| blob | 07869cb85248ced8548669451473dfe6a92a5a8b |
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 -0.297 2
674 HB1 opls_140 0.060 2
675 HB2 opls_140 0.060 2
676 CG opls_508 -0.261 3
677 ND1 opls_503 -0.291 4
678 HD1 opls_504 0.326 4
679 CD2 opls_507 0.504 5
680 HD2 opls_146 0.183 5
681 CE1 opls_506 0.182 6
682 HE1 opls_146 0.098 6
683 NE2 opls_511 -0.564 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 [ HIS1 ] ; Identical to HISD
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 -0.297 2
725 HB1 opls_140 0.060 2
726 HB2 opls_140 0.060 2
727 CG opls_508 -0.261 3
728 ND1 opls_503 -0.291 4
729 HD1 opls_504 0.326 4
730 CD2 opls_507 0.504 5
731 HD2 opls_146 0.183 5
732 CE1 opls_506 0.182 6
733 HE1 opls_146 0.098 6
734 NE2 opls_511 -0.564 7
735 C opls_235 0.500 8
736 O opls_236 -0.500 8
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 HD1
749 ND1 CE1
750 CD2 HD2
751 CD2 NE2
752 CE1 HE1
753 CE1 NE2
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 ND1 CD2 CG CB improper_Z_CA_X_Y
764 CG CE1 ND1 HD1 improper_Z_N_X_Y
765 CG NE2 CD2 HD2 improper_Z_CA_X_Y
766 ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
769 [ HISE ]
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 -0.297 2
776 HB1 opls_140 0.060 2
777 HB2 opls_140 0.060 2
778 CG opls_507 0.504 3
779 ND1 opls_511 -0.564 3
780 CD2 opls_508 -0.261 4
781 HD2 opls_146 0.183 4
782 CE1 opls_506 0.182 5
783 HE1 opls_146 0.098 5
784 NE2 opls_503 -0.291 6
785 HE2 opls_504 0.326 6
786 C opls_235 0.500 7
787 O opls_236 -0.500 7
788 [ bonds ]
789 N H
790 N CA
791 CA HA
792 CA CB
793 CA C
794 CB HB1
795 CB HB2
796 CB CG
797 CG ND1
798 CG CD2
799 ND1 CE1
800 CD2 HD2
801 CD2 NE2
802 CE1 HE1
803 CE1 NE2
804 NE2 HE2
805 C O
806 -C N
807 [ dihedrals ] ; override some with residue-specific ones
808 N CA CB CG dih_HIS_chi1_N_C_C_C
809 CG CB CA C dih_HIS_chi1_C_C_C_CO
810 CA CB CG ND1 dih_HIS_chi2_C_C_C_N
811 [ impropers ]
812 -C CA N H improper_Z_N_X_Y
813 CA +N C O improper_O_C_X_Y
814 CE1 CD2 NE2 HE2 improper_Z_N_X_Y
815 CG NE2 CD2 HD2 improper_Z_CA_X_Y
816 ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
817 ND1 CD2 CG CB improper_Z_CA_X_Y
820 [ HISH ] ; also known as HISP (or HIS+)
821 [ atoms ]
822 N opls_238 -0.500 1
823 H opls_241 0.300 1
824 CA opls_224B 0.140 1
825 HA opls_140 0.060 1
826 CB opls_505 -0.005 2
827 HB1 opls_140 0.060 2
828 HB2 opls_140 0.060 2
829 CG opls_510 0.215 3
830 ND1 opls_512 -0.540 4
831 HD1 opls_513 0.460 4
832 CD2 opls_510 0.215 5
833 HD2 opls_146 0.115 5
834 CE1 opls_509 0.385 6
835 HE1 opls_146 0.115 6
836 NE2 opls_512 -0.540 7
837 HE2 opls_513 0.460 7
838 C opls_235 0.500 8
839 O opls_236 -0.500 8
840 [ bonds ]
841 N H
842 N CA
843 CA HA
844 CA CB
845 CA C
846 CB HB1
847 CB HB2
848 CB CG
849 CG ND1
850 CG CD2
851 ND1 HD1
852 ND1 CE1
853 CD2 HD2
854 CD2 NE2
855 CE1 HE1
856 CE1 NE2
857 NE2 HE2
858 C O
859 -C N
860 [ dihedrals ] ; override some with residue-specific ones
861 N CA CB CG dih_HIP_chi1_N_C_C_C
862 CG CB CA C dih_HIP_chi1_C_C_C_CO
863 [ impropers ]
864 -C CA N H improper_Z_N_X_Y
865 CA +N C O improper_O_C_X_Y
866 CG CE1 ND1 HD1 improper_Z_N_X_Y
867 CE1 CD2 NE2 HE2 improper_Z_N_X_Y
868 CG NE2 CD2 HD2 improper_Z_CA_X_Y
869 ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
870 ND1 CD2 CG CB improper_Z_CA_X_Y
873 [ HOH ]
874 ; We believe SPC has slightly better properties than TIP3P...
875 [ atoms ]
876 OW opls_116 -0.82 0
877 HW1 opls_117 0.41 0
878 HW2 opls_117 0.41 0
879 [ bonds ]
880 OW HW1
881 OW HW2
883 [ HO4 ]
884 ; TIP4P
885 [ atoms ]
886 OW opls_113 0.00 0
887 HW1 opls_114 0.52 0
888 HW2 opls_114 0.52 0
889 MW opls_115 -1.04 0
890 [ bonds ]
891 OW HW1
892 OW HW2
894 [ HO5 ]
895 ; TIP5P
896 [ atoms ]
897 OW opls_118 0.00 0
898 HW1 opls_119 0.248 0
899 HW2 opls_119 0.248 0
900 LP1 opls_120 -0.248 0
901 LP2 opls_120 -0.248 0
902 [ bonds ]
903 OW HW1
904 OW HW2
906 [ ILE ]
907 [ atoms ]
908 N opls_238 -0.500 1
909 H opls_241 0.300 1
910 CA opls_224B 0.140 1
911 HA opls_140 0.060 1
912 CB opls_137 -0.060 2
913 HB opls_140 0.060 2
914 CG1 opls_136 -0.120 3
915 HG11 opls_140 0.060 3
916 HG12 opls_140 0.060 3
917 CG2 opls_135 -0.180 4
918 HG21 opls_140 0.060 4
919 HG22 opls_140 0.060 4
920 HG23 opls_140 0.060 4
921 CD opls_135 -0.180 5
922 HD1 opls_140 0.060 5
923 HD2 opls_140 0.060 5
924 HD3 opls_140 0.060 5
925 C opls_235 0.500 6
926 O opls_236 -0.500 6
927 [ bonds ]
928 N H
929 N CA
930 CA HA
931 CA CB
932 CA C
933 CB HB
934 CB CG1
935 CB CG2
936 CG1 HG11
937 CG1 HG12
938 CG1 CD
939 CG2 HG21
940 CG2 HG22
941 CG2 HG23
942 CD HD1
943 CD HD2
944 CD HD3
945 C O
946 -C N
947 [ dihedrals ] ; override some with residue-specific ones
948 N CA CB CG1 dih_ILE_chi1_N_C_C_C
949 N CA CB CG2 dih_ILE_chi1_N_C_C_C
950 CG1 CB CA C dih_ILE_chi1_C_C_C_CO
951 CG2 CB CA C dih_ILE_chi1_C_C_C_CO
952 [ impropers ]
953 -C CA N H improper_Z_N_X_Y
954 CA +N C O improper_O_C_X_Y
956 [ LEU ]
957 [ atoms ]
958 N opls_238 -0.500 1
959 H opls_241 0.300 1
960 CA opls_224B 0.140 1
961 HA opls_140 0.060 1
962 CB opls_136 -0.120 2
963 HB1 opls_140 0.060 2
964 HB2 opls_140 0.060 2
965 CG opls_137 -0.060 3
966 HG opls_140 0.060 3
967 CD1 opls_135 -0.180 4
968 HD11 opls_140 0.060 4
969 HD12 opls_140 0.060 4
970 HD13 opls_140 0.060 4
971 CD2 opls_135 -0.180 5
