| blob | d24ef05e5173956f03aa56c6cba390f58c9a9345 |
1 [ bondedtypes ]
2 ; Column 1 : default bondtype
3 ; Column 2 : default angletype
4 ; Column 3 : default proper dihedraltype
5 ; Column 4 : default improper dihedraltype
6 ; Column 5 : This controls the generation of dihedrals from the bonding.
7 ; All possible dihedrals are generated automatically. A value of
8 ; 1 here means that all these are retained. A value of
9 ; 0 here requires generated dihedrals be removed if
10 ; * there are any dihedrals on the same central atoms
11 ; specified in the residue topology, or
12 ; * there are other identical generated dihedrals
13 ; sharing the same central atoms, or
14 ; * there are other generated dihedrals sharing the
15 ; same central bond that have fewer hydrogen atoms
16 ; Column 6 : number of neighbors to exclude from non-bonded interactions
17 ; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
18 ; 0 = do not generate such
19 ; Column 8 : 1 = remove proper dihedrals if found centered on the same
20 ; bond as an improper dihedral
21 ; 0 = do not generate such
22 ; bondtype angletype dihedraltype impropertype all_dih nrexcl HH14 bRemoveDih
23 1 5 9 2 1 3 1 0
25 [ ALA ]
26 [ atoms ]
27 N NH1 -0.47 0
28 HN H 0.31 1
29 CA CT1 0.07 2
30 HA HB 0.09 3
31 CB CT3 -0.27 4
32 HB1 HA 0.09 5
33 HB2 HA 0.09 6
34 HB3 HA 0.09 7
35 C C 0.51 8
36 O O -0.51 9
37 [ bonds ]
38 CB CA
39 N HN
40 N CA
41 C CA
42 C +N
43 CA HA
44 CB HB1
45 CB HB2
46 CB HB3
47 O C
48 [ impropers ]
49 N -C CA HN
50 C CA +N O
51 [ cmap ]
52 -C N CA C +N
54 [ ARG ]
55 [ atoms ]
56 N NH1 -0.47 0
57 HN H 0.31 1
58 CA CT1 0.07 2
59 HA HB 0.09 3
60 CB CT2 -0.18 4
61 HB1 HA 0.09 5
62 HB2 HA 0.09 6
63 CG CT2 -0.18 7
64 HG1 HA 0.09 8
65 HG2 HA 0.09 9
66 CD CT2 0.20 10
67 HD1 HA 0.09 11
68 HD2 HA 0.09 12
69 NE NC2 -0.70 13
70 HE HC 0.44 14
71 CZ C 0.64 15
72 NH1 NC2 -0.80 16
73 HH11 HC 0.46 17
74 HH12 HC 0.46 18
75 NH2 NC2 -0.80 19
76 HH21 HC 0.46 20
77 HH22 HC 0.46 21
78 C C 0.51 22
79 O O -0.51 23
80 [ bonds ]
81 CB CA
82 CG CB
83 CD CG
84 NE CD
85 CZ NE
86 NH2 CZ
87 N HN
88 N CA
89 C CA
90 C +N
91 CA HA
92 CB HB1
93 CB HB2
94 CG HG1
95 CG HG2
96 CD HD1
97 CD HD2
98 NE HE
99 NH1 HH11
100 NH1 HH12
101 NH2 HH21
102 NH2 HH22
103 O C
104 CZ NH1
105 [ impropers ]
106 N -C CA HN
107 C CA +N O
108 CZ NH1 NH2 NE
109 [ cmap ]
110 -C N CA C +N
112 [ ASN ]
113 [ atoms ]
114 N NH1 -0.47 0
115 HN H 0.31 1
116 CA CT1 0.07 2
117 HA HB 0.09 3
118 CB CT2 -0.18 4
119 HB1 HA 0.09 5
120 HB2 HA 0.09 6
121 CG CC 0.55 7
122 OD1 O -0.55 8
123 ND2 NH2 -0.62 9
124 HD21 H 0.32 10
125 HD22 H 0.30 11
126 C C 0.51 12
127 O O -0.51 13
128 [ bonds ]
129 CB CA
130 CG CB
131 ND2 CG
132 N HN
133 N CA
134 C CA
135 C +N
136 CA HA
137 CB HB1
138 CB HB2
139 ND2 HD21
140 ND2 HD22
141 C O
142 CG OD1
143 [ impropers ]
144 N -C CA HN
145 C CA +N O
146 CG ND2 CB OD1
147 CG CB ND2 OD1
148 ND2 CG HD21 HD22
149 ND2 CG HD22 HD21
150 [ cmap ]
151 -C N CA C +N
153 [ ASP ]
154 [ atoms ]
155 N NH1 -0.47 0
156 HN H 0.31 1
157 CA CT1 0.07 2
158 HA HB 0.09 3
159 CB CT2 -0.28 4
160 HB1 HA 0.09 5
161 HB2 HA 0.09 6
162 CG CC 0.62 7
163 OD1 OC -0.76 8
164 OD2 OC -0.76 9
165 C C 0.51 10
166 O O -0.51 11
167 [ bonds ]
168 CB CA
169 CG CB
170 OD2 CG
171 N HN
172 N CA
173 C CA
174 C +N
175 CA HA
176 CB HB1
177 CB HB2
178 O C
179 CG OD1
180 [ impropers ]
181 N -C CA HN
182 C CA +N O
183 CG CB OD2 OD1
184 [ cmap ]
185 -C N CA C +N
187 [ ASPP ] ; protonated ASP
188 [ atoms ]
