; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
32 ; 0 = do not generate such
33 ; Column 8 : 1 = remove proper dihedrals if found centered on the same
34 ; bond as an improper dihedral
35 ; 0 = do not generate such
36 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
37 1 1 3 1 1 3 1 0
39 [ ACE ]
40 [ atoms ]
41 CH3 opls_135 -0.180 1
42 HH31 opls_140 0.060 1
43 HH32 opls_140 0.060 1
44 HH33 opls_140 0.060 1
45 C opls_235 0.500 2
46 O opls_236 -0.500 2
47 [ bonds ]
48 CH3 HH31
49 CH3 HH32
50 CH3 HH33
51 CH3 C
52 C O
53 [ impropers ]
54 CH3 +N C O improper_O_C_X_Y
56 [ ALA ]
57 [ atoms ]
58 N opls_238 -0.500 1
59 H opls_241 0.300 1
60 CA opls_224B 0.140 1
61 HA opls_140 0.060 1
62 CB opls_135 -0.180 2
63 HB1 opls_140 0.060 2
64 HB2 opls_140 0.060 2
65 HB3 opls_140 0.060 2
66 C opls_235 0.500 3
67 O opls_236 -0.500 3
68 [ bonds ]
69 N H
70 N CA
71 CA HA
72 CA CB
73 CA C
74 CB HB1
75 CB HB2
76 CB HB3
77 C O
78 -C N
79 [ impropers ]
80 -C CA N H improper_Z_N_X_Y
81 CA +N C O improper_O_C_X_Y
84 [ AIB ]
85 [ atoms ]
86 N opls_238 -0.500 1
87 H opls_241 0.300 1
88 CA opls_225B 0.200 1
89 CB1 opls_135 -0.180 2
90 HB11 opls_140 0.060 2
91 HB12 opls_140 0.060 2
92 HB13 opls_140 0.060 2
93 CB2 opls_135 -0.180 3
94 HB21 opls_140 0.060 3
95 HB22 opls_140 0.060 3
96 HB23 opls_140 0.060 3
97 C opls_235 0.500 4
98 O opls_236 -0.500 4
99 [ bonds ]
100 N H
101 N CA
102 CA CB1
103 CA CB2
104 CA C
105 CB1 HB11
106 CB1 HB12
107 CB1 HB13
108 CB2 HB21
109 CB2 HB22
110 CB2 HB23
111 C O
112 -C N
113 [ impropers ]
114 -C CA N H improper_Z_N_X_Y
115 CA +N C O improper_O_C_X_Y
118 [ ARG ]
119 [ atoms ]
120 N opls_238 -0.500 1
121 H opls_241 0.300 1
122 CA opls_224B 0.140 1
123 HA opls_140 0.060 1
124 CB opls_136 -0.120 2
125 HB1 opls_140 0.060 2
126 HB2 opls_140 0.060 2
127 CG opls_308 -0.050 3
128 HG1 opls_140 0.060 3
129 HG2 opls_140 0.060 3
130 CD opls_307 0.190 4
131 HD1 opls_140 0.060 4
132 HD2 opls_140 0.060 4
133 NE opls_303 -0.700 5
134 HE opls_304 0.440 5
135 CZ opls_302 0.640 5
136 NH1 opls_300 -0.800 6
137 HH11 opls_301 0.460 6
138 HH12 opls_301 0.460 6
139 NH2 opls_300 -0.800 7
140 HH21 opls_301 0.460 7
141 HH22 opls_301 0.460 7
142 C opls_235 0.500 8
143 O opls_236 -0.500 8
144 [ bonds ]
145 N H
146 N CA
147 CA HA
148 CA CB
149 CA C
150 CB HB1
151 CB HB2
152 CB CG
153 CG HG1
154 CG HG2
155 CG CD
156 CD HD1
157 CD HD2
158 CD NE
159 NE HE
160 NE CZ
161 CZ NH1
162 CZ NH2
163 NH1 HH11
164 NH1 HH12
165 NH2 HH21
166 NH2 HH22
167 C O
168 -C N
169 [ dihedrals ] ; override some with residue-specific ones
170 N CA CB CG dih_ARG_chi1_N_C_C_C
171 CG CB CA C dih_ARG_chi1_C_C_C_CO
172 [ impropers ]
173 -C CA N H improper_Z_N_X_Y
174 CA +N C O improper_O_C_X_Y
175 CD CZ NE HE improper_Z_N_X_Y
176 NE NH1 CZ NH2 improper_O_C_X_Y
177 CZ HH11 NH1 HH12 improper_Z_N_X_Y
178 CZ HH21 NH2 HH22 improper_Z_N_X_Y
180 [ ARGN ]
181 [ atoms ]
182 N opls_238 -0.500 1
183 H opls_241 0.300 1
184 CA opls_224B 0.140 1
185 HA opls_140 0.060 1
186 CB opls_136 -0.120 2
187 HB1 opls_140 0.060 2
188 HB2 opls_140 0.060 2
189 CG opls_308 -0.050 3
190 HG1 opls_140 0.060 3
191 HG2 opls_140 0.060 3
192 CD opls_748 0.040 4
193 HD1 opls_140 0.060 4
194 HD2 opls_140 0.060 4
195 NE opls_749 -0.620 5
196 HE opls_304 0.350 5; guessed charge
197 CZ opls_752 0.550 6
198 NH1 opls_750 -0.785 6
199 HH1 opls_301 0.340 6; guessed charge
200 NH2 opls_751 -0.785 7
201 HH21 opls_301 0.360 7; guessed charge
202 HH22 opls_301 0.360 7; guessed charge
203 C opls_235 0.500 8
204 O opls_236 -0.500 8
205 [ bonds ]
206 N H
207 N CA
208 CA HA
209 CA CB
210 CA C
211 CB HB1
212 CB HB2
213 CB CG
214 CG HG1
215 CG HG2
216 CG CD
217 CD HD1
218 CD HD2
219 CD NE
220 NE HE
221 NE CZ
222 CZ NH1
223 CZ NH2
224 NH1 HH1
225 NH2 HH21
226 NH2 HH22
227 C O
228 -C N
229 [ impropers ]
230 -C CA N H improper_Z_N_X_Y
231 CA +N C O improper_O_C_X_Y
232 CD CZ NE HE improper_Z_N_X_Y
233 NE NH1 CZ NH2 improper_O_C_X_Y
234 CZ HH21 NH2 HH22 improper_Z_N_X_Y
237 [ ASN ]
238 [ atoms ]
239 N opls_238 -0.500 0