972 HD21 opls_140 0.060 5
973 HD22 opls_140 0.060 5
974 HD23 opls_140 0.060 5
975 C opls_235 0.500 6
976 O opls_236 -0.500 6
977 [ bonds ]
978 N H
979 N CA
980 CA HA
981 CA CB
982 CA C
983 CB HB1
984 CB HB2
985 CB CG
986 CG HG
987 CG CD1
988 CG CD2
989 CD1 HD11
990 CD1 HD12
991 CD1 HD13
992 CD2 HD21
993 CD2 HD22
994 CD2 HD23
995 C O
996 -C N
997 [ dihedrals ] ; override some with residue-specific ones
998 N CA CB CG dih_LEU_chi1_N_C_C_C
999 CG CB CA C dih_LEU_chi1_C_C_C_CO
1000 [ impropers ]
1001 -C CA N H improper_Z_N_X_Y
1002 CA +N C O improper_O_C_X_Y
1004 [ LYS ]
1005 [ atoms ]
1006 N opls_238 -0.500 1
1007 H opls_241 0.300 1
1008 CA opls_224B 0.140 1
1009 HA opls_140 0.060 1
1010 CB opls_136 -0.120 2
1011 HB1 opls_140 0.060 2
1012 HB2 opls_140 0.060 2
1013 CG opls_136 -0.120 3
1014 HG1 opls_140 0.060 3
1015 HG2 opls_140 0.060 3
1016 CD opls_136 -0.120 4
1017 HD1 opls_140 0.060 4
1018 HD2 opls_140 0.060 4
1019 CE opls_906 0.060 5
1020 HE1 opls_911 0.060 5
1021 HE2 opls_911 0.060 5
1022 NZ opls_900 -0.900 6
1023 HZ1 opls_909 0.360 6
1024 HZ2 opls_909 0.360 6
1025 C opls_235 0.500 7
1026 O opls_236 -0.500 7
1027 [ bonds ]
1028 N H
1029 N CA
1030 CA HA
1031 CA CB
1032 CA C
1033 CB HB1
1034 CB HB2
1035 CB CG
1036 CG HG1
1037 CG HG2
1038 CG CD
1039 CD HD1
1040 CD HD2
1041 CD CE
1042 CE HE1
1043 CE HE2
1044 CE NZ
1045 NZ HZ1
1046 NZ HZ2
1047 C O
1048 -C N
1049 [ dihedrals ] ; override some with residue-specific ones
1050 N CA CB CG dih_LYS_chi1_N_C_C_C
1051 CG CB CA C dih_LYS_chi1_C_C_C_CO
1052 CD CE NZ HZ1 dih_LYS_chi5_C_C_N_H
1053 CD CE NZ HZ2 dih_LYS_chi5_C_C_N_H
1054 [ impropers ]
1055 -C CA N H improper_Z_N_X_Y
1056 CA +N C O improper_O_C_X_Y
1059 [ LYSH ]
1060 [ atoms ]
1061 N opls_238 -0.500 1
1062 H opls_241 0.300 1
1063 CA opls_224B 0.140 1
1064 HA opls_140 0.060 1
1065 CB opls_136 -0.120 2
1066 HB1 opls_140 0.060 2
1067 HB2 opls_140 0.060 2
1068 CG opls_136 -0.120 3