189 N NH1 -0.47 0
190 HN H 0.31 1
191 CA CT1 0.07 2
192 HA HB 0.09 3
193 CB CT2 -0.21 4 ;
194 HB1 HA 0.09 5 ; HB1 OD1
195 HB2 HA 0.09 6 ; | //
196 CG CD 0.75 7 ; -CB--CG
197 OD1 OB -0.55 8 ; | \
198 OD2 OH1 -0.61 9 ; HB2 OD2-HD2
199 HD2 H 0.44 10;
200 C C 0.51 11
201 O O -0.51 12
202 [ bonds ]
203 CB CA
204 CG CB
205 OD2 CG
206 OD2 HD2
207 N HN
208 N CA
209 C CA
210 C +N
211 CA HA
212 CB HB1
213 CB HB2
214 O C
215 CG OD1
216 [ impropers ]
217 N -C CA HN
218 C CA +N O
219 CG CB OD2 OD1
220 [ cmap ]
221 -C N CA C +N
223 [ CYS ]
224 [ atoms ]
225 N NH1 -0.47 0
226 HN H 0.31 1
227 CA CT1 0.07 2
228 HA HB 0.09 3
229 CB CT2 -0.11 4
230 HB1 HA 0.09 5
231 HB2 HA 0.09 6
232 SG S -0.23 7
233 HG1 HS 0.16 8
234 C C 0.51 9
235 O O -0.51 10
236 [ bonds ]
237 CB CA
238 SG CB
239 N HN
240 N CA
241 C CA
242 C +N
243 CA HA
244 CB HB1
245 CB HB2
246 SG HG1
247 O C
248 [ impropers ]
249 N -C CA HN
250 C CA +N O
251 [ cmap ]
252 -C N CA C +N
254 [ CYS2 ] ; disulfide cystine
255 [ atoms ]
256 N NH1 -0.47 0
257 HN H 0.31 1
258 CA CT1 0.07 2
259 HA HB 0.09 3
260 CB CT2 -0.10 4
261 HB1 HA 0.09 5
262 HB2 HA 0.09 6
263 SG SM -0.08 7
264 C C 0.51 8
265 O O -0.51 9
266 [ bonds ]
267 CB CA
268 SG CB
269 N HN
270 N CA
271 C CA
272 C +N
273 CA HA
274 CB HB1
275 CB HB2
276 O C
277 [ impropers ]
278 N -C CA HN
279 C CA +N O
280 [ cmap ]
281 -C N CA C +N
283 [ GLN ]
284 [ atoms ]
285 N NH1 -0.47 0
286 HN H 0.31 1
287 CA CT1 0.07 2
288 HA HB 0.09 3
289 CB CT2 -0.18 4
290 HB1 HA 0.09 5
291 HB2 HA 0.09 6
292 CG CT2 -0.18 7
293 HG1 HA 0.09 8
294 HG2 HA 0.09 9
295 CD CC 0.55 10
296 OE1 O -0.55 11
297 NE2 NH2 -0.62 12
298 HE21 H 0.32 13
299 HE22 H 0.30 14
300 C C 0.51 15
301 O O -0.51 16
302 [ bonds ]
303 CB CA
304 CG CB
305 CD CG
306 NE2 CD
307 N HN
308 N CA
309 C CA
310 C +N
311 CA HA
312 CB HB1
313 CB HB2
314 CG HG1
315 CG HG2
316 NE2 HE21
317 NE2 HE22
318 O C
319 CD OE1
320 [ impropers ]
321 N -C CA HN
322 C CA +N O
323 CD NE2 CG OE1
324 CD CG NE2 OE1
325 NE2 CD HE21 HE22
326 NE2 CD HE22 HE21
327 [ cmap ]
328 -C N CA C +N
330 [ GLU ]
331 [ atoms ]
332 N NH1 -0.47 0
333 HN H 0.31 1
334 CA CT1 0.07 2
335 HA HB 0.09 3
336 CB CT2 -0.18 4
337 HB1 HA 0.09 5
338 HB2 HA 0.09 6
339 CG CT2 -0.28 7
340 HG1 HA 0.09 8
341 HG2 HA 0.09 9
342 CD CC 0.62 10
343 OE1 OC -0.76 11
344 OE2 OC -0.76 12
345 C C 0.51 13
346 O O -0.51 14
347 [ bonds ]
348 CB CA
349 CG CB
350 CD CG
351 OE2 CD
352 N HN
353 N CA
354 C CA
355 C +N
356 CA HA
357 CB HB1
358 CB HB2
359 CG HG1
360 CG HG2
361 O C
362 CD OE1
363 [ impropers ]
364 N -C CA HN
365 C CA +N O
366 CD CG OE2 OE1
367 [ cmap ]
368 -C N CA C +N
370 [ GLUP ] ; protonated GLU
371 [ atoms ]
372 N NH1 -0.47 0
373 HN H 0.31 1
374 CA CT1 0.07 2
375 HA HB 0.09 3
376 CB CT2 -0.18 4
377 HB1 HA 0.09 5
378 HB2 HA 0.09 6
379 CG CT2 -0.21 7 ;
380 HG1 HA 0.09 8 ; HG1 OE1
381 HG2 HA 0.09 9 ; | //
382 CD CD 0.75 10; -CG--CD
383 OE1 OB -0.55 11; | \
384 OE2 OH1 -0.61 12; HG2 OE2-HE2
385 HE2 H 0.44 13;
386 C C 0.51 14
387 O O -0.51 15
388 [ bonds ]
389 CB CA
390 CG CB
391 CD CG
392 OE2 CD
393 OE2 HE2
394 N HN
395 N CA
396 C CA
397 C +N
398 CA HA
399 CB HB1
400 CB HB2
401 CG HG1
402 CG HG2
403 O C
404 CD OE1
405 [ impropers ]
406 N -C CA HN
407 C CA +N O
408 CD CG OE2 OE1
409 [ cmap ]
410 -C N CA C +N
412 [ GLY ]
413 [ atoms ]
414 N NH1 -0.47 0
415 HN H 0.31 1
416 CA CT2 -0.02 2
417 HA1 HB 0.09 3
418 HA2 HB 0.09 4
419 C C 0.51 5
420 O O -0.51 6
421 [ bonds ]
422 N HN
423 N CA
424 C CA