240 H opls_241 0.300 0
241 CA opls_224B 0.140 1
242 HA opls_140 0.060 1
243 CB opls_136 -0.120 2
244 HB1 opls_140 0.060 2
245 HB2 opls_140 0.060 2
246 CG opls_235 0.500 3
247 OD1 opls_236 -0.500 3
248 ND2 opls_237 -0.760 4
249 HD21 opls_240 0.380 4
250 HD22 opls_240 0.380 4
251 C opls_235 0.500 5
252 O opls_236 -0.500 5
253 [ bonds ]
254 N H
255 N CA
256 CA HA
257 CA CB
258 CA C
259 CB HB1
260 CB HB2
261 CB CG
262 CG OD1
263 CG ND2
264 ND2 HD21
265 ND2 HD22
266 C O
267 -C N
268 [ dihedrals ] ; override some with residue-specific ones
269 N CA CB CG dih_ASN_chi1_N_C_C_C
270 CG CB CA C dih_ASN_chi1_C_C_C_CO
271 CA CB CG ND2 dih_ASN_chi2_C_C_CO_N
272 [ impropers ]
273 -C CA N H improper_Z_N_X_Y
274 CA +N C O improper_O_C_X_Y
275 CB ND2 CG OD1 improper_O_C_X_Y
276 CG HD21 ND2 HD22 improper_Z_N_X_Y
278 [ ASP ]
279 [ atoms ]
280 N opls_238 -0.500 1
281 H opls_241 0.300 1
282 CA opls_224B 0.140 1
283 HA opls_140 0.060 1
284 CB opls_274 -0.220 2
285 HB1 opls_140 0.060 2
286 HB2 opls_140 0.060 2
287 CG opls_271 0.700 3
288 OD1 opls_272 -0.800 3
289 OD2 opls_272 -0.800 3
290 C opls_235 0.500 4
291 O opls_236 -0.500 4
292 [ bonds ]
293 N H
294 N CA
295 CA HA
296 CA CB
297 CA C
298 CB HB1
299 CB HB2
300 CB CG
301 CG OD1
302 CG OD2
303 C O
304 -C N
305 [ dihedrals ] ; override some with residue-specific ones
306 N CA CB CG dih_ASP_chi1_N_C_C_C
307 CG CB CA C dih_ASP_chi1_C_C_C_CO
308 [ impropers ]
309 -C CA N H improper_Z_N_X_Y
310 CA +N C O improper_O_C_X_Y
311 CB OD1 CG OD2 improper_O_C_X_Y
313 [ ASPH ]
314 [ atoms ]
315 N opls_238 -0.500 0
316 H opls_241 0.300 0
317 CA opls_224B 0.140 1
318 HA opls_140 0.060 1
319 CB opls_136 -0.120 2
320 HB1 opls_140 0.060 2
321 HB2 opls_140 0.060 2
322 CG opls_267 0.520 3
323 OD1 opls_269 -0.440 3
324 OD2 opls_268 -0.530 4
325 HD2 opls_270 0.450 4
326 C opls_235 0.500 5
327 O opls_236 -0.500 5
328 [ bonds ]
329 N H
330 N CA
331 CA HA
332 CA CB
333 CA C
334 CB HB1
335 CB HB2
336 CB CG
337 CG OD1
338 CG OD2
339 OD2 HD2
340 C O
341 -C N
342 [ dihedrals ] ; override some with residue-specific ones
343 N CA CB CG dih_ASP_chi1_N_C_C_C
344 CG CB CA C dih_ASP_chi1_C_C_C_CO
345 CB CG OD2 HD2 dih_sidechain_COOH_C_C_O_H
346 OD1 CG OD2 HD2 dih_sidechain_COOH_O_C_O_H
347 [ impropers ]
348 -C CA N H improper_Z_N_X_Y
349 CA +N C O improper_O_C_X_Y
350 CB OD1 CG OD2 improper_O_C_X_Y
353 [ CYS2 ] ; aka CYX
354 [ atoms ]
355 N opls_238 -0.500 1
356 H opls_241 0.300 1
357 CA opls_224B 0.140 1
358 HA opls_140 0.060 1
359 CB opls_214 0.0975 2
360 HB1 opls_140 0.060 2
361 HB2 opls_140 0.060 2
362 SG opls_203 -0.2175 2
363 C opls_235 0.500 3
364 O opls_236 -0.500 3
365 [ bonds ]
366 N H
367 N CA
368 CA HA
369 CA CB
370 CA C
371 CB HB1
372 CB HB2
373 CB SG
374 C O
375 -C N
376 [ dihedrals ] ; override some of the typebased dihedrals
377 N CA CB SG dih_CYS_chi1_N_C_C_S
378 C CA CB SG dih_CYS_chi1_CO_C_C_S
379 [ impropers ]
380 -C CA N H improper_Z_N_X_Y
381 CA +N C O improper_O_C_X_Y
383 [ CYSH ]
384 [ atoms ]
385 N opls_238 -0.500 1
386 H opls_241 0.300 1
387 CA opls_224B 0.140 1
388 HA opls_140 0.060 1
389 CB opls_206 0.060 2
390 HB1 opls_140 0.060 2
391 HB2 opls_140 0.060 2
392 SG opls_200 -0.335 3
393 HG opls_204 0.155 3
394 C opls_235 0.500 4
395 O opls_236 -0.500 4
396 [ bonds ]
397 N H
398 N CA
399 CA HA
400 CA CB
401 CA C
402 CB HB1
403 CB HB2
404 CB SG
405 SG HG
406 C O
407 -C N
408 [ dihedrals ] ; override some of the typebased dihedrals
409 N CA CB SG dih_CYS_chi1_N_C_C_S
410 C CA CB SG dih_CYS_chi1_CO_C_C_S
411 [ impropers ]
412 -C CA N H improper_Z_N_X_Y
413 CA +N C O improper_O_C_X_Y
415 [ GLN ]
416 [ atoms ]
417 N opls_238 -0.500 0
418 H opls_241 0.300 0
419 CA opls_224B 0.140 1
420 HA opls_140 0.060 1
421 CB opls_136 -0.120 2
422 HB1 opls_140 0.060 2
423 HB2 opls_140 0.060 2
424 CG opls_136 -0.120 3
425 HG1 opls_140 0.060 3
426 HG2 opls_140 0.060 3
427 CD opls_235 0.500 4
428 OE1 opls_236 -0.500 4
429 NE2 opls_237 -0.760 5
430 HE21 opls_240 0.380 5
431 HE22 opls_240 0.380 5