1069 HG1 opls_140 0.060 3
1070 HG2 opls_140 0.060 3
1071 CD opls_136 -0.120 4
1072 HD1 opls_140 0.060 4
1073 HD2 opls_140 0.060 4
1074 CE opls_292 0.190 5
1075 HE1 opls_140 0.060 5
1076 HE2 opls_140 0.060 5
1077 NZ opls_287 -0.300 6
1078 HZ1 opls_290 0.330 6
1079 HZ2 opls_290 0.330 6
1080 HZ3 opls_290 0.330 6
1081 C opls_235 0.500 7
1082 O opls_236 -0.500 7
1083 [ bonds ]
1084 N H
1085 N CA
1086 CA HA
1087 CA CB
1088 CA C
1089 CB HB1
1090 CB HB2
1091 CB CG
1092 CG HG1
1093 CG HG2
1094 CG CD
1095 CD HD1
1096 CD HD2
1097 CD CE
1098 CE HE1
1099 CE HE2
1100 CE NZ
1101 NZ HZ1
1102 NZ HZ2
1103 NZ HZ3
1104 C O
1105 -C N
1106 [ dihedrals ] ; override some with residue-specific ones
1107 N CA CB CG dih_LYS_chi1_N_C_C_C
1108 CG CB CA C dih_LYS_chi1_C_C_C_CO
1109 CD CE NZ HZ1 dih_LYS_chi5_C_C_N_H
1110 CD CE NZ HZ2 dih_LYS_chi5_C_C_N_H
1111 CD CE NZ HZ3 dih_LYS_chi5_C_C_N_H
1112 [ impropers ]
1113 -C CA N H improper_Z_N_X_Y
1114 CA +N C O improper_O_C_X_Y
1117 [ MET ]
1118 [ atoms ]
1119 N opls_238 -0.500 1
1120 H opls_241 0.300 1
1121 CA opls_224B 0.140 1
1122 HA opls_140 0.060 1
1123 CB opls_136 -0.120 2
1124 HB1 opls_140 0.060 2
1125 HB2 opls_140 0.060 2
1126 CG opls_210 0.048 3
1127 HG1 opls_140 0.060 3
1128 HG2 opls_140 0.060 3
1129 SD opls_202 -0.335 4
1130 CE opls_209 -0.013 5
1131 HE1 opls_140 0.060 5
1132 HE2 opls_140 0.060 5
1133 HE3 opls_140 0.060 5
1134 C opls_235 0.500 6
1135 O opls_236 -0.500 6
1136 [ bonds ]
1137 N H
1138 N CA
1139 CA HA
1140 CA CB
1141 CA C
1142 CB HB1
1143 CB HB2
1144 CB CG
1145 CG HG1
1146 CG HG2
1147 CG SD
1148 SD CE
1149 CE HE1
1150 CE HE2
1151 CE HE3
1152 C O
1153 -C N
1154 [ dihedrals ] ; override some with residue-specific ones
1155 N CA CB CG dih_MET_chi1_N_C_C_C
1156 CG CB CA C dih_MET_chi1_C_C_C_CO
1157 [ impropers ]
1158 -C CA N H improper_Z_N_X_Y
1159 CA +N C O improper_O_C_X_Y
1162 [ NAC ] ; metylamide, a.k.a NMA.