425 C +N
426 CA HA1
427 CA HA2
428 O C
429 [ impropers ]
430 N -C CA HN
431 C CA +N O
432 [ cmap ]
433 -C N CA C +N
435 [ HSD ]
436 [ atoms ]
437 N NH1 -0.47 0
438 HN H 0.31 1
439 CA CT1 0.07 2
440 HA HB 0.09 3
441 CB CT2 -0.09 4
442 HB1 HA 0.09 5
443 HB2 HA 0.09 6
444 ND1 NR1 -0.36 7
445 HD1 H 0.32 8
446 CG CPH1 -0.05 9
447 CE1 CPH2 0.25 10
448 HE1 HR1 0.13 11
449 NE2 NR2 -0.70 12
450 CD2 CPH1 0.22 13
451 HD2 HR3 0.10 14
452 C C 0.51 15
453 O O -0.51 16
454 [ bonds ]
455 CB CA
456 CG CB
457 ND1 CG
458 CE1 ND1
459 NE2 CD2
460 N HN
461 N CA
462 C CA
463 C +N
464 CA HA
465 CB HB1
466 CB HB2
467 ND1 HD1
468 CD2 HD2
469 CE1 HE1
470 O C
471 CG CD2
472 CE1 NE2
473 [ impropers ]
474 ND1 CG CE1 HD1
475 CD2 CG NE2 HD2
476 CE1 ND1 NE2 HE1
477 ND1 CE1 CG HD1
478 CD2 NE2 CG HD2
479 CE1 NE2 ND1 HE1
480 N -C CA HN
481 C CA +N O
482 [ cmap ]
483 -C N CA C +N
485 [ HSE ]
486 [ atoms ]
487 N NH1 -0.47 0
488 HN H 0.31 1
489 CA CT1 0.07 2
490 HA HB 0.09 3
491 CB CT2 -0.08 4
492 HB1 HA 0.09 5
493 HB2 HA 0.09 6
494 ND1 NR2 -0.70 7
495 CG CPH1 0.22 8
496 CE1 CPH2 0.25 9
497 HE1 HR1 0.13 10
498 NE2 NR1 -0.36 11
499 HE2 H 0.32 12
500 CD2 CPH1 -0.05 13
501 HD2 HR3 0.09 14
502 C C 0.51 15
503 O O -0.51 16
504 [ bonds ]
505 CB CA
506 CG CB
507 ND1 CG
508 NE2 CD2
509 N HN
510 N CA
511 C CA
512 C +N
513 NE2 CE1
514 CA HA
515 CB HB1
516 CB HB2
517 NE2 HE2
518 CD2 HD2
519 CE1 HE1
520 O C
521 CD2 CG
522 CE1 ND1
523 [ impropers ]
524 NE2 CD2 CE1 HE2
525 CD2 CG NE2 HD2
526 CE1 ND1 NE2 HE1
527 NE2 CE1 CD2 HE2
528 CD2 NE2 CG HD2
529 CE1 NE2 ND1 HE1
530 N -C CA HN
531 C CA +N O
532 [ cmap ]
533 -C N CA C +N
535 [ HSP ]
536 [ atoms ]
537 N NH1 -0.47 0
538 HN H 0.31 1
539 CA CT1 0.07 2
540 HA HB 0.09 3
541 CB CT2 -0.05 4
542 HB1 HA 0.09 5
543 HB2 HA 0.09 6
544 CD2 CPH1 0.19 7
545 HD2 HR1 0.13 8
546 CG CPH1 0.19 9
547 NE2 NR3 -0.51 10
548 HE2 H 0.44 11
549 ND1 NR3 -0.51 12
550 HD1 H 0.44 13
551 CE1 CPH2 0.32 14
552 HE1 HR2 0.18 15
553 C C 0.51 16
554 O O -0.51 17
555 [ bonds ]
556 CB CA
557 CG CB
558 ND1 CG
559 CE1 ND1
560 NE2 CD2
561 N HN
562 N CA
563 C CA
564 C +N
565 CA HA
566 CB HB1
567 CB HB2
568 ND1 HD1
569 NE2 HE2
570 CD2 HD2
571 CE1 HE1
572 O C
573 CD2 CG
574 NE2 CE1
575 [ impropers ]
576 ND1 CG CE1 HD1
577 ND1 CE1 CG HD1
578 NE2 CD2 CE1 HE2
579 NE2 CE1 CD2 HE2
580 N -C CA HN
581 C CA +N O
582 [ cmap ]
583 -C N CA C +N
585 [ ILE ]
586 [ atoms ]
587 N NH1 -0.47 0
588 HN H 0.31 1
589 CA CT1 0.07 2
590 HA HB 0.09 3
591 CB CT1 -0.09 4
592 HB HA 0.09 5
593 CG2 CT3 -0.27 6
594 HG21 HA 0.09 7
595 HG22 HA 0.09 8
596 HG23 HA 0.09 9
597 CG1 CT2 -0.18 10
598 HG11 HA 0.09 11
599 HG12 HA 0.09 12
600 CD CT3 -0.27 13
601 HD1 HA 0.09 14
602 HD2 HA 0.09 15
603 HD3 HA 0.09 16
604 C C 0.51 17
605 O O -0.51 18
606 [ bonds ]
607 CB CA
608 CG1 CB
609 CG2 CB
610 CD CG1
611 N HN
612 N CA
613 C CA
614 C +N
615 CA HA
616 CB HB
617 CG1 HG11
618 CG1 HG12
619 CG2 HG21
620 CG2 HG22
621 CG2 HG23
622 CD HD1
623 CD HD2
624 CD HD3
625 O C
626 [ impropers ]
627 N -C CA HN
628 C CA +N O
629 [ cmap ]
630 -C N CA C +N
632 [ LEU ]
633 [ atoms ]
634 N NH1 -0.47 0
635 HN H 0.31 1
636 CA CT1 0.07 2
637 HA HB 0.09 3
638 CB CT2 -0.18 4
639 HB1 HA 0.09 5
640 HB2 HA 0.09 6
641 CG CT1 -0.09 7
642 HG HA 0.09 8
643 CD1 CT3 -0.27 9
644 HD11 HA 0.09 10
645 HD12 HA 0.09 11
646 HD13 HA 0.09 12
647 CD2 CT3 -0.27 13
648 HD21 HA 0.09 14
649 HD22 HA 0.09 15
650 HD23 HA 0.09 16
651 C C 0.51 17
652 O O -0.51 18
653 [ bonds ]
654 CB CA
655 CG CB
