-
Notifications
You must be signed in to change notification settings - Fork 0
/
par_all27_prot_lipid_more.prm
3677 lines (3511 loc) · 178 KB
/
par_all27_prot_lipid_more.prm
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
*>CHARMM22 All-Hydrogen Parameter File for Proteins and Lipids <<
*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
*>>>>>>>>>>>>>>>>>>>>>> July, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
* All comments to ADM jr. via the CHARMM web site: www.charmm.org
* parameter set discussion forum
*
! references
!
!PROTEINS
!
!MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the
!treatment of backbone energetics in protein force fields: limitations
!of gas-phase quantum mechanics in reproducing protein conformational
!distributions in molecular dynamics simulations, Journal of
!Computational Chemistry, 25: 1400-1415, 2004.
!
!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom
!empirical potential for molecular modeling and dynamics Studies of
!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616.
!
!ZINC
!
!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and
!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS:
!Structure, Function, and Genetics 23:12-31 (1995)
!
!LIPIDS
!
!Feller, S.E. Gawrisch, G. and MacKerell, Jr., A.D. Polyunsaturated
!Fatty Acids in Lipid Bilayers: Intrinsic and Environmental
!Contributions to Their Unique Physical Properties. Journal of
!the American Chemical Society, 2002, 124:318-326
!
!Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential
!Energy Function for Molecular Simulations of Phospholipids, Journal
!of Physical Chemistry B, 2000, 104: 7510-7515.
!
!and
!
!Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus, M.
!Empirical Potential Energy Function for Phospholipids: Criteria for
!Parameter Optimization and Applications, in "Biological Membranes: A
!Molecular Perspective from Computation and Experiment," K.M. Merz and
!B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81.
!
!new ALKANES
!
!Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical Approach
!for the Optimization of Lennard-Jones Parameters. Journal of
!Computational Chemistry, 1998, 19: 334-338.
!
!ALKENES
!
!Feller, S.E., Yin, D., Pastor, R.W., and MacKerell, Jr., A.D.,
!Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration:
!Parameterization and Comparison with Diffraction Studies. Biophysical
!Journal, 73:2269-2279, 1997.
!
!new PHOSPHATE
!
!MacKerell, Jr., A.D. Influence of Water and Sodium on the Energetics
!of Dimethylphosphate and its Implications For DNA Structure, Journal
!de Chimie Physique, 1997, 94: 1436-1447.
!
!IONS
!
!all ions from Roux and coworkers
!
!Sodium
!
!Beglov, D. and Roux, B., Finite Representation of an Infinite
!Bulk System: Solvent Boundary Potential for Computer Simulations,
!Journal of Chemical Physics, 1994, 100: 9050-9063
!
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
!Carbon Dioxide
CST OST 937.96 1.1600 ! JES
!Heme to Sulfate (PSUL) link
SS FE 250.0 2.3200 !force constant a guess
!equilbrium bond length optimized to reproduce
!CSD survey values of
!2.341pm0.01 (mean, standard error)
!adm jr., 7/01
C C 600.000 1.3350 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
CA CA 305.000 1.3750 ! ALLOW ARO
! benzene, JES 8/25/89
CE1 CE1 440.000 1.3400 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CE2 500.000 1.3420 !
! for propene, yin/adm jr., 12/95
CE1 CT2 365.000 1.5020 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CT3 383.000 1.5040 !
! for butene, yin/adm jr., 12/95
CE2 CE2 510.000 1.3300 !