432 C opls_235 0.500 6
433 O opls_236 -0.500 6
434 [ bonds ]
435 N H
436 N CA
437 CA HA
438 CA CB
439 CA C
440 CB HB1
441 CB HB2
442 CB CG
443 CG HG1
444 CG HG2
445 CG CD
446 CD OE1
447 CD NE2
448 NE2 HE21
449 NE2 HE22
450 C O
451 -C N
452 [ dihedrals ] ; override some of the typebased dihedrals
453 N CA CB CG dih_GLN_chi1_N_C_C_C
454 CG CB CA C dih_GLN_chi1_C_C_C_CO
455 CB CG CD NE2 dih_GLN_chi3_C_C_CO_N
456 [ impropers ]
457 -C CA N H improper_Z_N_X_Y
458 CA +N C O improper_O_C_X_Y
459 CG NE2 CD OE1 improper_O_C_X_Y
460 CD HE21 NE2 HE22 improper_Z_N_X_Y
462 ; Charged Glutamine
463 ; See. Patriksson et al. Int. J. Mass. Spectrom. 248 pp 124-135 (2006)
464 [ QLN ]
465 [ atoms ]
466 N opls_238 -0.500 0
467 H opls_241 0.300 0
468 CA opls_224B 0.140 1
469 HA opls_140 0.060 1
470 CB opls_136 -0.120 2
471 HB1 opls_140 0.060 2
472 HB2 opls_140 0.060 2
473 CG opls_136 0.054 3
474 HG1 opls_140 0.131 3
475 HG2 opls_140 0.131 3
476 CD opls_235 0.544 4
477 OE1 opls_154 -0.496 4
478 HE1 opls_155 0.498 4
479 NE2 opls_237 -0.720 5
480 HE21 opls_240 0.429 5
481 HE22 opls_240 0.429 5
482 C opls_235 0.500 6
483 O opls_236 -0.500 6
484 [ bonds ]
485 N H
486 N CA
487 CA HA
488 CA CB
489 CA C
490 CB HB1
491 CB HB2
492 CB CG
493 CG HG1
494 CG HG2
495 CG CD
496 CD OE1
497 OE1 HE1
498 CD NE2
499 NE2 HE21
500 NE2 HE22
501 C O
502 -C N
503 [ dihedrals ] ; override some of the typebased dihedrals
504 N CA CB CG dih_GLN_chi1_N_C_C_C
505 CG CB CA C dih_GLN_chi1_C_C_C_CO
506 CB CG CD NE2 dih_GLN_chi3_C_C_CO_N
507 CG CD OE1 HE1 dih_GLN_chi4_C_C_O_H
508 [ impropers ]
509 -C CA N H improper_Z_N_X_Y
510 CA +N C O improper_O_C_X_Y
511 CG NE2 CD OE1 improper_O_C_X_Y
512 CD HE21 NE2 HE22 improper_Z_N_X_Y
513 HE1 OE1 CD NE2 improper_O_C_X_Y
516 [ GLU ]
517 [ atoms ]
518 N opls_238 -0.500 1
519 H opls_241 0.300 1
520 CA opls_224B 0.140 1
521 HA opls_140 0.060 1
522 CB opls_136 -0.120 2
523 HB1 opls_140 0.060 2
524 HB2 opls_140 0.060 2
525 CG opls_274 -0.220 3
526 HG1 opls_140 0.060 3
527 HG2 opls_140 0.060 3
528 CD opls_271 0.700 4
529 OE1 opls_272 -0.800 4
530 OE2 opls_272 -0.800 4
531 C opls_235 0.500 5
532 O opls_236 -0.500 5
533 [ bonds ]
534 N H
535 N CA
536 CA HA
537 CA CB
538 CA C
539 CB HB1
540 CB HB2
541 CB CG
542 CG HG1
543 CG HG2
544 CG CD
545 CD OE1
546 CD OE2
547 C O
548 -C N
549 [ dihedrals ] ; override some with residue-specific ones
550 N CA CB CG dih_GLU_chi1_N_C_C_C
551 CG CB CA C dih_GLU_chi1_C_C_C_CO
552 [ impropers ]
553 -C CA N H improper_Z_N_X_Y
554 CA +N C O improper_O_C_X_Y
555 CG OE1 CD OE2 improper_O_C_X_Y
558 [ PGLU ]
559 [ atoms ]
560 N opls_238 -0.500 1
561 H opls_241 0.300 1
562 CA opls_224B 0.140 1
563 HA opls_140 0.060 1
564 CB opls_136 -0.120 2
565 HB1 opls_140 0.060 2
566 HB2 opls_140 0.060 2
567 CG opls_274 -0.120 3
568 HG1 opls_140 0.060 3
569 HG2 opls_140 0.060 3
570 CD opls_235 0.500 4
571 OE opls_236 -0.500 4
572 C opls_235 0.500 5
573 O opls_236 -0.500 5
574 [ bonds ]
575 N H
576 N CA
577 CA HA
578 CA CB
579 CA C
580 CB HB1
581 CB HB2
582 CB CG
583 CG HG1
584 CG HG2
585 CG CD
586 CD OE
587 CD N
588 C O
589 -C N
590 [ dihedrals ] ; override some with residue-specific ones
591 N CA CB CG dih_GLU_chi1_N_C_C_C
592 CG CB CA C dih_GLU_chi1_C_C_C_CO
593 [ impropers ]
594 -C CA N H improper_Z_N_X_Y
595 CA +N C O improper_O_C_X_Y
596 ; CG OE1 CD OE2 improper_O_C_X_Y
599 [ GLUH ]
600 [ atoms ]
601 N opls_238 -0.500 1
602 H opls_241 0.300 1
603 CA opls_224B 0.140 1
604 HA opls_140 0.060 1
605 CB opls_136 -0.120 2
606 HB1 opls_140 0.060 2
607 HB2 opls_140 0.060 2
608 CG opls_136 -0.120 3
609 HG1 opls_140 0.060 3
610 HG2 opls_140 0.060 3
611 CD opls_267 0.520 4
612 OE1 opls_269 -0.440 4
613 OE2 opls_268 -0.530 5
614 HE2 opls_270 0.450 5
615 C opls_235 0.500 6
616 O opls_236 -0.500 6
617 [ bonds ]
618 N H
619 N CA
620 CA HA
621 CA CB
622 CA C
623 CB HB1
624 CB HB2
625 CB CG
626 CG HG1
627 CG HG2
628 CG CD
629 CD OE1
630 CD OE2
631 OE2 HE2
632 C O
633 -C N
634 [ dihedrals ] ; override some with residue-specific ones
635 N CA CB CG dih_GLU_chi1_N_C_C_C
636 CG CB CA C dih_GLU_chi1_C_C_C_CO
637 CG CD OE2 HE2 dih_sidechain_COOH_C_C_O_H
638 OE1 CD OE2 HE2 dih_sidechain_COOH_O_C_O_H
639 [ impropers ]
640 -C CA N H improper_Z_N_X_Y
641 CA +N C O improper_O_C_X_Y
642 CG OE1 CD OE2 improper_O_C_X_Y
645 [ GLY ]
646 [ atoms ]
647 N opls_238 -0.500 1
648 H opls_241 0.300 1
649 CA opls_223B 0.080 1
650 HA1 opls_140 0.060 1
651 HA2 opls_140 0.060 1
652 C opls_235 0.500 2
653 O opls_236 -0.500 2
654 [ bonds ]
655 N H
656 N CA
657 CA HA1
658 CA HA2
659 CA C
660 C O
661 -C N
662 [ impropers ]
663 -C CA N H improper_Z_N_X_Y
664 CA +N C O improper_O_C_X_Y
667 [ HISD ]
668 [ atoms ]
669 N opls_238 -0.500 1
670 H opls_241 0.300 1
671 CA opls_224B 0.140 1
672 HA opls_140 0.060 1
673 CB opls_505 -0.005 2
674 HB1 opls_140 0.060 2
675 HB2 opls_140 0.060 2
676 CG opls_508 0.015 3
677 ND1 opls_503 -0.570 4
678 HD1 opls_504 0.420 4
679 CD2 opls_507 -0.015 5
680 HD2 opls_146 0.115 5
681 CE1 opls_506 0.295 6
682 HE1 opls_146 0.115 6
683 NE2 opls_511 -0.490 7
684 C opls_235 0.500 8
685 O opls_236 -0.500 8
686 [ bonds ]
687 N H
688 N CA
689 CA HA
690 CA CB
691 CA C
692 CB HB1
693 CB HB2
694 CB CG
695 CG ND1
696 CG CD2
697 ND1 HD1
698 ND1 CE1
699 CD2 HD2
700 CD2 NE2
701 CE1 HE1
702 CE1 NE2
703 C O
704 -C N
705 [ dihedrals ] ; override some with residue-specific ones
706 N CA CB CG dih_HIS_chi1_N_C_C_C
707 CG CB CA C dih_HIS_chi1_C_C_C_CO
708 CA CB CG ND1 dih_HIS_chi2_C_C_C_N
709 [ impropers ]
710 -C CA N H improper_Z_N_X_Y
711 CA +N C O improper_O_C_X_Y
712 ND1 CD2 CG CB improper_Z_CA_X_Y
713 CG CE1 ND1 HD1 improper_Z_N_X_Y
714 CG NE2 CD2 HD2 improper_Z_CA_X_Y
715 ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
718 [ HISE ]
719 [ atoms ]
720 N opls_238 -0.500 1
721 H opls_241 0.300 1
722 CA opls_224B 0.140 1
723 HA opls_140 0.060 1
724 CB opls_505 -0.005 2
725 HB1 opls_140 0.060 2
726 HB2 opls_140 0.060 2
727 CG opls_507 -0.015 3
728 ND1 opls_511 -0.490 3
729 CD2 opls_508 0.015 4
730 HD2 opls_146 0.115 4
731 CE1 opls_506 0.295 5
732 HE1 opls_146 0.115 5
733 NE2 opls_503 -0.570 6
734 HE2 opls_504 0.420 6
735 C opls_235 0.500 7
736 O opls_236 -0.500 7
737 [ bonds ]
738 N H
739 N CA
740 CA HA
741 CA CB
742 CA C
743 CB HB1
744 CB HB2
745 CB CG
746 CG ND1
747 CG CD2
748 ND1 CE1
749 CD2 HD2
750 CD2 NE2
751 CE1 HE1
752 CE1 NE2
753 NE2 HE2
754 C O
755 -C N
756 [ dihedrals ] ; override some with residue-specific ones
757 N CA CB CG dih_HIS_chi1_N_C_C_C
758 CG CB CA C dih_HIS_chi1_C_C_C_CO
759 CA CB CG ND1 dih_HIS_chi2_C_C_C_N
760 [ impropers ]
761 -C CA N H improper_Z_N_X_Y
762 CA +N C O improper_O_C_X_Y
763 CE1 CD2 NE2 HE2 improper_Z_N_X_Y
764 CG NE2 CD2 HD2 improper_Z_CA_X_Y
765 ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
766 ND1 CD2 CG CB improper_Z_CA_X_Y
769 [ HISH ] ; also known as HISP (or HIS+)
770 [ atoms ]
771 N opls_238 -0.500 1
772 H opls_241 0.300 1
773 CA opls_224B 0.140 1
774 HA opls_140 0.060 1
775 CB opls_505 -0.005 2
776 HB1 opls_140 0.060 2
777 HB2 opls_140 0.060 2
778 CG opls_510 0.215 3
779 ND1 opls_512 -0.540 4
780 HD1 opls_513 0.460 4
781 CD2 opls_510 0.215 5
782 HD2 opls_146 0.115 5
783 CE1 opls_509 0.385 6
784 HE1 opls_146 0.115 6
785 NE2 opls_512 -0.540 7
786 HE2 opls_513 0.460 7
787 C opls_235 0.500 8
788 O opls_236 -0.500 8
789 [ bonds ]
790 N H
791 N CA
792 CA HA
793 CA CB
794 CA C
795 CB HB1
796 CB HB2
797 CB CG
798 CG ND1
799 CG CD2
800 ND1 HD1
801 ND1 CE1
802 CD2 HD2
803 CD2 NE2
804 CE1 HE1
805 CE1 NE2
806 NE2 HE2
807 C O
808 -C N
809 [ dihedrals ] ; override some with residue-specific ones
810 N CA CB CG dih_HIP_chi1_N_C_C_C
811 CG CB CA C dih_HIP_chi1_C_C_C_CO
812 [ impropers ]
813 -C CA N H improper_Z_N_X_Y
814 CA +N C O improper_O_C_X_Y
815 CG CE1 ND1 HD1 improper_Z_N_X_Y
816 CE1 CD2 NE2 HE2 improper_Z_N_X_Y
817 CG NE2 CD2 HD2 improper_Z_CA_X_Y
818 ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
819 ND1 CD2 CG CB improper_Z_CA_X_Y
822 [ HOH ]
823 ; We believe SPC has slightly better properties than TIP3P...
824 [ atoms ]
825 OW opls_116 -0.82 0
826 HW1 opls_117 0.41 0
827 HW2 opls_117 0.41 0
828 [ bonds ]
829 OW HW1
830 OW HW2
832 [ HO4 ]
833 ; TIP4P
834 [ atoms ]
835 OW opls_113 0.00 0
836 HW1 opls_114 0.52 0
837 HW2 opls_114 0.52 0
838 MW opls_115 -1.04 0
839 [ bonds ]
840 OW HW1
841 OW HW2
843 [ HO5 ]
844 ; TIP5P
845 [ atoms ]
846 OW opls_118 0.00 0
847 HW1 opls_119 0.248 0
848 HW2 opls_119 0.248 0
849 LP1 opls_120 -0.248 0
850 LP2 opls_120 -0.248 0
851 [ bonds ]
852 OW HW1
853 OW HW2
855 [ ILE ]
856 [ atoms ]
857 N opls_238 -0.500 1
858 H opls_241 0.300 1
859 CA opls_224B 0.140 1
860 HA opls_140 0.060 1
861 CB opls_137 -0.060 2
862 HB opls_140 0.060 2
863 CG1 opls_136 -0.120 3
864 HG11 opls_140 0.060 3
865 HG12 opls_140 0.060 3
866 CG2 opls_135 -0.180 4
867 HG21 opls_140 0.060 4
868 HG22 opls_140 0.060 4
869 HG23 opls_140 0.060 4
870 CD opls_135 -0.180 5
871 HD1 opls_140 0.060 5
872 HD2 opls_140 0.060 5
873 HD3 opls_140 0.060 5
874 C opls_235 0.500 6
875 O opls_236 -0.500 6
876 [ bonds ]
877 N H
878 N CA
879 CA HA
880 CA CB
881 CA C
882 CB HB
883 CB CG1
884 CB CG2
885 CG1 HG11
886 CG1 HG12
887 CG1 CD
888 CG2 HG21
889 CG2 HG22
890 CG2 HG23
891 CD HD1
892 CD HD2
893 CD HD3
894 C O
895 -C N
896 [ dihedrals ] ; override some with residue-specific ones
897 N CA CB CG1 dih_ILE_chi1_N_C_C_C
898 N CA CB CG2 dih_ILE_chi1_N_C_C_C
899 CG1 CB CA C dih_ILE_chi1_C_C_C_CO
900 CG2 CB CA C dih_ILE_chi1_C_C_C_CO
901 [ impropers ]
902 -C CA N H improper_Z_N_X_Y
903 CA +N C O improper_O_C_X_Y
905 [ LEU ]
906 [ atoms ]
907 N opls_238 -0.500 1
908 H opls_241 0.300 1
909 CA opls_224B 0.140 1
910 HA opls_140 0.060 1
911 CB opls_136 -0.120 2
912 HB1 opls_140 0.060 2
913 HB2 opls_140 0.060 2
914 CG opls_137 -0.060 3
915 HG opls_140 0.060 3
916 CD1 opls_135 -0.180 4
917 HD11 opls_140 0.060 4
918 HD12 opls_140 0.060 4
919 HD13 opls_140 0.060 4
920 CD2 opls_135 -0.180 5
921 HD21 opls_140 0.060 5
922 HD22 opls_140 0.060 5
923 HD23 opls_140 0.060 5
924 C opls_235 0.500 6
925 O opls_236 -0.500 6
926 [ bonds ]
927 N H
928 N CA
929 CA HA
930 CA CB
931 CA C
932 CB HB1
933 CB HB2
934 CB CG
935 CG HG
936 CG CD1
937 CG CD2
938 CD1 HD11
939 CD1 HD12
940 CD1 HD13
941 CD2 HD21
942 CD2 HD22
943 CD2 HD23
944 C O
945 -C N
946 [ dihedrals ] ; override some with residue-specific ones
947 N CA CB CG dih_LEU_chi1_N_C_C_C
948 CG CB CA C dih_LEU_chi1_C_C_C_CO
949 [ impropers ]
950 -C CA N H improper_Z_N_X_Y
951 CA +N C O improper_O_C_X_Y
953 [ LYS ]
954 [ atoms ]
955 N opls_238 -0.500 1
956 H opls_241 0.300 1
957 CA opls_224B 0.140 1
958 HA opls_140 0.060 1
959 CB opls_136 -0.120 2
960 HB1 opls_140 0.060 2
961 HB2 opls_140 0.060 2
962 CG opls_136 -0.120 3
963 HG1 opls_140 0.060 3
964 HG2 opls_140 0.060 3
965 CD opls_136 -0.120 4
966 HD1 opls_140 0.060 4
967 HD2 opls_140 0.060 4
968 CE opls_906 0.060 5
969 HE1 opls_911 0.060 5
970 HE2 opls_911 0.060 5
971 NZ opls_900 -0.900 6
972 HZ1 opls_909 0.360 6
973 HZ2 opls_909 0.360 6
974 C opls_235 0.500 7
975 O opls_236 -0.500 7
976 [ bonds ]
977 N H
978 N CA
979 CA HA
980 CA CB
981 CA C
982 CB HB1
983 CB HB2
984 CB CG
985 CG HG1
986 CG HG2
987 CG CD
988 CD HD1
989 CD HD2
990 CD CE
991 CE HE1
992 CE HE2
993 CE NZ
994 NZ HZ1
995 NZ HZ2
996 C O
997 -C N
998 [ dihedrals ] ; override some with residue-specific ones
999 N CA CB CG dih_LYS_chi1_N_C_C_C
1000 CG CB CA C dih_LYS_chi1_C_C_C_CO
1001 CD CE NZ HZ1 dih_LYS_chi5_C_C_N_H
1002 CD CE NZ HZ2 dih_LYS_chi5_C_C_N_H
1003 [ impropers ]
1004 -C CA N H improper_Z_N_X_Y
1005 CA +N C O improper_O_C_X_Y
1008 [ LYSH ]
1009 [ atoms ]
1010 N opls_238 -0.500 1
1011 H opls_241 0.300 1
1012 CA opls_224B 0.140 1
1013 HA opls_140 0.060 1
1014 CB opls_136 -0.120 2
1015 HB1 opls_140 0.060 2
1016 HB2 opls_140 0.060 2
1017 CG opls_136 -0.120 3