656 CD1 CG
657 CD2 CG
658 N HN
659 N CA
660 C CA
661 C +N
662 CA HA
663 CB HB1
664 CB HB2
665 CG HG
666 CD1 HD11
667 CD1 HD12
668 CD1 HD13
669 CD2 HD21
670 CD2 HD22
671 CD2 HD23
672 O C
673 [ impropers ]
674 N -C CA HN
675 C CA +N O
676 [ cmap ]
677 -C N CA C +N
679 [ LYS ]
680 [ atoms ]
681 N NH1 -0.47 0
682 HN H 0.31 1
683 CA CT1 0.07 2
684 HA HB 0.09 3
685 CB CT2 -0.18 4
686 HB1 HA 0.09 5
687 HB2 HA 0.09 6
688 CG CT2 -0.18 7
689 HG1 HA 0.09 8
690 HG2 HA 0.09 9
691 CD CT2 -0.18 10
692 HD1 HA 0.09 11
693 HD2 HA 0.09 12
694 CE CT2 0.21 13
695 HE1 HA 0.05 14
696 HE2 HA 0.05 15
697 NZ NH3 -0.30 16
698 HZ1 HC 0.33 17
699 HZ2 HC 0.33 18
700 HZ3 HC 0.33 19
701 C C 0.51 20
702 O O -0.51 21
703 [ bonds ]
704 CB CA
705 CG CB
706 CD CG
707 CE CD
708 NZ CE
709 N HN
710 N CA
711 C CA
712 C +N
713 CA HA
714 CB HB1
715 CB HB2
716 CG HG1
717 CG HG2
718 CD HD1
719 CD HD2
720 CE HE1
721 CE HE2
722 O C
723 NZ HZ1
724 NZ HZ2
725 NZ HZ3
726 [ impropers ]
727 N -C CA HN
728 C CA +N O
729 [ cmap ]
730 -C N CA C +N
732 [ LSN ] ; neutral lysine residue
733 [ atoms ]
734 N NH1 -0.47 0
735 HN H 0.31 1
736 CA CT1 0.07 2
737 HA HB 0.09 3
738 CB CT2 -0.18 4
739 HB1 HA 0.09 5
740 HB2 HA 0.09 6
741 CG CT2 -0.18 7
742 HG1 HA 0.09 8
743 HG2 HA 0.09 9
744 CD CT2 -0.18 10
745 HD1 HA 0.09 11
746 HD2 HA 0.09 12
747 CE CT2 0.13 13
748 HE1 HA 0.075 14
749 HE2 HA 0.075 15
750 NZ NH2 -0.96 16
751 HZ1 HC 0.34 17
752 HZ2 HC 0.34 18
753 C C 0.51 19
754 O O -0.51 20
755 [ bonds ]
756 CB CA
757 CG CB
758 CD CG
759 CE CD
760 NZ CE
761 N HN
762 N CA
763 C CA
764 C +N
765 CA HA
766 CB HB1
767 CB HB2
768 CG HG1
769 CG HG2
770 CD HD1
771 CD HD2
772 CE HE1
773 CE HE2
774 O C
775 NZ HZ1
776 NZ HZ2
777 [ impropers ]
778 N -C CA HN
779 C CA +N O
780 [ cmap ]
781 -C N CA C +N
783 [ MET ]
784 [ atoms ]
785 N NH1 -0.47 0
786 HN H 0.31 1
787 CA CT1 0.07 2
788 HA HB 0.09 3
789 CB CT2 -0.18 4
790 HB1 HA 0.09 5
791 HB2 HA 0.09 6
792 CG CT2 -0.14 7
793 HG1 HA 0.09 8
794 HG2 HA 0.09 9
795 SD S -0.09 10
796 CE CT3 -0.22 11
797 HE1 HA 0.09 12
798 HE2 HA 0.09 13
799 HE3 HA 0.09 14
800 C C 0.51 15
801 O O -0.51 16
802 [ bonds ]
803 CB CA
804 CG CB
805 SD CG
806 CE SD
807 N HN
808 N CA
809 C CA
810 C +N
811 CA HA
812 CB HB1
813 CB HB2
814 CG HG1
815 CG HG2
816 CE HE1
817 CE HE2
818 CE HE3
819 O C
820 [ impropers ]
821 N -C CA HN
822 C CA +N O
823 [ cmap ]
824 -C N CA C +N
826 [ PHE ]
827 [ atoms ]
828 N NH1 -0.47 0
829 HN H 0.31 1
830 CA CT1 0.07 2
831 HA HB 0.09 3
832 CB CT2 -0.18 4
833 HB1 HA 0.09 5
834 HB2 HA 0.09 6
835 CG CA 0.00 7
836 CD1 CA -0.115 8
837 HD1 HP 0.115 9
838 CE1 CA -0.115 10
839 HE1 HP 0.115 11
840 CZ CA -0.115 12
841 HZ HP 0.115 13
842 CD2 CA -0.115 14
843 HD2 HP 0.115 15
844 CE2 CA -0.115 16
845 HE2 HP 0.115 17
846 C C 0.51 18
847 O O -0.51 19
848 [ bonds ]
849 CB CA
850 CG CB
851 CD2 CG
852 CE1 CD1
853 CZ CE2
854 N HN
855 N CA
856 C CA
857 C +N
858 CA HA
859 CB HB1
860 CB HB2
861 CD1 HD1
862 CD2 HD2
863 CE1 HE1
864 O C
865 CD1 CG
866 CZ CE1
867 CE2 CD2
868 CE2 HE2
869 CZ HZ
870 [ impropers ]
871 N -C CA HN
872 C CA +N O
873 [ cmap ]
874 -C N CA C +N
876 [ PRO ]
877 [ atoms ]
878 N N -0.29 0
879 CD CP3 0.00 1
880 HD1 HA 0.09 2
881 HD2 HA 0.09 3
882 CA CP1 0.02 4
883 HA HB 0.09 5
884 CB CP2 -0.18 6
885 HB1 HA 0.09 7
886 HB2 HA 0.09 8
887 CG CP2 -0.18 9
888 HG1 HA 0.09 10
889 HG2 HA 0.09 11
890 C C 0.51 12
891 O O -0.51 13
892 [ bonds ]
893 C CA
894 C +N
895 N CA
896 CA CB
897 CB CG
898 CG CD
899 N CD
900 HA CA