! for ethene, yin/adm jr., 12/95
CP1 C 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CC 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CD 200.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 222.500 1.5270 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPB CE1 450.000 1.3800 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPA 299.800 1.4432 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB CPB 340.700 1.3464 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH1 CPH1 410.000 1.3600 ! ALLOW ARO
! histidine, adm jr., 6/27/90
CPM CPA 360.000 1.3716 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT CA 305.000 1.3680 ! ALLOW ARO
! adm jr., 12/30/91, for jwk
CPT CPT 360.000 1.4000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT1 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT1 222.500 1.5000 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT2 CA 230.000 1.4900 ! ALLOW ALI ARO
! phe,tyr, JES 8/25/89
CT2 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT2 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT3 CA 230.000 1.4900 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
CT3 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT3 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT3 CS 190.000 1.5310 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
CT3 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 222.500 1.5280 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT3 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CY CA 350.000 1.3650 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CY CPT 350.000 1.4400 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CT2 230.000 1.5100 ! ALLOW ARO
!JWK Kb from alkane freq.. b0 from TRP crystal
FE CM 258.000 1.9000 ! ALLOW HEM
! Heme (6-liganded): CO ligand (KK 05/13/91)
FE CPM 0.000 3.3814 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
H CD 330.000 1.1100 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
!HA C 330.000 1.1000 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
HA CA 340.000 1.0830 ! ALLOW ARO
! trp, adm jr., 10/02/89
HA CC 317.130 1.1000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
HA CP2 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CPM 367.600 1.0900 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT1 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 322.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CY 330.000 1.0800 ! ALLOW ARO
! JWK 05/14/91 new r0 from indole
HE1 CE1 360.500 1.1000 !
! for propene, yin/adm jr., 12/95
HE2 CE2 365.000 1.1000 !
! for ethene, yin/adm jr., 12/95
HB CP1 330.000 1.0800 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CT1 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT3 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HP CA 340.000 1.0800 ! ALLOW ARO
! phe,tyr JES 8/25/89
HP CY 350.000 1.0800 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HR1 CPH1 375.000 1.0830 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH2 340.000 1.0900 ! ALLOW ARO
! his, adm jr., 6/28/29
HR2 CPH2 333.000 1.0700 ! ALLOW ARO
! his, adm jr., 6/27/90
HR3 CPH1 365.000 1.0830 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HT HT 0.000 1.5139 ! ALLOW WAT
! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 320.000 1.4340 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 320.000 1.4550 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO
! 403.0->463.0, 1.305->1.365 guanidinium (KK)
NC2 CT2 261.000 1.4900 ! ALLOW ALI POL
! arg, (DS)
NC2 CT3 261.000 1.4900 ! ALLOW ALI POL
! methylguanidinium, adm jr., 3/26/92
NC2 HC 455.000 1.0000 ! ALLOW POL
! 405.0->455.0 GUANIDINIUM (KK)
NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO
! (DS)
NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
NH2 CT2 240.000 1.4550
! from NH2 CT3, neutral glycine, adm jr.
NH2 CT3 240.000 1.4550 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH2 H 480.000 1.0000 ! ALLOW POL
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 HC 460.000 1.0000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH3 CT1 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT2 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT3 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 HC 403.000 1.0400 ! ALLOW POL
! new stretch and bend; methylammonium (KK 03/10/92)
NP CP1 320.000 1.4850 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 320.000 1.5020 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP HC 460.000 1.0060 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NPH CPA 377.200 1.3757 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH FE 270.200 1.9580 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 CPH2 400.000 1.3600 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 H 466.000 1.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH2 400.000 1.3200 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 FE 65.000 2.2000 ! ALLOW HEM
! Heme (6-liganded): His ligand (KK 05/13/91)
NR3 CPH1 380.000 1.3700 ! ALLOW ARO
! his, adm jr., 6/28/90
NR3 CPH2 380.000 1.3200 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 H 453.000 1.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
NY CA 270.000 1.3700 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY CPT 270.000 1.3750 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY H 465.000 0.9760 ! ALLOW ARO
! indole JWK 08/28/89
O C 620.000 1.2300 ! ALLOW PEP POL ARO
! Peptide geometry, condensed phase (LK)
O CC 650.000 1.2300 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
OB CC 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr., 10/17/90, acetic acid vibrations and geom.