1163 [ atoms ]
1164 N opls_238 -0.500 1
1165 H opls_241 0.300 1
1166 CH3 opls_242 0.020 2
1167 HH31 opls_140 0.060 2
1168 HH32 opls_140 0.060 2
1169 HH33 opls_140 0.060 2
1170 [ bonds ]
1171 N H
1172 N CH3
1173 CH3 HH31
1174 CH3 HH32
1175 CH3 HH33
1176 -C N
1177 [ impropers ]
1178 -C CH3 N H improper_Z_N_X_Y
1181 [ NH2 ]
1182 [ atoms ]
1183 N opls_237 -0.760 1
1184 H1 opls_240 0.380 1
1185 H2 opls_240 0.380 1
1186 [ bonds ]
1187 -C N
1188 N H1
1189 N H2
1190 [ impropers ]
1191 -C H1 N H2 improper_Z_N_X_Y
1193 [ NHE ]
1194 ; same as NH2
1195 [ atoms ]
1196 N opls_237 -0.760 1
1197 H1 opls_240 0.380 1
1198 H2 opls_240 0.380 1
1199 [ bonds ]
1200 -C N
1201 N H1
1202 N H2
1203 [ impropers ]
1204 -C H1 N H2 improper_Z_N_X_Y
1206 [ PHE ]
1207 [ atoms ]
1208 N opls_238 -0.500 1
1209 H opls_241 0.300 1
1210 CA opls_224B 0.140 1
1211 HA opls_140 0.060 1
1212 CB opls_149 -0.005 2
1213 HB1 opls_140 0.060 2
1214 HB2 opls_140 0.060 2
1215 CG opls_145 -0.115 2
1216 CD1 opls_145 -0.115 3
1217 HD1 opls_146 0.115 3
1218 CD2 opls_145 -0.115 4
1219 HD2 opls_146 0.115 4
1220 CE1 opls_145 -0.115 5
1221 HE1 opls_146 0.115 5
1222 CE2 opls_145 -0.115 6
1223 HE2 opls_146 0.115 6
1224 CZ opls_145 -0.115 7
1225 HZ opls_146 0.115 7
1226 C opls_235 0.500 8
1227 O opls_236 -0.500 8
1228 [ bonds ]
1229 N H
1230 N CA
1231 CA HA
1232 CA CB
1233 CA C
1234 CB HB1
1235 CB HB2
1236 CB CG
1237 CG CD1
1238 CG CD2
1239 CD1 HD1
1240 CD1 CE1
1241 CD2 HD2
1242 CD2 CE2
1243 CE1 HE1
1244 CE1 CZ
1245 CE2 HE2
1246 CE2 CZ
1247 CZ HZ
1248 C O
1249 -C N
1250 [ impropers ]
1251 -C CA N H improper_Z_N_X_Y
1252 CA +N C O improper_O_C_X_Y
1253 CG CE2 CD2 HD2 improper_Z_CA_X_Y
1254 CD2 CZ CE2 HE2 improper_Z_CA_X_Y
1255 CE1 CE2 CZ HZ improper_Z_CA_X_Y
1256 CD1 CZ CE1 HE1 improper_Z_CA_X_Y
1257 CG CE1 CD1 HD1 improper_Z_CA_X_Y
1258 CD1 CD2 CG CB improper_Z_CA_X_Y
1261 [ PRO ]
1262 [ atoms ]
1263 N opls_239 -0.140 1
1264 CA opls_246 0.010 1
1265 HA opls_140 0.060 1
1266 CB opls_136 -0.120 2
1267 HB1 opls_140 0.060 2
1268 HB2 opls_140 0.060 2
1269 CG opls_136 -0.120 3
1270 HG1 opls_140 0.060 3
1271 HG2 opls_140 0.060 3
1272 CD opls_245 -0.050 4
1273 HD1 opls_140 0.060 4
1274 HD2 opls_140 0.060 4
1275 C opls_235 0.500 5
1276 O opls_236 -0.500 5
1277 [ bonds ]
1278 N CA
1279 CA HA
1280 CA CB
1281 CA C
1282 CB HB1
1283 CB HB2
1284 CB CG
1285 CG HG1
1286 CG HG2
1287 CG CD
1288 CD HD1
1289 CD HD2
1290 CD N
1291 C O
1292 -C N
1293 [ impropers ]
1294 -C CA N CD improper_Z_N_X_Y
1295 CA +N C O improper_O_C_X_Y
1298 [ SER ]
1299 [ atoms ]
1300 N opls_238 -0.500 1
1301 H opls_241 0.300 1
1302 CA opls_224B 0.140 1
1303 HA opls_140 0.060 1
1304 CB opls_157 0.145 2
1305 HB1 opls_140 0.060 2
1306 HB2 opls_140 0.060 2
1307 OG opls_154 -0.683 3
1308 HG opls_155 0.418 3
1309 C opls_235 0.500 4
1310 O opls_236 -0.500 4
1311 [ bonds ]
1312 N H
1313 N CA
1314 CA HA
1315 CA CB
1316 CA C
1317 CB HB1
1318 CB HB2
1319 CB OG
1320 OG HG
1321 C O
1322 -C N
1323 [ dihedrals ] ; override some of the typebased dihedrals
1324 N CA CB OG dih_SER_THR_chi1_N_C_C_O
1325 C CA CB OG dih_SER_THR_chi1_CO_C_C_O
1326 CA CB OG HG dih_SER_THR_chi2_C_C_OH_HO
1327 [ impropers ]
1328 -C CA N H improper_Z_N_X_Y
1329 CA +N C O improper_O_C_X_Y
1332 [ THR ]
1333 [ atoms ]
1334 N opls_238 -0.500 1
1335 H opls_241 0.300 1
1336 CA opls_224B 0.140 1
1337 HA opls_140 0.060 1
1338 CB opls_158 0.205 2
1339 HB opls_140 0.060 2
1340 OG1 opls_154 -0.683 2
1341 HG1 opls_155 0.418 2
1342 CG2 opls_135 -0.180 3
1343 HG21 opls_140 0.060 3
1344 HG22 opls_140 0.060 3
1345 HG23 opls_140 0.060 3
1346 C opls_235 0.500 4
1347 O opls_236 -0.500 4
1348 [ bonds ]
1349 N H
1350 N CA
1351 CA HA
1352 CA CB
1353 CA C
1354 CB HB
1355 CB OG1
1356 CB CG2
1357 OG1 HG1
1358 CG2 HG21
1359 CG2 HG22
1360 CG2 HG23
1361 C O
1362 -C N
1363 [ dihedrals ] ; override some of the typebased dihedrals
1364 N CA CB OG1 dih_SER_THR_chi1_N_C_C_O
1365 C CA CB OG1 dih_SER_THR_chi1_CO_C_C_O
1366 CA CB OG1 HG1 dih_SER_THR_chi2_C_C_OH_HO
1367 [ impropers ]
1368 -C CA N H improper_Z_N_X_Y
1369 CA +N C O improper_O_C_X_Y
1372 [ TRP ]
1373 [ atoms ]
1374 N opls_238 -0.500 1
1375 H opls_241 0.300 1
1376 CA opls_224B 0.140 1
1377 HA opls_140 0.060 1
1378 CB opls_136 -0.120 2
1379 HB1 opls_140 0.060 2
1380 HB2 opls_140 0.060 2
1381 CG opls_500 0.075 3
1382 CD1 opls_514 -0.115 4
1383 HD1 opls_146 0.115 4
1384 CD2 opls_501 -0.055 5
1385 NE1 opls_503 -0.570 6
1386 HE1 opls_504 0.420 6
1387 CE2 opls_502 0.130 6
1388 CE3 opls_145 -0.115 7
1389 HE3 opls_146 0.115 7
1390 CZ2 opls_145 -0.115 8
1391 HZ2 opls_146 0.115 8
1392 CZ3 opls_145 -0.115 9
1393 HZ3 opls_146 0.115 9
1394 CH2 opls_145 -0.115 10
1395 HH2 opls_146 0.115 10