901 HG1 CG
902 HG2 CG
903 HD1 CD
904 HD2 CD
905 HB1 CB
906 HB2 CB
907 O C
908 [ impropers ]
909 N -C CA CD
910 C CA +N O
911 [ cmap ]
912 -C N CA C +N
914 [ SER ]
915 [ atoms ]
916 N NH1 -0.47 0
917 HN H 0.31 1
918 CA CT1 0.07 2
919 HA HB 0.09 3
920 CB CT2 0.05 4
921 HB1 HA 0.09 5
922 HB2 HA 0.09 6
923 OG OH1 -0.66 7
924 HG1 H 0.43 8
925 C C 0.51 9
926 O O -0.51 10
927 [ bonds ]
928 CB CA
929 OG CB
930 N HN
931 N CA
932 C CA
933 C +N
934 CA HA
935 CB HB1
936 CB HB2
937 OG HG1
938 O C
939 [ impropers ]
940 N -C CA HN
941 C CA +N O
942 [ cmap ]
943 -C N CA C +N
945 [ THR ]
946 [ atoms ]
947 N NH1 -0.47 0
948 HN H 0.31 1
949 CA CT1 0.07 2
950 HA HB 0.09 3
951 CB CT1 0.14 4
952 HB HA 0.09 5
953 OG1 OH1 -0.66 6
954 HG1 H 0.43 7
955 CG2 CT3 -0.27 8
956 HG21 HA 0.09 9
957 HG22 HA 0.09 10
958 HG23 HA 0.09 11
959 C C 0.51 12
960 O O -0.51 13
961 [ bonds ]
962 CB CA
963 OG1 CB
964 CG2 CB
965 N HN
966 N CA
967 C CA
968 C +N
969 CA HA
970 CB HB
971 OG1 HG1
972 CG2 HG21
973 CG2 HG22
974 CG2 HG23
975 O C
976 [ impropers ]
977 N -C CA HN
978 C CA +N O
979 [ cmap ]
980 -C N CA C +N
982 [ TRP ]
983 [ atoms ]
984 N NH1 -0.47 0
985 HN H 0.31 1
986 CA CT1 0.07 2
987 HA HB 0.09 3
988 CB CT2 -0.18 4
989 HB1 HA 0.09 5
990 HB2 HA 0.09 6
991 CG CY -0.03 7
992 CD1 CA 0.035 8
993 HD1 HP 0.115 9
994 NE1 NY -0.61 10
995 HE1 H 0.38 11
996 CE2 CPT 0.13 12
997 CD2 CPT -0.02 13
998 CE3 CA -0.115 14
999 HE3 HP 0.115 15
1000 CZ3 CA -0.115 16
1001 HZ3 HP 0.115 17
1002 CZ2 CA -0.115 18
1003 HZ2 HP 0.115 19
1004 CH2 CA -0.115 20
1005 HH2 HP 0.115 21
1006 C C 0.51 22
1007 O O -0.51 23
1008 [ bonds ]
1009 CB CA
1010 CG CB
1011 CD2 CG
1012 NE1 CD1
1013 CZ2 CE2
1014 N HN
1015 N CA
1016 C CA
1017 C +N
1018 CZ3 CH2
1019 CD2 CE3
1020 NE1 CE2
1021 CA HA
1022 CB HB1
1023 CB HB2
1024 CD1 HD1
1025 NE1 HE1
1026 CE3 HE3
1027 CZ2 HZ2
1028 CZ3 HZ3
1029 CH2 HH2
1030 O C
1031 CD1 CG
1032 CE2 CD2
1033 CZ3 CE3
1034 CH2 CZ2
1035 [ impropers ]
1036 N -C CA HN
1037 C CA +N O
1038 [ cmap ]
1039 -C N CA C +N
1041 [ TYR ]
1042 [ atoms ]
1043 N NH1 -0.47 0
1044 HN H 0.31 1
1045 CA CT1 0.07 2
1046 HA HB 0.09 3
1047 CB CT2 -0.18 4
1048 HB1 HA 0.09 5
1049 HB2 HA 0.09 6
1050 CG CA 0.00 7
1051 CD1 CA -0.115 8
1052 HD1 HP 0.115 9
1053 CE1 CA -0.115 10
1054 HE1 HP 0.115 11
1055 CZ CA 0.11 12
1056 OH OH1 -0.54 13
1057 HH H 0.43 14
1058 CD2 CA -0.115 15
1059 HD2 HP 0.115 16
1060 CE2 CA -0.115 17
1061 HE2 HP 0.115 18
1062 C C 0.51 19
1063 O O -0.51 20
1064 [ bonds ]
1065 CB CA
1066 CG CB
1067 CD2 CG
1068 CE1 CD1
1069 CZ CE2
1070 OH CZ
1071 N HN
1072 N CA
1073 C CA
1074 C +N
1075 CA HA
1076 CB HB1
1077 CB HB2
1078 CD1 HD1
1079 CD2 HD2
1080 CE1 HE1
1081 CE2 HE2
1082 OH HH
1083 O C
1084 CD1 CG
1085 CE1 CZ
1086 CE2 CD2
1087 [ impropers ]
1088 N -C CA HN
1089 C CA +N O
1090 [ cmap ]
1091 -C N CA C +N
1093 [ VAL ]
1094 [ atoms ]
1095 N NH1 -0.47 0
1096 HN H 0.31 1
1097 CA CT1 0.07 2
1098 HA HB 0.09 3
1099 CB CT1 -0.09 4
1100 HB HA 0.09 5
1101 CG1 CT3 -0.27 6
1102 HG11 HA 0.09 7
1103 HG12 HA 0.09 8
1104 HG13 HA 0.09 9
1105 CG2 CT3 -0.27 10
1106 HG21 HA 0.09 11
1107 HG22 HA 0.09 12
1108 HG23 HA 0.09 13
1109 C C 0.51 14
1110 O O -0.51 15
1111 [ bonds ]
1112 CB CA
1113 CG1 CB
1114 CG2 CB
1115 N HN
1116 N CA
1117 C CA
1118 C +N
1119 CA HA
1120 CB HB
1121 CG1 HG11
1122 CG1 HG12
1123 CG1 HG13
1124 CG2 HG21
1125 CG2 HG22
1126 CG2 HG23
1127 O C
1128 [ impropers ]
1129 N -C CA HN
1130 C CA +N O
1131 [ cmap ]
1132 -C N CA C +N
1134 [ ALAD ] ; Alanine dipeptide
1135 [ atoms ]
1136 CL CT3 -0.27 0
1137 HL1 HA 0.09 1
1138 HL2 HA 0.09 2
1139 HL3 HA 0.09 3
1140 CLP C 0.51 4
1141 OL O -0.51 5
1142 NL NH1 -0.47 6
1143 HL H 0.31 7
1144 CA CT1 0.07 8
1145 HA HB 0.09 9
1146 CB CT3 -0.27 10
1147 HB1 HA 0.09 11
1148 HB2 HA 0.09 12
1149 HB3 HA 0.09 13
1150 CRP C 0.51 14
1151 OR O -0.51 15
1152 NR NH1 -0.47 16
1153 HR H 0.31 17
1154 CR CT3 -0.11 18
1155 HR1 HA 0.09 19
1156 HR2 HA 0.09 20
1157 HR3 HA 0.09 21
1158 [ bonds ]
1159 CL CLP
1160 CLP NL
1161 NL CA
1162 CA CRP
1163 CRP NR
1164 NR CR
1165 CLP OL
1166 CRP OR
1167 NL HL
1168 NR HR
1169 CA HA
1170 CA CB
1171 CL HL1
1172 CL HL2
1173 CL HL3
1174 CB HB1
1175 CB HB2
1176 CB HB3
1177 CR HR1
1178 CR HR2
1179 CR HR3
1180 [ impropers ]
1181 CLP CL NL OL
1182 NL CLP CA HL
1183 CRP CA NR OR
1184 NR CRP CR HR
1185 [ cmap ]
1186 CLP NL CA CRP NR
1188 [ HEME ]
1189 [ atoms ]
1190 FE FE 0.24 0
1191 NA NPH -0.18 1
1192 NB NPH -0.18 2
1193 NC NPH -0.18 3
1194 ND NPH -0.18 4
1195 C1A CPA 0.12 5
1196 C2A CPB -0.06 6
1197 C3A CPB -0.06 7
1198 C4A CPA 0.12 8
1199 C1B CPA 0.12 9
1200 C2B CPB -0.06 10
1201 C3B CPB -0.06 11
1202 C4B CPA 0.12 12
1203 C1C CPA 0.12 13
1204 C2C CPB -0.06 14
1205 C3C CPB -0.06 15
1206 C4C CPA 0.12 16
1207 C1D CPA 0.12 17
1208 C2D CPB -0.06 18
1209 C3D CPB -0.06 19
1210 C4D CPA 0.12 20
1211 CHA CPM -0.10 21
1212 HA HA 0.10 22
1213 CHB CPM -0.10 23
1214 HB HA 0.10 24
1215 CHC CPM -0.10 25
1216 HC HA 0.10 26
1217 CHD CPM -0.10 27
1218 HD HA 0.10 28
1219 CMA CT3 -0.27 29
1220 HMA1 HA 0.09 30
1221 HMA2 HA 0.09 31
1222 HMA3 HA 0.09 32
1223 CAA CT2 -0.18 33
1224 HAA1 HA 0.09 34
1225 HAA2 HA 0.09 35
1226 CBA CT2 -0.28 36
1227 HBA1 HA 0.09 37
1228 HBA2 HA 0.09 38
1229 CGA CC 0.62 39
1230 O1A OC -0.76 40
1231 O2A OC -0.76 41
1232 CMB CT3 -0.27 42
1233 HMB1 HA 0.09 43
1234 HMB2 HA 0.09 44
1235 HMB3 HA 0.09 45
1236 CAB CE1 -0.15 46
1237 HAB HE1 0.15 47
1238 CBB CE2 -0.42 48
1239 HBB1 HE2 0.21 49
1240 HBB2 HE2 0.21 50
1241 CMC CT3 -0.27 51
1242 HMC1 HA 0.09 52
1243 HMC2 HA 0.09 53
1244 HMC3 HA 0.09 54
1245 CAC CE1 -0.15 55
1246 HAC HE1 0.15 56
1247 CBC CE2 -0.42 57
1248 HBC1 HE2 0.21 58
1249 HBC2 HE2 0.21 59
1250 CMD CT3 -0.27 60
1251 HMD1 HA 0.09 61
1252 HMD2 HA 0.09 62
1253 HMD3 HA 0.09 63
1254 CAD CT2 -0.18 64
1255 HAD1 HA 0.09 65
1256 HAD2 HA 0.09 66
1257 CBD CT2 -0.28 67
1258 HBD1 HA 0.09 68
1259 HBD2 HA 0.09 69
1260 CGD CC 0.62 70
1261 O1D OC -0.76 71
1262 O2D OC -0.76 72
1263 [ bonds ]
1264 FE NA
1265 FE NB
1266 FE NC
1267 FE ND
1268 NA C1A
1269 C1A C2A
1270 C2A C3A
1271 C3A C4A
1272 NA C4A
1273 C2A CAA
1274 CAA CBA
1275 CBA CGA
1276 CGA O1A
1277 CGA O2A
1278 C3A CMA
1279 CHB C4A
1280 CHB C1B
1281 NB C1B
1282 C1B C2B
1283 C2B C3B
1284 C3B C4B
1285 NB C4B
1286 C2B CMB
1287 C3B CAB
1288 CAB CBB
1289 CHC C4B
1290 CHC C1C
1291 NC C1C
1292 C1C C2C
1293 C2C C3C
1294 C3C C4C
1295 NC C4C
1296 C2C CMC
1297 C3C CAC
1298 CAC CBC
1299 CHD C4C
1300 CHD C1D
1301 ND C1D
1302 C1D C2D
1303 C2D C3D
1304 C3D C4D
1305 ND C4D
1306 C2D CMD
1307 C3D CAD
1308 CAD CBD
1309 CBD CGD
1310 CGD O1D
1311 CGD O2D
1312 CHA C4D
1313 CHA C1A
1314 CHA HA
1315 CHB HB
1316 CHC HC
1317 CHD HD
1318 CAA HAA1
1319 CAA HAA2
1320 CBA HBA1
1321 CBA HBA2
1322 CMA HMA1
1323 CMA HMA2
1324 CMA HMA3
1325 CMB HMB1
1326 CMB HMB2
1327 CMB HMB3
1328 CAB HAB
1329 CBB HBB1
1330 CBB HBB2
1331 CMC HMC1
1332 CMC HMC2
1333 CMC HMC3
1334 CAC HAC
1335 CBC HBC1
1336 CBC HBC2
1337 CMD HMD1
1338 CMD HMD2
1339 CMD HMD3
1340 CAD HAD1
1341 CAD HAD2
1342 CBD HBD1
1343 CBD HBD2
1344 [ angles ]
1345 ; ai aj ak th0 cth ub0 cub
1346 NA FE NC 180.0 0.0 0.0 0.0
1347 NB FE ND 180.0 0.0 0.0 0.0
1348 [ impropers ]
1349 C2A C1A C3A CAA
1350 C3A C2A C4A CMA
1351 C2B C1B C3B CMB
1352 C3B C2B C4B CAB
1353 C2C C1C C3C CMC
1354 C3C C2C C4C CAC
1355 C2D C1D C3D CMD
1356 C3D C2D C4D CAD
1357 CGA CBA O2A O1A
1358 CGD CBD O2D O1D
1359 C4A NA C1A C2A
1360 C1A NA C4A C3A
1361 C4B NB C1B C2B
1362 C1B NB C4B C3B
1363 C4C NC C1C C2C
1364 C1C NC C4C C3C
1365 C4D ND C1D C2D
1366 C1D ND C4D C3D
1367 NA C1A C2A C3A
1368 NA C4A C3A C2A
1369 NB C1B C2B C3B
1370 NB C4B C3B C2B
1371 NC C1C C2C C3C
1372 NC C4C C3C C2C
1373 ND C1D C2D C3D
1374 ND C4D C3D C2D
1375 NA C1A CHA C4D
1376 NA C4A CHB C1B
1377 NB C1B CHB C4A
1378 NB C4B CHC C1C
1379 NC C1C CHC C4B
1380 NC C4C CHD C1D
1381 ND C1D CHD C4C
1382 ND C4D CHA C1A
1383 CHA C1A C4D HA
1384 CHB C1B C4A HB
1385 CHC C1C C4B HC
1386 CHD C1D C4C HD
1387 C1A C2A CHA NA
1388 C4A C3A CHB NA
1389 C1B C2B CHB NB
1390 C4B C3B CHC NB
1391 C1C C2C CHC NC
1392 C4C C3C CHD NC
1393 C1D C2D CHD ND
1394 C4D C3D CHA ND
1395 NA C1A C4A FE
1396 NB C1B C4B FE
1397 NC C1C C4C FE
1398 ND C1D C4D FE
1400 [ HEO2 ]
1401 [ atoms ]
1402 FE FE 0.24 0
1403 NA NPH -0.18 1
1404 NB NPH -0.18 2
1405 NC NPH -0.18 3
1406 ND NPH -0.18 4
1407 C1A CPA 0.12 5
1408 C2A CPB -0.06 6
1409 C3A CPB -0.06 7
1410 C4A CPA 0.12 8
1411 C1B CPA 0.12 9
1412 C2B CPB -0.06 10
1413 C3B CPB -0.06 11
1414 C4B CPA 0.12 12
1415 C1C CPA 0.12 13
1416 C2C CPB -0.06 14
1417 C3C CPB -0.06 15
1418 C4C CPA 0.12 16
1419 C1D CPA 0.12 17
1420 C2D CPB -0.06 18
1421 C3D CPB -0.06 19
1422 C4D CPA 0.12 20
1423 CHA CPM -0.10 21
1424 HA HA 0.10 22
1425 CHB CPM -0.10 23
1426 HB HA 0.10 24
1427 CHC CPM -0.10 25
1428 HC HA 0.10 26
1429 CHD CPM -0.10 27
1430 HD HA 0.10 28
1431 CMA CT3 -0.27 29
1432 HMA1 HA 0.09 30
1433 HMA2 HA 0.09 31
1434 HMA3 HA 0.09 32
1435 CAA CT2 -0.18 33
1436 HAA1 HA 0.09 34
1437 HAA2 HA 0.09 35
1438 CBA CT2 -0.28 36
1439 HBA1 HA 0.09 37
1440 HBA2 HA 0.09 38
1441 CGA CC 0.62 39
1442 O1A OC -0.76 40
1443 O2A OC -0.76 41
1444 CMB CT3 -0.27 42
1445 HMB1 HA 0.09 43
1446 HMB2 HA 0.09 44
1447 HMB3 HA 0.09 45
1448 CAB CE1 -0.15 46
1449 HAB HE1 0.15 47
1450 CBB CE2 -0.42 48
1451 HBB1 HE2 0.21 49
1452 HBB2 HE2 0.21 50
1453 CMC CT3 -0.27 51
1454 HMC1 HA 0.09 52
1455 HMC2 HA 0.09 53
1456 HMC3 HA 0.09 54
1457 CAC CE1 -0.15 55
1458 HAC HE1 0.15 56
1459 CBC CE2 -0.42 57
1460 HBC1 HE2 0.21 58
1461 HBC2 HE2 0.21 59
1462 CMD CT3 -0.27 60
1463 HMD1 HA 0.09 61
1464 HMD2 HA 0.09 62
1465 HMD3 HA 0.09 63
1466 CAD CT2 -0.18 64
1467 HAD1 HA 0.09 65
1468 HAD2 HA 0.09 66
1469 CBD CT2 -0.28 67
1470 HBD1 HA 0.09 68
1471 HBD2 HA 0.09 69
1472 CGD CC 0.62 70
1473 O1D OC -0.76 71
1474 O2D OC -0.76 72
1475 O1 OM 0.021 73
1476 O2 OM -0.021 74
1477 [ bonds ]
1478 FE NA
1479 FE NB
1480 FE NC
1481 FE ND
1482 NA C1A
1483 C1A C2A
1484 C2A C3A
1485 C3A C4A
1486 NA C4A
1487 C2A CAA
1488 CAA CBA
1489 CBA CGA
1490 CGA O1A
1491 CGA O2A
1492 C3A CMA
1493 CHB C4A
1494 CHB C1B
1495 NB C1B
1496 C1B C2B
1497 C2B C3B
1498 C3B C4B
1499 NB C4B
1500 C2B CMB
1501 C3B CAB
1502 CAB CBB
1503 CHC C4B
1504 CHC C1C
1505 NC C1C
1506 C1C C2C
1507 C2C C3C
1508 C3C C4C
1509 NC C4C
1510 C2C CMC
1511 C3C CAC
1512 CAC CBC
1513 CHD C4C
1514 CHD C1D
1515 ND C1D
1516 C1D C2D
1517 C2D C3D
1518 C3D C4D
1519 ND C4D
1520 C2D CMD
1521 C3D CAD
1522 CAD CBD
1523 CBD CGD
1524 CGD O1D
1525 CGD O2D
1526 CHA C4D
1527 CHA C1A
1528 CHA HA
1529 CHB HB
1530 CHC HC
1531 CHD HD
1532 CAA HAA1
1533 CAA HAA2
1534 CBA HBA1
1535 CBA HBA2
1536 CMA HMA1
1537 CMA HMA2
1538 CMA HMA3
1539 CMB HMB1
1540 CMB HMB2
1541 CMB HMB3
1542 CAB HAB
1543 CBB HBB1
1544 CBB HBB2
1545 CMC HMC1
1546 CMC HMC2
1547 CMC HMC3
1548 CAC HAC
1549 CBC HBC1
1550 CBC HBC2
1551 CMD HMD1
1552 CMD HMD2
1553 CMD HMD3
1554 CAD HAD1
1555 CAD HAD2
1556 CBD HBD1
1557 CBD HBD2
1558 O1 O2
1559 O1 FE
1560 [ angles ]
1561 ; ai aj ak th0 cth ub0 cub
1562 NA FE NC 180.0 0.0 0.0 0.0
1563 NB FE ND 180.0 0.0 0.0 0.0
1564 FE O1 O2 122.0 50.00 0.0 0.0
1565 [ impropers ]
1566 C2A C1A C3A CAA
1567 C3A C2A C4A CMA
1568 C2B C1B C3B CMB
1569 C3B C2B C4B CAB
1570 C2C C1C C3C CMC
1571 C3C C2C C4C CAC
1572 C2D C1D C3D CMD
1573 C3D C2D C4D CAD
1574 CGA CBA O2A O1A
1575 CGD CBD O2D O1D
1576 C4A NA C1A C2A
1577 C1A NA C4A C3A
1578 C4B NB C1B C2B
1579 C1B NB C4B C3B
1580 C4C NC C1C C2C
1581 C1C NC C4C C3C
1582 C4D ND C1D C2D
1583 C1D ND C4D C3D
1584 NA C1A C2A C3A
1585 NA C4A C3A C2A
1586 NB C1B C2B C3B
1587 NB C4B C3B C2B
1588 NC C1C C2C C3C
1589 NC C4C C3C C2C
1590 ND C1D C2D C3D
1591 ND C4D C3D C2D
1592 NA C1A CHA C4D
1593 NA C4A CHB C1B
1594 NB C1B CHB C4A
1595 NB C4B CHC C1C
1596 NC C1C CHC C4B
1597 NC C4C CHD C1D
1598 ND C1D CHD C4C
1599 ND C4D CHA C1A
1600 CHA C1A C4D HA
1601 CHB C1B C4A HB
1602 CHC C1C C4B HC
1603 CHD C1D C4C HD
1604 C1A C2A CHA NA
1605 C4A C3A CHB NA
1606 C1B C2B CHB NB
1607 C4B C3B CHC NB
1608 C1C C2C CHC NC
1609 C4C C3C CHD NC
1610 C1D C2D CHD ND
1611 C4D C3D CHA ND
1612 NA C1A C4A FE
1613 NB C1B C4B FE
1614 NC C1C C4C FE
1615 ND C1D C4D FE
1617 [ O2 ] ; O2 ligand for HEME
1618 [ atoms ]
1619 O1 OM 0.021 0
1620 O2 OM -0.021 1
1621 [ bonds ]
1622 O1 O2
1624 [ CO ] ; CO ligand for HEME
1625 [ atoms ]
1626 C CM 0.021 0
1627 O OM -0.021 1
1628 [ bonds ]
1629 C O
1631 [ HOH ]
1632 [ atoms ]
1633 OW OT -0.834 0
1634 HW1 HT 0.417 1
1635 HW2 HT 0.417 2
1636 [ bonds ]
1637 OW HW1
1638 OW HW2
1639 HW1 HW2
1641 [ TIP3 ]
1642 [ atoms ]
1643 OH2 OT -0.834 0
1644 H1 HT 0.417 1
1645 H2 HT 0.417 2
1646 [ bonds ]
1647 OH2 H1
1648 OH2 H2
1649 H1 H2
1651 [ TP3M ]
1652 [ atoms ]
1653 OH2 OT -0.834 0
1654 H1 HT 0.417 1
1655 H2 HT 0.417 2
1656 [ bonds ]
1657 OH2 H1
1658 OH2 H2
1660 [ HO4 ]
1661 ; TIP4P
1662 [ atoms ]
1663 OW OWT4 0.00 0
1664 HW1 HWT4 0.52 0
1665 HW2 HWT4 0.52 0
1666 MW MWT4 -1.04 0
1667 [ bonds ]
1668 OW HW1
1669 OW HW2
1671 [ SOD ]
1672 [ atoms ]
1673 SOD SOD 1.00 0
1675 [ MG ]
1676 [ atoms ]
1677 MG MG 2.00 0
1679 [ POT ]
1680 [ atoms ]
1681 POT POT 1.00 0
1683 [ CES ]
1684 [ atoms ]
1685 CES CES 1.00 0
1687 [ CAL ]
1688 [ atoms ]
1689 CAL CAL 2.00 0
1691 [ CLA ]
1692 [ atoms ]
1693 CLA CLA -1.00 0
1695 [ ZN2 ]
1696 [ atoms ]
1697 ZN ZN 2.00 0
1699 [ ACE ]
1700 [ atoms ]
1701 CH3 CT3 -0.270 0
1702 HH31 HA 0.090 1
1703 HH32 HA 0.090 2
1704 HH33 HA 0.090 3
1705 C C 0.510 4
1706 O O -0.510 5
1707 [ bonds ]
1708 C CH3
1709 C +N
1710 CH3 HH31
1711 CH3 HH32
1712 CH3 HH33
1713 O C
1714 [ impropers ]
1715 C CH3 +N O
1717 [ CT3 ]
1718 ; this can also be done with the .c.tdb, but the atom naming is different
1719 ; and this can matter
1720 [ atoms ]
1721 N NH1 -0.470 0
1722 HN H 0.310 1
1723 CH3 CT3 -0.110 2
1724 HH31 HA 0.090 3
1725 HH32 HA 0.090 4
1726 HH33 HA 0.090 5
1727 [ bonds ]
1728 -C N
1729 N HN
1730 N CH3
1731 CH3 HH31
1732 CH3 HH32
1733 CH3 HH33
1735 [ impropers ]
1736 N -C CH3 HN
1737 -C CH3 N -O