OB CD 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 8/27/91, phenoxide
OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 7/23/91, acetic acid
OC CT2 450.000 1.3300 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT3 450.000 1.3300 ! ALLOW ALC
! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
OH1 CA 334.300 1.4110 ! ALLOW ARO ALC
! MeOH, EMB 10/10/89,
OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC
! adm jr. 5/02/91, acetic acid pure solvent
OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 H 545.000 0.9600 ! ALLOW ALC ARO
! EMB 11/21/89 methanol vib fit
OM CM 1115.000 1.1280 ! ALLOW HEM
! Heme (6-liganded): CO ligand (KK 05/13/91)
OM FE 250.000 1.8000 ! ALLOW HEM
! Heme (6-liganded): O2 ligand (KK 05/13/91)
OM OM 600.000 1.2300 ! ALLOW HEM
! Heme (6-liganded): O2 ligand (KK 05/13/91)
OS CD 150.000 1.3340 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
OS CT3 340.000 1.4300 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OT HT 450.000 0.9572 ! ALLOW WAT
! FROM TIPS3P GEOM
S CT2 198.000 1.8180 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S CT3 240.000 1.8160 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S HS 275.000 1.3250 ! ALLOW SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
SM CT2 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SM CT3 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SM SM 173.000 2.0290 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SS CS 205.000 1.8360 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
!lipid section
CTL3 CL 200.0 1.522 ! methyl acetate
CTL2 CL 200.0 1.522 ! methyl acetate
CTL1 CL 200.0 1.522 ! methyl acetate
OBL CL 750.0 1.220 ! methyl acetate
OCL CL 525.0 1.260 ! acetate, protein
OSL CL 150.0 1.334 ! methyl acetate
OHL CL 230.0 1.40 ! methyl acetate
HOL OHL 545.0 0.960 ! acetic acid
CTL1 HAL1 309.00 1.111 ! alkanes, 3/92
CTL2 HAL2 309.00 1.111 ! alkanes, 4/98
CTL3 HAL3 322.00 1.111 ! alkanes, 4/98
CTL3 OSL 340.0 1.43 ! phosphate
CTL2 OSL 340.0 1.43 ! phosphate
CTL1 OSL 340.0 1.43 ! phosphate
OSL PL 270.0 1.60 ! phosphate
O2L PL 580.0 1.48 ! phosphate
OHL PL 237.0 1.59 ! phosphate
NH3L HCL 410.0 1.04 ! ethanolamine
NH3L CTL2 261.0 1.51 ! ethanolamine
NTL CTL2 215.00 1.51 ! tetramethylammonium
NTL CTL5 215.00 1.51 ! tetramethylammonium
CTL5 HL 300.00 1.08 ! tetramethylammonium
CTL2 HL 300.00 1.08 ! tetramethylammonium
CTL1 CTL1 222.500 1.500 ! alkanes, 3/92
CTL1 CTL2 222.500 1.538 ! alkanes, 3/92
CTL1 CTL3 222.500 1.538 ! alkanes, 3/92
CTL2 CTL2 222.500 1.530 ! alkanes, 3/92
CTL2 CTL3 222.500 1.528 ! alkanes, 3/92
CTL3 CTL3 222.500 1.530 ! alkanes, 3/92
OHL CTL1 428.0 1.420 ! glycerol
OHL CTL2 428.0 1.420 ! glycerol
OHL CTL3 428.0 1.420 ! glycerol
SL O2L 540.0 1.448 ! methylsulfate
SL OSL 250.0 1.575 ! methylsulfate
!HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM)
!HT OT 450.0 0.9572 ! from TIPS3P geometry
CEL2 CEL2 510.000 1.330 ! ethene yin,adm jr., 12/95
HEL2 CEL2 365.000 1.100 ! propene; from ethene, yin,adm jr., 12/95
CEL1 CTL3 383.000 1.504 ! butene, yin,adm jr., 12/95
CEL1 CEL2 500.000 1.342 ! propene, yin,adm jr., 12/95
HEL1 CEL1 360.500 1.100 ! propene, yin,adm jr., 12/95
CEL1 CTL2 365.000 1.502 ! butene; from propene, yin,adm jr., 12/95
CEL1 CEL1 440.000 1.340 ! butene, yin,adm jr., 12/95
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
!Carbon Dioxide, JES
OST CST OST 3000.00 180.0000 ! CO2, JES
!Heme to Sulfate (PSUL) link
CS SS FE 50.0 100.6 !force constant a guess
!equilibrium angle optimized to reproduce
!CSD survey values
!107.5pm0.6 (mean, standard error)
!adm jr., 7/01
SS FE NPH 100.0 90.0 !force constant a guess
!adm jr., 7/01
!
CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO
! JES 8/25/89
CE1 CE1 CT2 48.00 123.50 !
! for 2-butene, yin/adm jr., 12/95
CE1 CE1 CT3 48.00 123.50 !
! for 2-butene, yin/adm jr., 12/95
CE1 CT2 CT3 32.00 112.20 !
! for 1-butene; from propene, yin/adm jr., 12/95
CE2 CE1 CT2 48.00 126.00 !
! for 1-butene; from propene, yin/adm jr., 12/95
CE2 CE1 CT3 47.00 125.20 !
! for propene, yin/adm jr., 12/95
CP1 N C 60.000 117.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 C 52.000 112.3000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N C 60.000 117.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N CP1 100.000 114.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 NP CP1 100.000 111.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPA CPB CE1 70.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPA CPM CPA 94.200 125.1200 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPA NPH CPA 139.300 103.9000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB CE1 CE2 70.000 121.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPB CE1 70.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPB CPA 30.800 106.5100 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO
! his, adm jr., 6/27/90
CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
CPM CPA CPB 61.600 124.0700 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT CA CA 60.000 118.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT CPT CA 60.000 122.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT NY CA 110.000 108.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
! PARALLH19 (JES)
CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO
! PARALLH19 (JES)
CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! from CT2 CT1 C, for lactams, adm jr.
CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT2 CY CA 45.800 129.4000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CT2 CY CPT 45.800 124.0000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
! 107.5->120.0 to make planar Arg (KK)
CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO
! toluene, adm jr., 3/7/92
CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/09/92, for ALA cter
CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
! ethylbenzene, adm jr., 3/7/92
CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
! methylguanidinium, adm jr., 3/26/92
CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CY CPT CA 160.000 130.6000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CPT CPT 110.000 107.4000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CT2 CT1 58.350 114.0000 ! ALLOW ARO
! from TRP crystal, JWK
CY CT2 CT3 58.350 114.0000 ! ALLOW ARO
! from TRP crystal, JWK
FE NPH CPA 96.150 128.0500 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO
! NMA Vib Modes (LK)
H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO
! his, adm jr. 8/13/90 acetamide geometry and vibrations
H NH2 H 23.000 120.0000 ! ALLOW POL
! adm jr. 8/13/90 acetamide geometry and vibrations
H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NY CA 28.000 126.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H NY CPT 28.000 126.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO
! JES 8/25/89 phenol
H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
!HA C C 50.000 120.5000 ! ALLOW PEP POL ARO
! Heme vinyl substituent (KK from propene (JCS))
!HA C CPB 50.000 120.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
!HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO
! Heme vinyl substituent (KK from propene (JCS))
HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO
! trp, adm jr., 10/02/89
HA CA CPT 41.000 122.0000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CPM CPA 12.700 117.4400 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA CPM FE 0.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd
! based on HA CT2 HA
HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO
! PARALLH19 (JES)
HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT2 CE1 45.00 111.50 !
! for 1-butene; from propene, yin/adm jr., 12/95
HA CT2 CPB 50.000 109.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 CY 33.430 109.5000 ! ALLOW ARO
! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA
HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT3 CE1 42.00 111.50 !
! for 2-butene, yin/adm jr., 12/95
HA CT3 CPB 50.000 109.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HE1 CE1 CE1 52.00 119.50 !
! for 2-butene, yin/adm jr., 12/95
HE1 CE1 CE2 42.00 118.00 !
! for propene, yin/adm jr., 12/95
HE1 CE1 CT2 40.00 116.00 !