1396 C opls_235 0.500 11
1397 O opls_236 -0.500 11
1398 [ bonds ]
1399 N H
1400 N CA
1401 CA HA
1402 CA CB
1403 CA C
1404 CB HB1
1405 CB HB2
1406 CB CG
1407 CG CD1
1408 CG CD2
1409 CD1 HD1
1410 CD1 NE1
1411 CD2 CE2
1412 CD2 CE3
1413 NE1 HE1
1414 NE1 CE2
1415 CE2 CZ2
1416 CE3 HE3
1417 CE3 CZ3
1418 CZ2 HZ2
1419 CZ2 CH2
1420 CZ3 HZ3
1421 CZ3 CH2
1422 CH2 HH2
1423 C O
1424 -C N
1425 [ dihedrals ] ; override some with residue-specific ones
1426 N CA CB CG dih_TRP_chi1_N_C_C_C
1427 CG CB CA C dih_TRP_chi1_C_C_C_CO
1428 [ impropers ]
1429 -C CA N H improper_Z_N_X_Y
1430 CA +N C O improper_O_C_X_Y
1431 CD1 CE2 NE1 HE1 improper_Z_N_X_Y
1432 CE2 CH2 CZ2 HZ2 improper_Z_CA_X_Y
1433 CZ2 CZ3 CH2 HH2 improper_Z_CA_X_Y
1434 CH2 CE3 CZ3 HZ3 improper_Z_CA_X_Y
1435 CZ3 CD2 CE3 HE3 improper_Z_CA_X_Y
1436 CG NE1 CD1 HD1 improper_Z_CA_X_Y
1437 CD1 CD2 CG CB improper_Z_CA_X_Y
1440 [ TYR ]
1441 [ atoms ]
1442 N opls_238 -0.500 1
1443 H opls_241 0.300 1
1444 CA opls_224B 0.140 1
1445 HA opls_140 0.060 1
1446 CB opls_149 -0.005 2
1447 HB1 opls_140 0.060 2
1448 HB2 opls_140 0.060 2
1449 CG opls_145 -0.115 2
1450 CD1 opls_145 -0.115 4
1451 HD1 opls_146 0.115 4
1452 CD2 opls_145 -0.115 5
1453 HD2 opls_146 0.115 5
1454 CE1 opls_145 -0.115 6
1455 HE1 opls_146 0.115 6
1456 CE2 opls_145 -0.115 7
1457 HE2 opls_146 0.115 7
1458 CZ opls_166 0.150 8
1459 OH opls_167 -0.585 8
1460 HH opls_168 0.435 8
1461 C opls_235 0.500 9
1462 O opls_236 -0.500 9
1463 [ bonds ]
1464 N H
1465 N CA
1466 CA HA
1467 CA CB
1468 CA C
1469 CB HB1
1470 CB HB2
1471 CB CG
1472 CG CD1
1473 CG CD2
1474 CD1 HD1
1475 CD1 CE1
1476 CD2 HD2
1477 CD2 CE2
1478 CE1 HE1
1479 CE1 CZ
1480 CE2 HE2
1481 CE2 CZ
1482 CZ OH
1483 OH HH
1484 C O
1485 -C N
1486 [ impropers ]
1487 -C CA N H improper_Z_N_X_Y
1488 CA +N C O improper_O_C_X_Y
1489 CG CE2 CD2 HD2 improper_Z_CA_X_Y
1490 CD2 CZ CE2 HE2 improper_Z_CA_X_Y
1491 CD1 CZ CE1 HE1 improper_Z_CA_X_Y
1492 CG CE1 CD1 HD1 improper_Z_CA_X_Y
1493 CD1 CD2 CG CB improper_Z_CA_X_Y
1494 CE1 CE2 CZ OH improper_Z_CA_X_Y
1497 [ VAL ]
1498 [ atoms ]
1499 N opls_238 -0.500 1
1500 H opls_241 0.300 1
1501 CA opls_224B 0.140 1
1502 HA opls_140 0.060 1
1503 CB opls_137 -0.060 2
1504 HB opls_140 0.060 2
1505 CG1 opls_135 -0.180 3
1506 HG11 opls_140 0.060 3
1507 HG12 opls_140 0.060 3
1508 HG13 opls_140 0.060 3
1509 CG2 opls_135 -0.180 4
1510 HG21 opls_140 0.060 4
1511 HG22 opls_140 0.060 4
1512 HG23 opls_140 0.060 4
1513 C opls_235 0.500 5
1514 O opls_236 -0.500 5
1515 [ bonds ]
1516 N H
1517 N CA
1518 CA HA
1519 CA CB
1520 CA C
1521 CB HB
1522 CB CG1
1523 CB CG2
1524 CG1 HG11
1525 CG1 HG12
1526 CG1 HG13
1527 CG2 HG21
1528 CG2 HG22
1529 CG2 HG23
1530 C O
1531 -C N
1532 [ dihedrals ] ; override some with residue-specific ones
1533 N CA CB CG1 dih_VAL_chi1_N_C_C_C
1534 N CA CB CG2 dih_VAL_chi1_N_C_C_C
1535 CG1 CB CA C dih_VAL_chi1_C_C_C_CO
1536 CG2 CB CA C dih_VAL_chi1_C_C_C_CO
1537 [ impropers ]
1538 -C CA N H improper_Z_N_X_Y
1539 CA +N C O improper_O_C_X_Y
1542 [ F ]
1543 [ atoms ]
1544 F opls_400 -1.000 0
1546 [ CL ]
1547 [ atoms ]
1548 CL opls_401 -1.000 0
1550 [ BR ]
1551 [ atoms ]
1552 BR opls_402 -1.000 0
1555 ; Aqvists cation parameters
1557 [ LI ]
1558 [ atoms ]
1559 LI opls_406 1.000 0 ; Jorgensen ion type would be opls_404
1561 [ NA ]
1562 [ atoms ]
1563 NA opls_407 1.000 0 ; Jorgensen ion type would be opls_405
1565 [ K ]
1566 [ atoms ]
1567 K opls_408 1.000 0
1569 [ RB ]
1570 [ atoms ]
1571 RB opls_409 1.000 0
1573 [ CS ]
1574 [ atoms ]
1575 CS opls_410 1.000 0
1577 [ MG ]
1578 [ atoms ]
1579 MG opls_411 2.000 0
1581 [ CA ]
1582 [ atoms ]
1583 CA opls_412 2.000 0
1585 [ SR ]
1586 [ atoms ]
1587 SR opls_413 2.000 0
1589 [ BA ]
1590 [ atoms ]
1591 BA opls_414 2.000 0
1594 ; Ethanol - CA is the carbon bound to the OH group
1595 [ EtOH ]
1596 [ atoms ]
1597 CB opls_135 -0.180 1
1598 HB1 opls_140 0.060 1
1599 HB2 opls_140 0.060 1
1600 HB3 opls_140 0.060 1
1601 CA opls_157 0.145 2
1602 HA1 opls_140 0.060 2
1603 HA2 opls_140 0.060 2
1604 OH opls_154 -0.683 2
1605 HO opls_155 0.418 2
1606 [ bonds ]
1607 CB HB1
1608 CB HB2
1609 CB HB3
1610 CB CA
1611 CA HA1
1612 CA HA2
1613 CA OH
1614 OH HO
1617 ; New All atom DMSO model, DvdS, 17/06/2006
1618 ; Use at your own risk!
1619 [ DMSO ]
1620 [ atoms ]
1621 OD opls_125 -0.459 1
1622 SD opls_124 0.139 1
1623 CD1 opls_139 -0.020 1
1624 HD11 opls_140 0.060 1
1625 HD12 opls_140 0.060 1
1626 HD13 opls_140 0.060 1
1627 CD2 opls_139 -0.020 1
1628 HD21 opls_140 0.060 1
1629 HD22 opls_140 0.060 1
1630 HD23 opls_140 0.060 1
1632 [ bonds ]
1633 OD SD
1634 SD CD1
1635 SD CD2
1636 CD1 HD11
1637 CD1 HD12
1638 CD1 HD13
1639 CD2 HD21
1640 CD2 HD22
1641 CD2 HD23