1018 HG1 opls_140 0.060 3
1019 HG2 opls_140 0.060 3
1020 CD opls_136 -0.120 4
1021 HD1 opls_140 0.060 4
1022 HD2 opls_140 0.060 4
1023 CE opls_292 0.190 5
1024 HE1 opls_140 0.060 5
1025 HE2 opls_140 0.060 5
1026 NZ opls_287 -0.300 6
1027 HZ1 opls_290 0.330 6
1028 HZ2 opls_290 0.330 6
1029 HZ3 opls_290 0.330 6
1030 C opls_235 0.500 7
1031 O opls_236 -0.500 7
1032 [ bonds ]
1033 N H
1034 N CA
1035 CA HA
1036 CA CB
1037 CA C
1038 CB HB1
1039 CB HB2
1040 CB CG
1041 CG HG1
1042 CG HG2
1043 CG CD
1044 CD HD1
1045 CD HD2
1046 CD CE
1047 CE HE1
1048 CE HE2
1049 CE NZ
1050 NZ HZ1
1051 NZ HZ2
1052 NZ HZ3
1053 C O
1054 -C N
1055 [ dihedrals ] ; override some with residue-specific ones
1056 N CA CB CG dih_LYS_chi1_N_C_C_C
1057 CG CB CA C dih_LYS_chi1_C_C_C_CO
1058 CD CE NZ HZ1 dih_LYS_chi5_C_C_N_H
1059 CD CE NZ HZ2 dih_LYS_chi5_C_C_N_H
1060 CD CE NZ HZ3 dih_LYS_chi5_C_C_N_H
1061 [ impropers ]
1062 -C CA N H improper_Z_N_X_Y
1063 CA +N C O improper_O_C_X_Y
1066 [ MET ]
1067 [ atoms ]
1068 N opls_238 -0.500 1
1069 H opls_241 0.300 1
1070 CA opls_224B 0.140 1
1071 HA opls_140 0.060 1
1072 CB opls_136 -0.120 2
1073 HB1 opls_140 0.060 2
1074 HB2 opls_140 0.060 2
1075 CG opls_210 0.048 3
1076 HG1 opls_140 0.060 3
1077 HG2 opls_140 0.060 3
1078 SD opls_202 -0.335 4
1079 CE opls_209 -0.013 5
1080 HE1 opls_140 0.060 5
1081 HE2 opls_140 0.060 5
1082 HE3 opls_140 0.060 5
1083 C opls_235 0.500 6
1084 O opls_236 -0.500 6
1085 [ bonds ]
1086 N H
1087 N CA
1088 CA HA
1089 CA CB
1090 CA C
1091 CB HB1
1092 CB HB2
1093 CB CG
1094 CG HG1
1095 CG HG2
1096 CG SD
1097 SD CE
1098 CE HE1
1099 CE HE2
1100 CE HE3
1101 C O
1102 -C N
1103 [ dihedrals ] ; override some with residue-specific ones
1104 N CA CB CG dih_MET_chi1_N_C_C_C
1105 CG CB CA C dih_MET_chi1_C_C_C_CO
1106 [ impropers ]
1107 -C CA N H improper_Z_N_X_Y
1108 CA +N C O improper_O_C_X_Y
1111 [ NAC ] ; metylamide, a.k.a NMA.
1112 [ atoms ]
1113 N opls_238 -0.500 1
1114 H opls_241 0.300 1
1115 CH3 opls_242 0.020 2
1116 HH31 opls_140 0.060 2
1117 HH32 opls_140 0.060 2
1118 HH33 opls_140 0.060 2
1119 [ bonds ]
1120 N H
1121 N CH3
1122 CH3 HH31
1123 CH3 HH32
1124 CH3 HH33
1125 -C N
1126 [ impropers ]
1127 -C CH3 N H improper_Z_N_X_Y
1130 [ NH2 ]
1131 [ atoms ]
1132 N opls_237 -0.760 1
1133 H1 opls_240 0.380 1
1134 H2 opls_240 0.380 1
1135 [ bonds ]
1136 -C N
1137 N H1
1138 N H2
1139 [ impropers ]
1140 -C H1 N H2 improper_Z_N_X_Y
1142 [ NHE ]
1143 ; same as NH2
1144 [ atoms ]
1145 N opls_237 -0.760 1
1146 H1 opls_240 0.380 1
1147 H2 opls_240 0.380 1
1148 [ bonds ]
1149 -C N
1150 N H1
1151 N H2
1152 [ impropers ]
1153 -C H1 N H2 improper_Z_N_X_Y
1155 [ PHE ]
1156 [ atoms ]
1157 N opls_238 -0.500 1
1158 H opls_241 0.300 1
1159 CA opls_224B 0.140 1
1160 HA opls_140 0.060 1
1161 CB opls_149 -0.005 2
1162 HB1 opls_140 0.060 2
1163 HB2 opls_140 0.060 2
1164 CG opls_145 -0.115 2
1165 CD1 opls_145 -0.115 3
1166 HD1 opls_146 0.115 3
1167 CD2 opls_145 -0.115 4
1168 HD2 opls_146 0.115 4
1169 CE1 opls_145 -0.115 5
1170 HE1 opls_146 0.115 5
1171 CE2 opls_145 -0.115 6
1172 HE2 opls_146 0.115 6
1173 CZ opls_145 -0.115 7
1174 HZ opls_146 0.115 7
1175 C opls_235 0.500 8
1176 O opls_236 -0.500 8
1177 [ bonds ]
1178 N H
1179 N CA
1180 CA HA
1181 CA CB
1182 CA C
1183 CB HB1
1184 CB HB2
1185 CB CG
1186 CG CD1
1187 CG CD2
1188 CD1 HD1
1189 CD1 CE1
1190 CD2 HD2
1191 CD2 CE2
1192 CE1 HE1
1193 CE1 CZ
1194 CE2 HE2
1195 CE2 CZ
1196 CZ HZ
1197 C O
1198 -C N
1199 [ impropers ]
1200 -C CA N H improper_Z_N_X_Y
1201 CA +N C O improper_O_C_X_Y
1202 CG CE2 CD2 HD2 improper_Z_CA_X_Y
1203 CD2 CZ CE2 HE2 improper_Z_CA_X_Y
1204 CE1 CE2 CZ HZ improper_Z_CA_X_Y
1205 CD1 CZ CE1 HE1 improper_Z_CA_X_Y
1206 CG CE1 CD1 HD1 improper_Z_CA_X_Y
1207 CD1 CD2 CG CB improper_Z_CA_X_Y
1210 [ PRO ]
1211 [ atoms ]
1212 N opls_239 -0.140 1
1213 CA opls_246 0.010 1
1214 HA opls_140 0.060 1
1215 CB opls_136 -0.120 2
1216 HB1 opls_140 0.060 2
1217 HB2 opls_140 0.060 2
1218 CG opls_136 -0.120 3
1219 HG1 opls_140 0.060 3
1220 HG2 opls_140 0.060 3
1221 CD opls_245 -0.050 4
1222 HD1 opls_140 0.060 4
1223 HD2 opls_140 0.060 4
1224 C opls_235 0.500 5
1225 O opls_236 -0.500 5
1226 [ bonds ]
1227 N CA
1228 CA HA
1229 CA CB
1230 CA C
1231 CB HB1
1232 CB HB2
1233 CB CG
1234 CG HG1
1235 CG HG2
1236 CG CD
1237 CD HD1
1238 CD HD2
1239 CD N
1240 C O
1241 -C N
1242 [ impropers ]
1243 -C CA N CD improper_Z_N_X_Y
1244 CA +N C O improper_O_C_X_Y
1247 [ SER ]
1248 [ atoms ]
1249 N opls_238 -0.500 1
1250 H opls_241 0.300 1
1251 CA opls_224B 0.140 1
1252 HA opls_140 0.060 1
1253 CB opls_157 0.145 2
1254 HB1 opls_140 0.060 2
1255 HB2 opls_140 0.060 2
1256 OG opls_154 -0.683 3
1257 HG opls_155 0.418 3
1258 C opls_235 0.500 4
1259 O opls_236 -0.500 4
1260 [ bonds ]
1261 N H
1262 N CA
1263 CA HA
1264 CA CB
1265 CA C
1266 CB HB1
1267 CB HB2
1268 CB OG
1269 OG HG
1270 C O
1271 -C N
1272 [ dihedrals ] ; override some of the typebased dihedrals
1273 N CA CB OG dih_SER_THR_chi1_N_C_C_O
1274 C CA CB OG dih_SER_THR_chi1_CO_C_C_O
1275 CA CB OG HG dih_SER_THR_chi2_C_C_OH_HO
1276 [ impropers ]
1277 -C CA N H improper_Z_N_X_Y
1278 CA +N C O improper_O_C_X_Y
1281 [ THR ]
1282 [ atoms ]
1283 N opls_238 -0.500 1
1284 H opls_241 0.300 1
1285 CA opls_224B 0.140 1
1286 HA opls_140 0.060 1
1287 CB opls_158 0.205 2
1288 HB opls_140 0.060 2
1289 OG1 opls_154 -0.683 2
1290 HG1 opls_155 0.418 2
1291 CG2 opls_135 -0.180 3
1292 HG21 opls_140 0.060 3
1293 HG22 opls_140 0.060 3
1294 HG23 opls_140 0.060 3
1295 C opls_235 0.500 4
1296 O opls_236 -0.500 4
1297 [ bonds ]
1298 N H
1299 N CA
1300 CA HA
1301 CA CB
1302 CA C
1303 CB HB
1304 CB OG1
1305 CB CG2
1306 OG1 HG1
1307 CG2 HG21
1308 CG2 HG22
1309 CG2 HG23
1310 C O
1311 -C N
1312 [ dihedrals ] ; override some of the typebased dihedrals
1313 N CA CB OG1 dih_SER_THR_chi1_N_C_C_O
1314 C CA CB OG1 dih_SER_THR_chi1_CO_C_C_O
1315 CA CB OG1 HG1 dih_SER_THR_chi2_C_C_OH_HO
1316 [ impropers ]
1317 -C CA N H improper_Z_N_X_Y
1318 CA +N C O improper_O_C_X_Y
1321 [ TRP ]
1322 [ atoms ]
1323 N opls_238 -0.500 1
1324 H opls_241 0.300 1
1325 CA opls_224B 0.140 1
1326 HA opls_140 0.060 1
1327 CB opls_136 -0.120 2
1328 HB1 opls_140 0.060 2
1329 HB2 opls_140 0.060 2
1330 CG opls_500 0.075 3
1331 CD1 opls_514 -0.115 4
1332 HD1 opls_146 0.115 4
1333 CD2 opls_501 -0.055 5
1334 NE1 opls_503 -0.570 6
1335 HE1 opls_504 0.420 6
1336 CE2 opls_502 0.130 6
1337 CE3 opls_145 -0.115 7
1338 HE3 opls_146 0.115 7
1339 CZ2 opls_145 -0.115 8
1340 HZ2 opls_146 0.115 8
1341 CZ3 opls_145 -0.115 9
1342 HZ3 opls_146 0.115 9
1343 CH2 opls_145 -0.115 10
1344 HH2 opls_146 0.115 10
1345 C opls_235 0.500 11
1346 O opls_236 -0.500 11
1347 [ bonds ]
1348 N H
1349 N CA
1350 CA HA
1351 CA CB
1352 CA C
1353 CB HB1
1354 CB HB2
1355 CB CG
1356 CG CD1
1357 CG CD2
1358 CD1 HD1
1359 CD1 NE1
1360 CD2 CE2
1361 CD2 CE3
1362 NE1 HE1
1363 NE1 CE2
1364 CE2 CZ2
1365 CE3 HE3
1366 CE3 CZ3
1367 CZ2 HZ2
1368 CZ2 CH2
1369 CZ3 HZ3
1370 CZ3 CH2
1371 CH2 HH2
1372 C O
1373 -C N
1374 [ dihedrals ] ; override some with residue-specific ones
1375 N CA CB CG dih_TRP_chi1_N_C_C_C
1376 CG CB CA C dih_TRP_chi1_C_C_C_CO
1377 [ impropers ]
1378 -C CA N H improper_Z_N_X_Y
1379 CA +N C O improper_O_C_X_Y
1380 CD1 CE2 NE1 HE1 improper_Z_N_X_Y
1381 CE2 CH2 CZ2 HZ2 improper_Z_CA_X_Y
1382 CZ2 CZ3 CH2 HH2 improper_Z_CA_X_Y
1383 CH2 CE3 CZ3 HZ3 improper_Z_CA_X_Y
1384 CZ3 CD2 CE3 HE3 improper_Z_CA_X_Y
1385 CG NE1 CD1 HD1 improper_Z_CA_X_Y
1386 CD1 CD2 CG CB improper_Z_CA_X_Y
1389 [ TYR ]
1390 [ atoms ]
1391 N opls_238 -0.500 1
1392 H opls_241 0.300 1
1393 CA opls_224B 0.140 1
1394 HA opls_140 0.060 1
1395 CB opls_149 -0.005 2
1396 HB1 opls_140 0.060 2
1397 HB2 opls_140 0.060 2
1398 CG opls_145 -0.115 2
1399 CD1 opls_145 -0.115 4
1400 HD1 opls_146 0.115 4
1401 CD2 opls_145 -0.115 5
1402 HD2 opls_146 0.115 5
1403 CE1 opls_145 -0.115 6
1404 HE1 opls_146 0.115 6
1405 CE2 opls_145 -0.115 7
1406 HE2 opls_146 0.115 7
1407 CZ opls_166 0.150 8
1408 OH opls_167 -0.585 8
1409 HH opls_168 0.435 8
1410 C opls_235 0.500 9
1411 O opls_236 -0.500 9
1412 [ bonds ]
1413 N H
1414 N CA
1415 CA HA
1416 CA CB
1417 CA C
1418 CB HB1
1419 CB HB2
1420 CB CG
1421 CG CD1
1422 CG CD2
1423 CD1 HD1
1424 CD1 CE1
1425 CD2 HD2
1426 CD2 CE2
1427 CE1 HE1
1428 CE1 CZ
1429 CE2 HE2
1430 CE2 CZ
1431 CZ OH
1432 OH HH
1433 C O
1434 -C N
1435 [ impropers ]
1436 -C CA N H improper_Z_N_X_Y
1437 CA +N C O improper_O_C_X_Y
1438 CG CE2 CD2 HD2 improper_Z_CA_X_Y
1439 CD2 CZ CE2 HE2 improper_Z_CA_X_Y
1440 CD1 CZ CE1 HE1 improper_Z_CA_X_Y
1441 CG CE1 CD1 HD1 improper_Z_CA_X_Y
1442 CD1 CD2 CG CB improper_Z_CA_X_Y
1443 CE1 CE2 CZ OH improper_Z_CA_X_Y
1446 [ VAL ]
1447 [ atoms ]
1448 N opls_238 -0.500 1
1449 H opls_241 0.300 1
1450 CA opls_224B 0.140 1
1451 HA opls_140 0.060 1
1452 CB opls_137 -0.060 2
1453 HB opls_140 0.060 2
1454 CG1 opls_135 -0.180 3
1455 HG11 opls_140 0.060 3
1456 HG12 opls_140 0.060 3
1457 HG13 opls_140 0.060 3
1458 CG2 opls_135 -0.180 4
1459 HG21 opls_140 0.060 4
1460 HG22 opls_140 0.060 4
1461 HG23 opls_140 0.060 4
1462 C opls_235 0.500 5
1463 O opls_236 -0.500 5
1464 [ bonds ]
1465 N H
1466 N CA
1467 CA HA
1468 CA CB
1469 CA C
1470 CB HB
1471 CB CG1
1472 CB CG2
1473 CG1 HG11
1474 CG1 HG12
1475 CG1 HG13
1476 CG2 HG21
1477 CG2 HG22
1478 CG2 HG23
1479 C O
1480 -C N
1481 [ dihedrals ] ; override some with residue-specific ones
1482 N CA CB CG1 dih_VAL_chi1_N_C_C_C
1483 N CA CB CG2 dih_VAL_chi1_N_C_C_C
1484 CG1 CB CA C dih_VAL_chi1_C_C_C_CO
1485 CG2 CB CA C dih_VAL_chi1_C_C_C_CO
1486 [ impropers ]
1487 -C CA N H improper_Z_N_X_Y
1488 CA +N C O improper_O_C_X_Y
1491 [ F ]
1492 [ atoms ]
1493 F opls_400 -1.000 0
1495 [ CL ]
1496 [ atoms ]
1497 CL opls_401 -1.000 0
1499 [ BR ]
1500 [ atoms ]
1501 BR opls_402 -1.000 0
1504 ; Aqvists cation parameters
1506 [ LI ]
1507 [ atoms ]
1508 LI opls_406 1.000 0 ; Jorgensen ion type would be opls_404
1510 [ NA ]
1511 [ atoms ]
1512 NA opls_407 1.000 0 ; Jorgensen ion type would be opls_405
1514 [ K ]
1515 [ atoms ]
1516 K opls_408 1.000 0
1518 [ RB ]
1519 [ atoms ]
1520 RB opls_409 1.000 0
1522 [ CS ]
1523 [ atoms ]
1524 CS opls_410 1.000 0
1526 [ MG ]
1527 [ atoms ]
1528 MG opls_411 2.000 0
1530 [ CA ]
1531 [ atoms ]
1532 CA opls_412 2.000 0
1534 [ SR ]
1535 [ atoms ]
1536 SR opls_413 2.000 0
1538 [ BA ]
1539 [ atoms ]
1540 BA opls_414 2.000 0
1543 ; Ethanol - CA is the carbon bound to the OH group
1544 [ EtOH ]
1545 [ atoms ]
1546 CB opls_135 -0.180 1
1547 HB1 opls_140 0.060 1
1548 HB2 opls_140 0.060 1
1549 HB3 opls_140 0.060 1
1550 CA opls_157 0.145 2
1551 HA1 opls_140 0.060 2
1552 HA2 opls_140 0.060 2
1553 OH opls_154 -0.683 2
1554 HO opls_155 0.418 2
1555 [ bonds ]
1556 CB HB1
1557 CB HB2
1558 CB HB3
1559 CB CA
1560 CA HA1
1561 CA HA2
1562 CA OH
1563 OH HO
1566 ; New All atom DMSO model, DvdS, 17/06/2006
1567 ; Use at your own risk!
1568 [ DMSO ]
1569 [ atoms ]
1570 OD opls_125 -0.459 1
1571 SD opls_124 0.139 1
1572 CD1 opls_139 -0.020 1
1573 HD11 opls_140 0.060 1
1574 HD12 opls_140 0.060 1
1575 HD13 opls_140 0.060 1
1576 CD2 opls_139 -0.020 1
1577 HD21 opls_140 0.060 1
1578 HD22 opls_140 0.060 1
1579 HD23 opls_140 0.060 1
1581 [ bonds ]
1582 OD SD
1583 SD CD1
1584 SD CD2
1585 CD1 HD11
1586 CD1 HD12
1587 CD1 HD13
1588 CD2 HD21
1589 CD2 HD22
1590 CD2 HD23