! for 1-butene; from propene, yin/adm jr., 12/95
HE1 CE1 CT3 22.00 117.00 !
! for propene, yin/adm jr., 12/95
HE1 CE1 CPB 50.000 120.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HE2 CE2 CE1 45.00 120.50 !
! for propene, yin/adm jr., 12/95
HE2 CE2 CE2 55.50 120.50 !
! for ethene, yin/adm jr., 12/95
HE2 CE2 HE2 19.00 119.00 !
! for propene, yin/adm jr., 12/95
HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CT1 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB CT1 CT1 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CT2 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CT3 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB CT2 HB 36.000 115.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT3 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO
! 35.3->49.0 GUANIDINIUM (KK)
HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI
! 107.5->120.0 to make planar Arg (KK)
HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI
! methylguanidinium, adm jr., 3/26/92
HC NC2 HC 25.000 120.0000 ! ALLOW POL
! 40.0->25.0 GUANIDINIUM (KK)
HC NH2 CT2 50.000 111.0000 ! ALLOW POL
! from HC NH2 CT3, neutral glycine, adm jr.
HC NH2 CT3 50.000 111.0000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
HC NH2 HC 39.000 106.5000 ! ALLOW POL
! 40.0->25.0 GUANIDINIUM (KK)
HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 HC 44.000 109.5000 ! ALLOW POL
! new stretch and bend; methylammonium (KK 03/10/92)
HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP HC 51.000 107.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO
! JES 8/25/89 benzene
HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO
! adm jr., 6/27/90, his
HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI
! methanethiol pure solvent, adm jr., 6/22/92
HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI
! methanethiol pure solvent, adm jr., 6/22/92
HT OT HT 55.000 104.5200 ! ALLOW WAT
! TIP3P GEOMETRY, ADM JR.
N C CP1 20.000 112.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 C 50.000 108.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CC 50.000 108.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CP2 70.000 110.8000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 CP2 70.000 110.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO
! changed from 60.0/120.3 for guanidinium (KK)
NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL
! arg, (DS)
NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL
! arg, (DS)
NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL
! methylguanidinium, adm jr., 3/26/92
NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/20/92, for asn,asp,gln,glu and cters
NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! from NH1 CT1 CT2, for lactams, adm jr.
NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
! from NH1 CT3 HA, for lactams, adm jr.
NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
! NMA crystal (JCS)
NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
NH2 CT2 HA 38.000 109.50 50.00 2.14000
!from NH2 CT3 HA, neutral lysine
NH2 CT2 HB 38.000 109.50 50.00 2.14000
!from NH2 CT3 HA, neutral glycine, adm jr.
NH2 CT2 CD 52.000 108.0000
!from CT2 CT2 CD, neutral glycine, adm jr.
NH2 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL
!from NH3 CT2 CT2, neutral lysine
NH2 CT3 HA 38.000 109.50 50.00 2.14000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! new aliphatics, adm jr., 2/3/92
NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL
! new aliphatics, adm jr., 2/3/92
NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL
! new aliphatics, adm jr., 2/3/92
NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL
! new aliphatics, adm jr., 2/3/92
NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP
! new aliphatics, adm jr., 2/3/92
NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! alanine (JCS)
NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL
! alanine (JCS)
NH3 CT2 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT2 HB 51.500 107.5000 ! ALLOW ALI POL PEP
! for use on NTER -- from NH3 CT2HA (JCS) -- (LK)
NH3 CT3 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NP CP1 C 50.000 106.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 CC 50.000 106.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 CP2 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 HB 51.500 107.5000 ! ALLOW ALI POL PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 CP2 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 HA 51.500 109.1500 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NPH CPA CPB 122.000 111.5400 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH CPA CPM 88.000 124.3900 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH FE CM 50.000 90.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
NPH FE CPM 0.000 45.0000 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
NPH FE NPH 14.390 90.0000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR2 FE CM 50.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
NR2 FE NPH 50.000 90.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO