packmol-memgen-minimal 1.1.16__py3-none-any.whl

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Files changed (71) hide show
  1. packmol_memgen/__init__.py +2 -0
  2. packmol_memgen/__version__.py +34 -0
  3. packmol_memgen/data/LICENSE.Apache-2.0 +201 -0
  4. packmol_memgen/data/extra_solvents.lib +789 -0
  5. packmol_memgen/data/frcmod.lipid_ext +97 -0
  6. packmol_memgen/data/frcmod.solvents +129 -0
  7. packmol_memgen/data/insane_lipids.txt +138 -0
  8. packmol_memgen/data/insane_solvents.txt +45 -0
  9. packmol_memgen/data/leaprc.extra_solvents +42 -0
  10. packmol_memgen/data/leaprc.lipid_ext +48 -0
  11. packmol_memgen/data/lipid_ext.lib +12312 -0
  12. packmol_memgen/data/martini_v3.0.0.itp +356605 -0
  13. packmol_memgen/data/memgen.parm +4082 -0
  14. packmol_memgen/data/pdbs.tar.gz +0 -0
  15. packmol_memgen/data/solvent.parm +14 -0
  16. packmol_memgen/example/example.sh +31 -0
  17. packmol_memgen/lib/__init__.py +0 -0
  18. packmol_memgen/lib/amber.py +77 -0
  19. packmol_memgen/lib/charmmlipid2amber/__init__.py +0 -0
  20. packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.csv +7164 -0
  21. packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py +225 -0
  22. packmol_memgen/lib/pdbremix/LICENSE +21 -0
  23. packmol_memgen/lib/pdbremix/__init__.py +0 -0
  24. packmol_memgen/lib/pdbremix/_version.py +1 -0
  25. packmol_memgen/lib/pdbremix/amber.py +1103 -0
  26. packmol_memgen/lib/pdbremix/asa.py +227 -0
  27. packmol_memgen/lib/pdbremix/data/aminoacid.pdb +334 -0
  28. packmol_memgen/lib/pdbremix/data/binaries.json +26 -0
  29. packmol_memgen/lib/pdbremix/data/charmm22.parameter +2250 -0
  30. packmol_memgen/lib/pdbremix/data/charmm22.topology +1635 -0
  31. packmol_memgen/lib/pdbremix/data/color_b.py +682 -0
  32. packmol_memgen/lib/pdbremix/data/hin.lib +130 -0
  33. packmol_memgen/lib/pdbremix/data/hydroxide.lib +88 -0
  34. packmol_memgen/lib/pdbremix/data/make_chi.py +92 -0
  35. packmol_memgen/lib/pdbremix/data/opls.parameter +1108 -0
  36. packmol_memgen/lib/pdbremix/data/opls.topology +1869 -0
  37. packmol_memgen/lib/pdbremix/data/phd.frcmod +82 -0
  38. packmol_memgen/lib/pdbremix/data/phd.leaprc +4 -0
  39. packmol_memgen/lib/pdbremix/data/phd.prepin +35 -0
  40. packmol_memgen/lib/pdbremix/data/template.pdb +334 -0
  41. packmol_memgen/lib/pdbremix/data/znb.frcmod +24 -0
  42. packmol_memgen/lib/pdbremix/data/znb.leaprc +7 -0
  43. packmol_memgen/lib/pdbremix/data/znb.lib +69 -0
  44. packmol_memgen/lib/pdbremix/data.py +264 -0
  45. packmol_memgen/lib/pdbremix/fetch.py +102 -0
  46. packmol_memgen/lib/pdbremix/force.py +627 -0
  47. packmol_memgen/lib/pdbremix/gromacs.py +978 -0
  48. packmol_memgen/lib/pdbremix/lib/__init__.py +0 -0
  49. packmol_memgen/lib/pdbremix/lib/docopt.py +579 -0
  50. packmol_memgen/lib/pdbremix/lib/pyqcprot.py +305 -0
  51. packmol_memgen/lib/pdbremix/namd.py +1078 -0
  52. packmol_memgen/lib/pdbremix/pdbatoms.py +543 -0
  53. packmol_memgen/lib/pdbremix/pdbtext.py +120 -0
  54. packmol_memgen/lib/pdbremix/protein.py +311 -0
  55. packmol_memgen/lib/pdbremix/pymol.py +480 -0
  56. packmol_memgen/lib/pdbremix/rmsd.py +203 -0
  57. packmol_memgen/lib/pdbremix/simulate.py +420 -0
  58. packmol_memgen/lib/pdbremix/spacehash.py +73 -0
  59. packmol_memgen/lib/pdbremix/trajectory.py +286 -0
  60. packmol_memgen/lib/pdbremix/util.py +273 -0
  61. packmol_memgen/lib/pdbremix/v3.py +16 -0
  62. packmol_memgen/lib/pdbremix/v3array.py +482 -0
  63. packmol_memgen/lib/pdbremix/v3numpy.py +350 -0
  64. packmol_memgen/lib/pdbremix/volume.py +155 -0
  65. packmol_memgen/lib/utils.py +1017 -0
  66. packmol_memgen/main.py +2827 -0
  67. packmol_memgen_minimal-1.1.16.dist-info/METADATA +664 -0
  68. packmol_memgen_minimal-1.1.16.dist-info/RECORD +71 -0
  69. packmol_memgen_minimal-1.1.16.dist-info/WHEEL +4 -0
  70. packmol_memgen_minimal-1.1.16.dist-info/entry_points.txt +2 -0
  71. packmol_memgen_minimal-1.1.16.dist-info/licenses/LICENSE +338 -0
packmol_memgen/lib/pdbremix/data/charmm22.parameter ADDED
@@ -0,0 +1,2250 @@
1
+ *>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<<
2
+ *>>>>>>>>>>>>>>>>>>>>> December 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
3
+ * All comments to ADM jr. via the CHARMM web site: www.charmm.org
4
+ * parameter set discussion forum
5
+ *
6
+
7
+ !includes revised aliphatic carbon parameters see (CT*x) for use with
8
+ !trifluoroethanol
9
+
10
+ ! references
11
+ !
12
+ !PROTEINS
13
+ !
14
+ !MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
15
+ !Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
16
+ !Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
17
+ !C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
18
+ !W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
19
+ !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom
20
+ !empirical potential for molecular modeling and dynamics Studies of
21
+ !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616.
22
+ !
23
+ !IONS (see lipid and nucleic acid topology and parameter files for
24
+ !additional ions
25
+ !
26
+ !ZINC
27
+ !
28
+ !Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and
29
+ !Solution: A Simple but Accurate Nonbonded Representation, PROTEINS:
30
+ !Structure, Function, and Genetics 23:12-31 (1995)
31
+ !
32
+
33
+ BONDS
34
+ !
35
+ !V(bond) = Kb(b - b0)**2
36
+ !
37
+ !Kb: kcal/mole/A**2
38
+ !b0: A
39
+ !
40
+ !atom type Kb b0
41
+ !
42
+ !Carbon Dioxide
43
+ CST OST 937.96 1.1600 ! JES
44
+ !Heme to Sulfate (PSUL) link
45
+ SS FE 250.0 2.3200 !force constant a guess
46
+ !equilbrium bond length optimized to reproduce
47
+ !CSD survey values of
48
+ !2.341pm0.01 (mean, standard error)
49
+ !adm jr., 7/01
50
+ C C 600.000 1.3350 ! ALLOW ARO HEM
51
+ ! Heme vinyl substituent (KK, from propene (JCS))
52
+ CA CA 305.000 1.3750 ! ALLOW ARO
53
+ ! benzene, JES 8/25/89
54
+ CE1 CE1 440.000 1.3400 !
55
+ ! for butene; from propene, yin/adm jr., 12/95
56
+ CE1 CE2 500.000 1.3420 !
57
+ ! for propene, yin/adm jr., 12/95
58
+ CE1 CT2 365.000 1.5020 !
59
+ ! for butene; from propene, yin/adm jr., 12/95
60
+ CE1 CT3 383.000 1.5040 !
61
+ ! for butene, yin/adm jr., 12/95
62
+ CE2 CE2 510.000 1.3300 !
63
+ ! for ethene, yin/adm jr., 12/95
64
+ CP1 C 250.000 1.4900 ! ALLOW PRO
65
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
66
+ CP1 CC 250.000 1.4900 ! ALLOW PRO
67
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
68
+ CP1 CD 200.000 1.4900 ! ALLOW PRO
69
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
70
+ CP2 CP1 222.500 1.5270 ! ALLOW PRO
71
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
72
+ CP2 CP2 222.500 1.5370 ! ALLOW PRO
73
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
74
+ CP3 CP2 222.500 1.5370 ! ALLOW PRO
75
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
76
+ CPB CE1 450.000 1.3800 ! ALLOW HEM
77
+ ! Heme (6-liganded): substituents (KK 05/13/91)
78
+ CPB CPA 299.800 1.4432 ! ALLOW HEM
79
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
80
+ CPB CPB 340.700 1.3464 ! ALLOW HEM
81
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
82
+ CPH1 CPH1 410.000 1.3600 ! ALLOW ARO
83
+ ! histidine, adm jr., 6/27/90
84
+ CPM CPA 360.000 1.3716 ! ALLOW HEM
85
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
86
+ CPT CA 305.000 1.3680 ! ALLOW ARO
87
+ ! adm jr., 12/30/91, for jwk
88
+ CPT CPT 360.000 1.4000 ! ALLOW ARO
89
+ !adm jr., 12/30/91, for jwk
90
+ CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
91
+ ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
92
+ CT1 CC 200.000 1.5220 ! ALLOW POL
93
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
94
+ CT1 CD 200.000 1.5220 ! ALLOW POL
95
+ ! adm jr. 5/02/91, acetic acid pure solvent
96
+ CT1 CT1 222.500 1.5000 ! ALLOW ALI
97
+ ! alkane update, adm jr., 3/2/92
98
+ CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
99
+ ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
100
+ CT2 CA 230.000 1.4900 ! ALLOW ALI ARO
101
+ ! phe,tyr, JES 8/25/89
102
+ CT2 CC 200.000 1.5220 ! ALLOW POL
103
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
104
+ CT2 CD 200.000 1.5220 ! ALLOW POL
105
+ ! adm jr. 5/02/91, acetic acid pure solvent
106
+ CT2 CPB 230.000 1.4900 ! ALLOW HEM
107
+ ! Heme (6-liganded): substituents (KK 05/13/91)
108
+ CT2 CPH1 229.630 1.5000 ! ALLOW ARO
109
+ ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
110
+ CT2 CT1 222.500 1.5380 ! ALLOW ALI
111
+ ! alkane update, adm jr., 3/2/92
112
+ CT2 CT2 222.500 1.5300 ! ALLOW ALI
113
+ ! alkane update, adm jr., 3/2/92
114
+ CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
115
+ ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
116
+ CT3 CA 230.000 1.4900 ! ALLOW ALI ARO
117
+ ! toluene, adm jr. 3/7/92
118
+ CT3 CC 200.000 1.5220 ! ALLOW POL
119
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
120
+ CT3 CD 200.000 1.5220 ! ALLOW POL
121
+ ! adm jr. 5/02/91, acetic acid pure solvent
122
+ CT3 CPB 230.000 1.4900 ! ALLOW HEM
123
+ ! Heme (6-liganded): substituents (KK 05/13/91)
124
+ CT3 CPH1 229.630 1.5000 ! ALLOW ARO
125
+ ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
126
+ CT3 CS 190.000 1.5310 ! ALLOW SUL
127
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
128
+ CT3 CT1 222.500 1.5380 ! ALLOW ALI
129
+ ! alkane update, adm jr., 3/2/92
130
+ CT3 CT2 222.500 1.5280 ! ALLOW ALI
131
+ ! alkane update, adm jr., 3/2/92
132
+ CT3 CT3 222.500 1.5300 ! ALLOW ALI
133
+ ! alkane update, adm jr., 3/2/92
134
+ CY CA 350.000 1.3650 ! ALLOW ARO
135
+ !adm jr., 5/08/91, indole CCDB structure search
136
+ CY CPT 350.000 1.4400 ! ALLOW ARO
137
+ !adm jr., 12/30/91, for jwk
138
+ CY CT2 230.000 1.5100 ! ALLOW ARO
139
+ !JWK Kb from alkane freq.. b0 from TRP crystal
140
+ FE CM 258.000 1.9000 ! ALLOW HEM
141
+ ! Heme (6-liganded): CO ligand (KK 05/13/91)
142
+ FE CPM 0.000 3.3814 ! ALLOW HEM
143
+ ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
144
+ H CD 330.000 1.1100 ! ALLOW PEP POL ARO
145
+ ! adm jr. 5/02/91, acetic acid pure solvent
146
+ !HA C 330.000 1.1000 ! ALLOW ARO HEM
147
+ ! Heme vinyl substituent (KK, from propene (JCS))
148
+ HA CA 340.000 1.0830 ! ALLOW ARO
149
+ ! trp, adm jr., 10/02/89
150
+ HA CC 317.130 1.1000 ! ALLOW POL
151
+ ! adm jr., 5/13/91, formamide geometry and vibrations
152
+ HA CP2 309.000 1.1110 ! ALLOW PRO
153
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
154
+ HA CP3 309.000 1.1110 ! ALLOW PRO
155
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
156
+ HA CPM 367.600 1.0900 ! ALLOW HEM
157
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
158
+ HA CS 300.000 1.1110 ! ALLOW SUL
159
+ ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
160
+ HA CT1 309.000 1.1110 ! ALLOW ALI
161
+ ! alkane update, adm jr., 3/2/92
162
+ HA CT2 309.000 1.1110 ! ALLOW ALI
163
+ ! alkane update, adm jr., 3/2/92
164
+ HA CT3 322.000 1.1110 ! ALLOW ALI
165
+ ! alkane update, adm jr., 3/2/92
166
+ HA CY 330.000 1.0800 ! ALLOW ARO
167
+ ! JWK 05/14/91 new r0 from indole
168
+ HE1 CE1 360.500 1.1000 !
169
+ ! for propene, yin/adm jr., 12/95
170
+ HE2 CE2 365.000 1.1000 !
171
+ ! for ethene, yin/adm jr., 12/95
172
+ HB CP1 330.000 1.0800 ! ALLOW PRO
173
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
174
+ HB CT1 330.000 1.0800 ! ALLOW PEP
175
+ ! Alanine Dipeptide ab initio calc's (LK)
176
+ HB CT2 330.000 1.0800 ! ALLOW PEP
177
+ ! Alanine Dipeptide ab initio calc's (LK)
178
+ HB CT3 330.000 1.0800 ! ALLOW PEP
179
+ ! Alanine Dipeptide ab initio calc's (LK)
180
+ HP CA 340.000 1.0800 ! ALLOW ARO
181
+ ! phe,tyr JES 8/25/89
182
+ HP CY 350.000 1.0800 ! ALLOW ARO
183
+ !adm jr., 12/30/91, for jwk
184
+ HR1 CPH1 375.000 1.0830 ! ALLOW ARO
185
+ ! his, adm jr., 6/27/90
186
+ HR1 CPH2 340.000 1.0900 ! ALLOW ARO
187
+ ! his, adm jr., 6/28/29
188
+ HR2 CPH2 333.000 1.0700 ! ALLOW ARO
189
+ ! his, adm jr., 6/27/90
190
+ HR3 CPH1 365.000 1.0830 ! ALLOW ARO
191
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
192
+ HT HT 0.000 1.5139 ! ALLOW WAT
193
+ ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
194
+ N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO
195
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
196
+ N CP1 320.000 1.4340 ! ALLOW PRO
197
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
198
+ N CP3 320.000 1.4550 ! ALLOW PRO
199
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
200
+ NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO
201
+ ! 403.0->463.0, 1.305->1.365 guanidinium (KK)
202
+ NC2 CT2 261.000 1.4900 ! ALLOW ALI POL
203
+ ! arg, (DS)
204
+ NC2 CT3 261.000 1.4900 ! ALLOW ALI POL
205
+ ! methylguanidinium, adm jr., 3/26/92
206
+ NC2 HC 455.000 1.0000 ! ALLOW POL
207
+ ! 405.0->455.0 GUANIDINIUM (KK)
208
+ NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO
209
+ ! Alanine Dipeptide ab initio calc's (LK)
210
+ NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO
211
+ ! NMA Gas & Liquid Phase IR Spectra (LK)
212
+ NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO
213
+ ! NMA Gas & Liquid Phase IR Spectra (LK)
214
+ NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO
215
+ ! NMA Gas & Liquid Phase IR Spectra (LK)
216
+ NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO
217
+ ! Alanine Dipeptide ab initio calc's (LK)
218
+ NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO
219
+ ! (DS)
220
+ NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO
221
+ ! adm jr. 4/10/91, acetamide
222
+ NH2 CT2 240.000 1.4550
223
+ ! from NH2 CT3, neutral glycine, adm jr.
224
+ NH2 CT3 240.000 1.4550 ! ALLOW POL
225
+ ! methylamine geom/freq, adm jr., 6/2/92
226
+ NH2 H 480.000 1.0000 ! ALLOW POL
227
+ ! adm jr. 8/13/90 acetamide geometry and vibrations
228
+ NH2 HC 460.000 1.0000 ! ALLOW POL
229
+ ! methylamine geom/freq, adm jr., 6/2/92
230
+ NH3 CT1 200.000 1.4800 ! ALLOW ALI POL
231
+ ! new stretch and bend; methylammonium (KK 03/10/92)
232
+ NH3 CT2 200.000 1.4800 ! ALLOW ALI POL
233
+ ! new stretch and bend; methylammonium (KK 03/10/92)
234
+ NH3 CT3 200.000 1.4800 ! ALLOW ALI POL
235
+ ! new stretch and bend; methylammonium (KK 03/10/92)
236
+ NH3 HC 403.000 1.0400 ! ALLOW POL
237
+ ! new stretch and bend; methylammonium (KK 03/10/92)
238
+ NP CP1 320.000 1.4850 ! ALLOW PRO
239
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
240
+ NP CP3 320.000 1.5020 ! ALLOW PRO
241
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
242
+ NP HC 460.000 1.0060 ! ALLOW PRO
243
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
244
+ NPH CPA 377.200 1.3757 ! ALLOW HEM
245
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
246
+ NPH FE 270.200 1.9580 ! ALLOW HEM
247
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
248
+ NR1 CPH1 400.000 1.3800 ! ALLOW ARO
249
+ ! his, ADM JR., 7/20/89
250
+ NR1 CPH2 400.000 1.3600 ! ALLOW ARO
251
+ ! his, ADM JR., 7/20/89
252
+ NR1 H 466.000 1.0000 ! ALLOW ARO
253
+ ! his, ADM JR., 7/20/89
254
+ NR2 CPH1 400.000 1.3800 ! ALLOW ARO
255
+ ! his, ADM JR., 7/20/89
256
+ NR2 CPH2 400.000 1.3200 ! ALLOW ARO
257
+ ! his, ADM JR., 7/20/89
258
+ NR2 FE 65.000 2.2000 ! ALLOW HEM
259
+ ! Heme (6-liganded): His ligand (KK 05/13/91)
260
+ NR3 CPH1 380.000 1.3700 ! ALLOW ARO
261
+ ! his, adm jr., 6/28/90
262
+ NR3 CPH2 380.000 1.3200 ! ALLOW ARO
263
+ ! his, adm jr., 6/27/90
264
+ NR3 H 453.000 1.0000 ! ALLOW ARO
265
+ ! his, adm jr., 6/27/90
266
+ NY CA 270.000 1.3700 ! ALLOW ARO
267
+ !adm jr., 12/30/91, for jwk
268
+ NY CPT 270.000 1.3750 ! ALLOW ARO
269
+ !adm jr., 12/30/91, for jwk
270
+ NY H 465.000 0.9760 ! ALLOW ARO
271
+ ! indole JWK 08/28/89
272
+ O C 620.000 1.2300 ! ALLOW PEP POL ARO
273
+ ! Peptide geometry, condensed phase (LK)
274
+ O CC 650.000 1.2300 ! ALLOW PEP POL ARO
275
+ ! adm jr. 4/10/91, acetamide
276
+ OB CC 750.000 1.2200 ! ALLOW PEP POL ARO
277
+ ! adm jr., 10/17/90, acetic acid vibrations and geom.
278
+ OB CD 750.000 1.2200 ! ALLOW PEP POL ARO
279
+ ! adm jr. 5/02/91, acetic acid pure solvent
280
+ OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION
281
+ ! adm jr. 8/27/91, phenoxide
282
+ OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION
283
+ ! adm jr. 7/23/91, acetic acid
284
+ OC CT2 450.000 1.3300 ! ALLOW ALC
285
+ ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
286
+ OC CT3 450.000 1.3300 ! ALLOW ALC
287
+ ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
288
+ OH1 CA 334.300 1.4110 ! ALLOW ARO ALC
289
+ ! MeOH, EMB 10/10/89,
290
+ OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC
291
+ ! adm jr. 5/02/91, acetic acid pure solvent
292
+ OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO
293
+ ! methanol vib fit EMB 11/21/89
294
+ OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO
295
+ ! methanol vib fit EMB 11/21/89
296
+ OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO
297
+ ! methanol vib fit EMB 11/21/89
298
+ OH1 H 545.000 0.9600 ! ALLOW ALC ARO
299
+ ! EMB 11/21/89 methanol vib fit
300
+ OM CM 1115.000 1.1280 ! ALLOW HEM
301
+ ! Heme (6-liganded): CO ligand (KK 05/13/91)
302
+ OM FE 250.000 1.8000 ! ALLOW HEM
303
+ ! Heme (6-liganded): O2 ligand (KK 05/13/91)
304
+ OM OM 600.000 1.2300 ! ALLOW HEM
305
+ ! Heme (6-liganded): O2 ligand (KK 05/13/91)
306
+ OS CD 150.000 1.3340 ! ALLOW POL PEP
307
+ ! adm jr. 5/02/91, acetic acid pure solvent
308
+ OS CT3 340.000 1.4300 ! ALLOW POL PEP
309
+ ! adm jr., 4/05/91, for PRES CT1 from methylacetate
310
+ OT HT 450.000 0.9572 ! ALLOW WAT
311
+ ! FROM TIPS3P GEOM
312
+ S CT2 198.000 1.8180 ! ALLOW ALI SUL ION
313
+ ! fitted to C-S s 9/26/92 (FL)
314
+ S CT3 240.000 1.8160 ! ALLOW ALI SUL ION
315
+ ! fitted to C-S s 9/26/92 (FL)
316
+ S HS 275.000 1.3250 ! ALLOW SUL ION
317
+ ! methanethiol pure solvent, adm jr., 6/22/92
318
+ SM CT2 214.000 1.8160 ! ALLOW SUL ION
319
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
320
+ SM CT3 214.000 1.8160 ! ALLOW SUL ION
321
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
322
+ SM SM 173.000 2.0290 ! ALLOW SUL ION
323
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
324
+ SS CS 205.000 1.8360 ! ALLOW SUL
325
+ ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
326
+
327
+ ANGLES
328
+ !
329
+ !V(angle) = Ktheta(Theta - Theta0)**2
330
+ !
331
+ !V(Urey-Bradley) = Kub(S - S0)**2
332
+ !
333
+ !Ktheta: kcal/mole/rad**2
334
+ !Theta0: degrees
335
+ !Kub: kcal/mole/A**2 (Urey-Bradley)
336
+ !S0: A
337
+ !
338
+ !atom types Ktheta Theta0 Kub S0
339
+ !
340
+ !Carbon Dioxide, JES
341
+ OST CST OST 3000.00 180.0000 ! CO2, JES
342
+ !Heme to Sulfate (PSUL) link
343
+ CS SS FE 50.0 100.6 !force constant a guess
344
+ !equilibrium angle optimized to reproduce
345
+ !CSD survey values
346
+ !107.5pm0.6 (mean, standard error)
347
+ !adm jr., 7/01
348
+ SS FE NPH 100.0 90.0 !force constant a guess
349
+ !adm jr., 7/01
350
+ !
351
+ CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO
352
+ ! JES 8/25/89
353
+ CE1 CE1 CT2 48.00 123.50 !
354
+ ! for 2-butene, yin/adm jr., 12/95
355
+ CE1 CE1 CT3 48.00 123.50 !
356
+ ! for 2-butene, yin/adm jr., 12/95
357
+ CE1 CT2 CT3 32.00 112.20 !
358
+ ! for 1-butene; from propene, yin/adm jr., 12/95
359
+ CE2 CE1 CT2 48.00 126.00 !
360
+ ! for 1-butene; from propene, yin/adm jr., 12/95
361
+ CE2 CE1 CT3 47.00 125.20 !
362
+ ! for propene, yin/adm jr., 12/95
363
+ CP1 N C 60.000 117.0000 ! ALLOW PRO
364
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
365
+ CP2 CP1 C 52.000 112.3000 ! ALLOW PRO
366
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
367
+ CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO
368
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
369
+ CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP
370
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
371
+ CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO
372
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
373
+ CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO
374
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
375
+ CP3 N C 60.000 117.0000 ! ALLOW PRO
376
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
377
+ CP3 N CP1 100.000 114.2000 ! ALLOW PRO
378
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
379
+ CP3 NP CP1 100.000 111.0000 ! ALLOW PRO
380
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
381
+ CPA CPB CE1 70.000 126.7400 ! ALLOW HEM
382
+ ! Heme (6-liganded): substituents (KK 05/13/91)
383
+ CPA CPM CPA 94.200 125.1200 ! ALLOW HEM
384
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
385
+ CPA NPH CPA 139.300 103.9000 ! ALLOW HEM
386
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
387
+ CPB CE1 CE2 70.000 121.5000 ! ALLOW HEM
388
+ ! Heme (6-liganded): substituents (KK 05/13/91)
389
+ CPB CPB CE1 70.000 126.7500 ! ALLOW HEM
390
+ ! Heme (6-liganded): substituents (KK 05/13/91)
391
+ CPB CPB CPA 30.800 106.5100 ! ALLOW HEM
392
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
393
+ CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO
394
+ ! his, adm jr., 6/27/90
395
+ CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO
396
+ ! his, adm jr., 6/27/90
397
+ CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO
398
+ ! his, ADM JR., 7/20/89
399
+ CPM CPA CPB 61.600 124.0700 ! ALLOW HEM
400
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
401
+ CPT CA CA 60.000 118.0000 ! ALLOW ARO
402
+ !adm jr., 12/30/91, for jwk
403
+ CPT CPT CA 60.000 122.0000 ! ALLOW ARO
404
+ !adm jr., 12/30/91, for jwk
405
+ CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO
406
+ !adm jr., 12/30/91, for jwk
407
+ CPT NY CA 110.000 108.0000 ! ALLOW ARO
408
+ !adm jr., 12/30/91, for jwk
409
+ CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
410
+ ! Alanine Dipeptide ab initio calc's (LK)
411
+ CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
412
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
413
+ CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
414
+ ! alkane update, adm jr., 3/2/92
415
+ CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
416
+ ! PARALLH19 (JES)
417
+ CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
418
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
419
+ CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
420
+ ! adm jr. 5/02/91, acetic acid pure solvent
421
+ CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
422
+ ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
423
+ CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
424
+ ! alkane frequencies (MJF), alkane geometries (SF)
425
+ CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
426
+ ! NMA Vib Modes (LK)
427
+ CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO
428
+ ! PARALLH19 (JES)
429
+ CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM
430
+ ! Heme (6-liganded): substituents (KK 05/13/91)
431
+ CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM
432
+ ! Heme (6-liganded): substituents (KK 05/13/91)
433
+ CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
434
+ ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
435
+ CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
436
+ ! Alanine Dipeptide ab initio calc's (LK)
437
+ CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
438
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
439
+ CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
440
+ ! adm jr. 5/02/91, acetic acid pure solvent
441
+ CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
442
+ ! alkane update, adm jr., 3/2/92
443
+ CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
444
+ ! from CT2 CT1 C, for lactams, adm jr.
445
+ CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
446
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
447
+ CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
448
+ ! adm jr. 5/02/91, acetic acid pure solvent
449
+ CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM
450
+ ! Heme (6-liganded): substituents (KK 05/13/91)
451
+ CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
452
+ ! alkane frequencies (MJF), alkane geometries (SF)
453
+ CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI
454
+ ! alkane update, adm jr., 3/2/92
455
+ CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
456
+ ! alkane frequencies (MJF), alkane geometries (SF)
457
+ CT2 CY CA 45.800 129.4000 ! ALLOW ARO
458
+ !adm jr., 5/08/91, indole CCDB structure search
459
+ CT2 CY CPT 45.800 124.0000 ! ALLOW ARO
460
+ !adm jr., 5/08/91, indole CCDB structure search
461
+ CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
462
+ ! 107.5->120.0 to make planar Arg (KK)
463
+ CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
464
+ ! NMA Vib Modes (LK)
465
+ CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
466
+ ! adm jr. 5/02/91, acetic acid pure solvent
467
+ CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO
468
+ ! toluene, adm jr., 3/7/92
469
+ CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM
470
+ ! Heme (6-liganded): substituents (KK 05/13/91)
471
+ CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM
472
+ ! Heme (6-liganded): substituents (KK 05/13/91)
473
+ CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
474
+ ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
475
+ CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
476
+ ! Alanine Dipeptide ab initio calc's (LK)
477
+ CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
478
+ ! adm jr. 4/09/92, for ALA cter
479
+ CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI
480
+ ! alkane update, adm jr., 3/2/92
481
+ CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI
482
+ ! alkane update, adm jr., 3/2/92
483
+ CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
484
+ ! alkane update, adm jr., 3/2/92
485
+ CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
486
+ ! ethylbenzene, adm jr., 3/7/92
487
+ CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
488
+ ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
489
+ CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
490
+ ! alkane frequencies (MJF), alkane geometries (SF)
491
+ CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI
492
+ ! alkane update, adm jr., 3/2/92
493
+ CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
494
+ ! alkane update, adm jr., 3/2/92
495
+ CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
496
+ ! methylguanidinium, adm jr., 3/26/92
497
+ CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
498
+ ! NMA Vib Modes (LK)
499
+ CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
500
+ ! adm jr. 5/02/91, acetic acid pure solvent
501
+ CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION
502
+ ! expt. MeEtS, 3/26/92 (FL)
503
+ CY CPT CA 160.000 130.6000 ! ALLOW ARO
504
+ !adm jr., 12/30/91, for jwk
505
+ CY CPT CPT 110.000 107.4000 ! ALLOW ARO
506
+ !adm jr., 12/30/91, for jwk
507
+ CY CT2 CT1 58.350 114.0000 ! ALLOW ARO
508
+ ! from TRP crystal, JWK
509
+ CY CT2 CT3 58.350 114.0000 ! ALLOW ARO
510
+ ! from TRP crystal, JWK
511
+ FE NPH CPA 96.150 128.0500 ! ALLOW HEM
512
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
513
+ FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM
514
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
515
+ FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM
516
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
517
+ H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO
518
+ ! NMA Vib Modes (LK)
519
+ H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI
520
+ ! NMA Vibrational Modes (LK)
521
+ H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI
522
+ ! NMA Vibrational Modes (LK)
523
+ H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI
524
+ ! NMA Vibrational Modes (LK)
525
+ H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO
526
+ ! his, adm jr. 8/13/90 acetamide geometry and vibrations
527
+ H NH2 H 23.000 120.0000 ! ALLOW POL
528
+ ! adm jr. 8/13/90 acetamide geometry and vibrations
529
+ H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO
530
+ ! his, adm jr., 6/27/90
531
+ H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO
532
+ ! his, adm jr., 6/27/90
533
+ H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO
534
+ ! his, adm jr., 6/27/90
535
+ H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO
536
+ ! his, adm jr., 6/27/90
537
+ H NY CA 28.000 126.0000 ! ALLOW ARO
538
+ !adm jr., 12/30/91, for jwk
539
+ H NY CPT 28.000 126.0000 ! ALLOW ARO
540
+ !adm jr., 12/30/91, for jwk
541
+ H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO
542
+ ! JES 8/25/89 phenol
543
+ H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL
544
+ ! adm jr. 5/02/91, acetic acid pure solvent
545
+ H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI
546
+ ! methanol vib fit EMB 11/21/89
547
+ H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI
548
+ ! methanol vib fit EMB 11/21/89
549
+ H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI
550
+ ! methanol vib fit EMB 11/21/89
551
+ !HA C C 50.000 120.5000 ! ALLOW PEP POL ARO
552
+ ! Heme vinyl substituent (KK from propene (JCS))
553
+ !HA C CPB 50.000 120.0000 ! ALLOW HEM
554
+ ! Heme (6-liganded): substituents (KK 05/13/91)
555
+ !HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO
556
+ ! Heme vinyl substituent (KK from propene (JCS))
557
+ HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO
558
+ ! trp, adm jr., 10/02/89
559
+ HA CA CPT 41.000 122.0000 ! ALLOW ARO
560
+ !adm jr., 5/08/91, indole CCDB structure search
561
+ HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
562
+ ! JWK 05/14/91 new theta0 and r0UB from indole
563
+ HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO
564
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
565
+ HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
566
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
567
+ HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
568
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
569
+ HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
570
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
571
+ HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
572
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
573
+ HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
574
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
575
+ HA CPM CPA 12.700 117.4400 ! ALLOW HEM
576
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
577
+ HA CPM FE 0.000 180.0000 ! ALLOW HEM
578
+ ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
579
+ HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL
580
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
581
+ HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL
582
+ ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
583
+ HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
584
+ ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
585
+ HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
586
+ ! adm jr. 5/02/91, acetic acid pure solvent
587
+ HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI
588
+ ! alkane update, adm jr., 3/2/92
589
+ HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI
590
+ ! alkane update, adm jr., 3/2/92
591
+ HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI
592
+ ! alkane update, adm jr., 3/2/92
593
+ HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd
594
+ ! based on HA CT2 HA
595
+ HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
596
+ ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
597
+ HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO
598
+ ! PARALLH19 (JES)
599
+ HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
600
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
601
+ HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
602
+ ! adm jr. 5/02/91, acetic acid pure solvent
603
+ HA CT2 CE1 45.00 111.50 !
604
+ ! for 1-butene; from propene, yin/adm jr., 12/95
605
+ HA CT2 CPB 50.000 109.5000 ! ALLOW HEM
606
+ ! Heme (6-liganded): substituents (KK 05/13/91)
607
+ HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO
608
+ ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
609
+ HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
610
+ ! alkane frequencies (MJF), alkane geometries (SF)
611
+ HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI
612
+ ! alkane update, adm jr., 3/2/92
613
+ HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI
614
+ ! alkane update, adm jr., 3/2/92
615
+ HA CT2 CY 33.430 109.5000 ! ALLOW ARO
616
+ ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA
617
+ HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI
618
+ ! alkane update, adm jr., 3/2/92
619
+ HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
620
+ ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
621
+ HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO
622
+ ! toluene, adm jr. 3/7/92
623
+ HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
624
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
625
+ HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
626
+ ! adm jr. 5/02/91, acetic acid pure solvent
627
+ HA CT3 CE1 42.00 111.50 !
628
+ ! for 2-butene, yin/adm jr., 12/95
629
+ HA CT3 CPB 50.000 109.5000 ! ALLOW HEM
630
+ ! Heme (6-liganded): substituents (KK 05/13/91)
631
+ HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO
632
+ ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
633
+ HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL
634
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
635
+ HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
636
+ ! alkane frequencies (MJF), alkane geometries (SF)
637
+ HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI
638
+ ! alkane update, adm jr., 3/2/92
639
+ HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI
640
+ ! alkane update, adm jr., 3/2/92
641
+ HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI
642
+ ! alkane update, adm jr., 3/2/92
643
+ HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO
644
+ ! JWK 05/14/91 new theta0 and r0UB from indole
645
+ HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
646
+ ! JWK 05/14/91 new theta0 and r0UB from indole
647
+ HE1 CE1 CE1 52.00 119.50 !
648
+ ! for 2-butene, yin/adm jr., 12/95
649
+ HE1 CE1 CE2 42.00 118.00 !
650
+ ! for propene, yin/adm jr., 12/95
651
+ HE1 CE1 CT2 40.00 116.00 !
652
+ ! for 1-butene; from propene, yin/adm jr., 12/95
653
+ HE1 CE1 CT3 22.00 117.00 !
654
+ ! for propene, yin/adm jr., 12/95
655
+ HE1 CE1 CPB 50.000 120.0000 ! ALLOW HEM
656
+ ! Heme (6-liganded): substituents (KK 05/13/91)
657
+ HE2 CE2 CE1 45.00 120.50 !
658
+ ! for propene, yin/adm jr., 12/95
659
+ HE2 CE2 CE2 55.50 120.50 !
660
+ ! for ethene, yin/adm jr., 12/95
661
+ HE2 CE2 HE2 19.00 119.00 !
662
+ ! for propene, yin/adm jr., 12/95
663
+ HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO
664
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
665
+ HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO
666
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
667
+ HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO
668
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
669
+ HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO
670
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
671
+ HB CT1 C 50.000 109.5000 ! ALLOW PEP
672
+ ! Alanine Dipeptide ab initio calc's (LK)
673
+ HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL
674
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
675
+ HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL
676
+ ! adm jr. 5/02/91, acetic acid pure solvent
677
+ HB CT1 CT1 35.000 111.0000 ! ALLOW PEP
678
+ ! Alanine Dipeptide ab initio calc's (LK)
679
+ HB CT1 CT2 35.000 111.0000 ! ALLOW PEP
680
+ ! Alanine Dipeptide ab initio calc's (LK)
681
+ HB CT1 CT3 35.000 111.0000 ! ALLOW PEP
682
+ ! Alanine Dipeptide ab initio calc's (LK)
683
+ HB CT2 C 50.000 109.5000 ! ALLOW PEP
684
+ ! Alanine Dipeptide ab initio calc's (LK)
685
+ HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL
686
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
687
+ HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL
688
+ ! adm jr. 5/02/91, acetic acid pure solvent
689
+ HB CT2 HB 36.000 115.0000 ! ALLOW PEP
690
+ ! Alanine Dipeptide ab initio calc's (LK)
691
+ HB CT3 C 50.000 109.5000 ! ALLOW PEP
692
+ ! Alanine Dipeptide ab initio calc's (LK)
693
+ HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO
694
+ ! 35.3->49.0 GUANIDINIUM (KK)
695
+ HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI
696
+ ! 107.5->120.0 to make planar Arg (KK)
697
+ HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI
698
+ ! methylguanidinium, adm jr., 3/26/92
699
+ HC NC2 HC 25.000 120.0000 ! ALLOW POL
700
+ ! 40.0->25.0 GUANIDINIUM (KK)
701
+ HC NH2 CT2 50.000 111.0000 ! ALLOW POL
702
+ ! from HC NH2 CT3, neutral glycine, adm jr.
703
+ HC NH2 CT3 50.000 111.0000 ! ALLOW POL
704
+ ! methylamine geom/freq, adm jr., 6/2/92
705
+ HC NH2 HC 39.000 106.5000 ! ALLOW POL
706
+ ! 40.0->25.0 GUANIDINIUM (KK)
707
+ HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
708
+ ! new stretch and bend; methylammonium (KK 03/10/92)
709
+ HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
710
+ ! new stretch and bend; methylammonium (KK 03/10/92)
711
+ HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
712
+ ! new stretch and bend; methylammonium (KK 03/10/92)
713
+ HC NH3 HC 44.000 109.5000 ! ALLOW POL
714
+ ! new stretch and bend; methylammonium (KK 03/10/92)
715
+ HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
716
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
717
+ HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
718
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
719
+ HC NP HC 51.000 107.5000 ! ALLOW PRO
720
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
721
+ HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO
722
+ ! JES 8/25/89 benzene
723
+ HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO
724
+ !adm jr., 12/30/91, for jwk
725
+ HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
726
+ ! JWK 05/14/91 new theta0 and r0UB from indole
727
+ HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO
728
+ !adm jr., 12/30/91, for jwk
729
+ HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
730
+ ! JWK 05/14/91 new theta0 and r0UB from indole
731
+ HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO
732
+ ! adm jr., 6/27/90, his
733
+ HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO
734
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
735
+ HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI
736
+ ! methanethiol pure solvent, adm jr., 6/22/92
737
+ HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI
738
+ ! methanethiol pure solvent, adm jr., 6/22/92
739
+ HT OT HT 55.000 104.5200 ! ALLOW WAT
740
+ ! TIP3P GEOMETRY, ADM JR.
741
+ N C CP1 20.000 112.5000 ! ALLOW PRO
742
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
743
+ N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
744
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
745
+ N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
746
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
747
+ N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
748
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
749
+ N CP1 C 50.000 108.2000 ! ALLOW PRO
750
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
751
+ N CP1 CC 50.000 108.2000 ! ALLOW PRO
752
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
753
+ N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP
754
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
755
+ N CP1 CP2 70.000 110.8000 ! ALLOW PRO
756
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
757
+ N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO
758
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
759
+ N CP3 CP2 70.000 110.5000 ! ALLOW PRO
760
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
761
+ N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO
762
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
763
+ NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO
764
+ ! changed from 60.0/120.3 for guanidinium (KK)
765
+ NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL
766
+ ! arg, (DS)
767
+ NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL
768
+ ! arg, (DS)
769
+ NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL
770
+ ! methylguanidinium, adm jr., 3/26/92
771
+ NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO
772
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
773
+ NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO
774
+ ! NMA Vib Modes (LK)
775
+ NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO
776
+ ! NMA Vib Modes (LK)
777
+ NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO
778
+ ! NMA Vib Modes (LK)
779
+ NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
780
+ ! Alanine Dipeptide ab initio calc's (LK)
781
+ NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
782
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
783
+ NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
784
+ ! adm jr. 5/02/91, acetic acid pure solvent
785
+ NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO
786
+ ! Alanine Dipeptide ab initio calc's (LK)
787
+ NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
788
+ ! Alanine Dipeptide ab initio calc's (LK)
789
+ NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO
790
+ ! Alanine Dipeptide ab initio calc's (LK)
791
+ NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP
792
+ ! Alanine Dipeptide ab initio calc's (LK)
793
+ NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
794
+ ! Alanine Dipeptide ab initio calc's (LK)
795
+ NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
796
+ ! adm jr. 5/20/92, for asn,asp,gln,glu and cters
797
+ NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
798
+ ! adm jr. 5/02/91, acetic acid pure solvent
799
+ NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
800
+ ! from NH1 CT1 CT2, for lactams, adm jr.
801
+ NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
802
+ ! from NH1 CT3 HA, for lactams, adm jr.
803
+ NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP
804
+ ! Alanine Dipeptide ab initio calc's (LK)
805
+ NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
806
+ ! NMA crystal (JCS)
807
+ NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
808
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
809
+ NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
810
+ ! adm jr. 8/13/90 acetamide geometry and vibrations
811
+ NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
812
+ ! adm jr. 8/13/90 acetamide geometry and vibrations
813
+ NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
814
+ ! adm jr. 8/13/90 acetamide geometry and vibrations
815
+ NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL
816
+ ! adm jr., 5/13/91, formamide geometry and vibrations
817
+ NH2 CT2 HA 38.000 109.50 50.00 2.14000
818
+ !from NH2 CT3 HA, neutral lysine
819
+ NH2 CT2 HB 38.000 109.50 50.00 2.14000
820
+ !from NH2 CT3 HA, neutral glycine, adm jr.
821
+ NH2 CT2 CD 52.000 108.0000
822
+ !from CT2 CT2 CD, neutral glycine, adm jr.
823
+ NH2 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL
824
+ !from NH3 CT2 CT2, neutral lysine
825
+ NH2 CT3 HA 38.000 109.50 50.00 2.14000 ! ALLOW POL
826
+ ! methylamine geom/freq, adm jr., 6/2/92
827
+ NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI
828
+ ! new aliphatics, adm jr., 2/3/92
829
+ NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI
830
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
831
+ NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL
832
+ ! new aliphatics, adm jr., 2/3/92
833
+ NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL
834
+ ! new aliphatics, adm jr., 2/3/92
835
+ NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL
836
+ ! new aliphatics, adm jr., 2/3/92
837
+ NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP
838
+ ! new aliphatics, adm jr., 2/3/92
839
+ NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI
840
+ ! alanine (JCS)
841
+ NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI
842
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
843
+ NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI
844
+ ! adm jr. 5/02/91, acetic acid pure solvent
845
+ NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL
846
+ ! alanine (JCS)
847
+ NH3 CT2 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL
848
+ ! new stretch and bend; methylammonium (KK 03/10/92)
849
+ NH3 CT2 HB 51.500 107.5000 ! ALLOW ALI POL PEP
850
+ ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK)
851
+ NH3 CT3 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL
852
+ ! new stretch and bend; methylammonium (KK 03/10/92)
853
+ NP CP1 C 50.000 106.0000 ! ALLOW PRO
854
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
855
+ NP CP1 CC 50.000 106.0000 ! ALLOW PRO
856
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
857
+ NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP
858
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
859
+ NP CP1 CP2 70.000 108.5000 ! ALLOW PRO
860
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
861
+ NP CP1 HB 51.500 107.5000 ! ALLOW ALI POL PEP PRO
862
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
863
+ NP CP3 CP2 70.000 108.5000 ! ALLOW PRO
864
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
865
+ NP CP3 HA 51.500 109.1500 ! ALLOW PEP PRO
866
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
867
+ NPH CPA CPB 122.000 111.5400 ! ALLOW HEM
868
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
869
+ NPH CPA CPM 88.000 124.3900 ! ALLOW HEM
870
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
871
+ NPH FE CM 50.000 90.0000 ! ALLOW HEM
872
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
873
+ NPH FE CPM 0.000 45.0000 ! ALLOW HEM
874
+ ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
875
+ NPH FE NPH 14.390 90.0000 ! ALLOW HEM
876
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
877
+ NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO
878
+ ! his, ADM JR., 7/20/89
879
+ NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO
880
+ ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
881
+ NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO
882
+ ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
883
+ NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO
884
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
885
+ NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO
886
+ ! his, adm jr., 6/27/90
887
+ NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO
888
+ ! his, ADM JR., 7/20/89
889
+ NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO
890
+ ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
891
+ NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO
892
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
893
+ NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO
894
+ ! his, adm jr., 6/27/90
895
+ NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO
896
+ ! his, adm jr., 6/27/90
897
+ NR2 FE CM 50.000 180.0000 ! ALLOW HEM
898
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
899
+ NR2 FE NPH 50.000 90.0000 ! ALLOW HEM
900
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
901
+ NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO
902
+ ! his, ADM JR., 7/20/89
903
+ NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO
904
+ ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
905
+ NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO
906
+ ! his, adm jr., 6/27/90
907
+ NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO
908
+ ! his, adm jr., 6/27/90
909
+ NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO
910
+ ! his, ADM JR., 7/20/89
911
+ NY CA CY 120.000 110.00 25.00 2.24000 ! ALLOW ARO
912
+ !adm jr., 12/30/91, for jwk
913
+ NY CA HA 32.000 125.00 25.00 2.17700 ! ALLOW ARO
914
+ ! JWK 05/14/91 new theta0 and r0UB from indole
915
+ NY CA HP 32.000 125.00 25.00 2.17700 ! ALLOW ARO
916
+ ! JWK 05/14/91 new theta0 and r0UB from indole
917
+ NY CPT CA 160.000 130.6000 ! ALLOW ARO
918
+ !adm jr., 12/30/91, for jwk
919
+ NY CPT CPT 110.000 107.4000 ! ALLOW ARO
920
+ !adm jr., 12/30/91, for jwk
921
+ O C CP1 80.000 118.0000 ! ALLOW PEP PRO
922
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
923
+ O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO
924
+ ! Alanine Dipeptide ab initio calc's (LK)
925
+ O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO
926
+ ! Alanine Dipeptide ab initio calc's (LK)
927
+ O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO
928
+ ! Alanine Dipeptide ab initio calc's (LK)
929
+ O C H 50.000 121.7000 ! ALLOW PEP POL ARO
930
+ ! acetaldehyde (JCS)
931
+ O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO
932
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
933
+ O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO
934
+ ! NMA Vib Modes (LK)
935
+ O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO
936
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
937
+ O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
938
+ ! adm jr. 4/10/91, acetamide update
939
+ O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
940
+ ! adm jr. 4/10/91, acetamide update
941
+ O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
942
+ ! adm jr. 4/10/91, acetamide update
943
+ O CC HA 44.000 122.0000 ! ALLOW POL
944
+ ! adm jr., 5/13/91, formamide geometry and vibrations
945
+ O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO
946
+ ! adm jr. 4/10/91, acetamide update
947
+ OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO
948
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
949
+ OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
950
+ ! adm jr. 5/02/91, acetic acid pure solvent
951
+ OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
952
+ ! adm jr. 5/02/91, acetic acid pure solvent
953
+ OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
954
+ ! adm jr. 5/02/91, acetic acid pure solvent
955
+ OC CA CA 40.000 120.0000 ! ALLOW POL ARO
956
+ ! adm jr. 8/27/91, phenoxide
957
+ OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO
958
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
959
+ OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
960
+ ! adm jr. 7/23/91, correction, ACETATE (KK)
961
+ OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
962
+ ! adm jr. 7/23/91, correction, ACETATE (KK)
963
+ OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
964
+ ! adm jr. 7/23/91, correction, ACETATE (KK)
965
+ OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO
966
+ ! adm jr. 7/23/91, correction, ACETATE (KK)
967
+ OC CT2 CT3 65.000 122.0000 ! ALLOW ALC
968
+ ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
969
+ OC CT2 HA 65.000 118.3000 ! ALLOW ALC
970
+ ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
971
+ OC CT3 HA 65.000 118.3000 ! ALLOW ALC
972
+ ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
973
+ OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC
974
+ ! PARALLH19 WITH [122.3] (JES)
975
+ OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
976
+ ! adm jr, 10/17/90, acetic acid vibrations
977
+ OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
978
+ ! adm jr, 10/17/90, acetic acid vibrations
979
+ OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC
980
+ ! adm jr, 10/17/90, acetic acid vibrations
981
+ OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
982
+ ! MeOH, EMB, 10/10/89
983
+ OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
984
+ ! MeOH, EMB, 10/10/89
985
+ OH1 CT1 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
986
+ ! MeOH, EMB, 10/10/89
987
+ OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
988
+ ! MeOH, EMB, 10/10/89
989
+ OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO
990
+ ! MeOH, EMB, 10/10/89
991
+ OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
992
+ ! MeOH, EMB, 10/10/89
993
+ OH1 CT2 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
994
+ ! MeOH, EMB, 10/10/89
995
+ OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
996
+ ! MeOH, EMB, 10/10/89
997
+ OM CM FE 35.000 180.0000 ! ALLOW HEM
998
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
999
+ OM FE NPH 5.000 90.0000 ! ALLOW HEM
1000
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
1001
+ OM OM FE 0.000 180.0000 ! ALLOW HEM
1002
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
1003
+ OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO
1004
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1005
+ OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
1006
+ ! adm jr., 4/05/91, for PRES CT1 from methylacetate
1007
+ OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
1008
+ ! adm jr., 4/05/91, for PRES CT1 from methylacetate
1009
+ OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
1010
+ ! adm jr., 4/05/91, for PRES CT1 from methylacetate
1011
+ OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL
1012
+ ! adm jr. 3/19/92, from lipid methyl acetate
1013
+ OS CT2 HA 60.000 109.5000 ! ALLOW PEP POL
1014
+ ! adm jr. 4/05/91, for PRES CT1 from methyl acetate
1015
+ OS CT3 HA 60.000 109.5000 ! ALLOW PEP POL
1016
+ ! adm jr. 4/05/91, for PRES CT1 from methyl acetate
1017
+ S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
1018
+ ! as in expt.MeEtS & DALC crystal, 5/15/92
1019
+ S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION
1020
+ ! expt. MeEtS, 3/26/92 (FL)
1021
+ S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION
1022
+ ! expt. MeEtS, 3/26/92 (FL)
1023
+ S CT2 HA 46.100 111.3000 ! ALLOW ALI SUL ION
1024
+ ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
1025
+ S CT3 HA 46.100 111.3000 ! ALLOW ALI SUL ION
1026
+ ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
1027
+ SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
1028
+ ! as in expt.MeEtS & DALC crystal, 5/15/92
1029
+ SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION
1030
+ ! new S-S atom type 8/24/90
1031
+ SM CT3 HA 38.000 111.0000 ! ALLOW ALI SUL ION
1032
+ ! new S-S atom type 8/24/90
1033
+ SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION
1034
+ ! expt. dimethyldisulfide, 3/26/92 (FL)
1035
+ SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION
1036
+ ! expt. dimethyldisulfide, 3/26/92 (FL)
1037
+ SS CS CT3 55.000 118.0000 ! ALLOW SUL
1038
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
1039
+ SS CS HA 40.000 112.3000 ! ALLOW SUL
1040
+ ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
1041
+
1042
+ DIHEDRALS
1043
+ !
1044
+ !V(dihedral) = Kchi(1 + cos(n(chi) - delta))
1045
+ !
1046
+ !Kchi: kcal/mole
1047
+ !n: multiplicity
1048
+ !delta: degrees
1049
+ !
1050
+ !atom types Kchi n delta
1051
+ !
1052
+ !Heme to Sulfate (PSUL) link
1053
+ X FE SS X 0.0000 4 0.00 ! guess
1054
+ !adm jr., 7/01
1055
+ X CS SS X 0.0000 3 0.20 ! guess
1056
+ !from methanethiol, HS S CT3 HA
1057
+ !adm jr., 7/01
1058
+
1059
+ C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP
1060
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
1061
+ C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP
1062
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
1063
+ C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP
1064
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1065
+ CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO
1066
+ ! JES 8/25/89
1067
+ CA CPT CPT CA 3.1000 2 180.00 ! ALLOW ARO
1068
+ ! JWK 05/14/91 fit to indole
1069
+ CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO
1070
+ ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
1071
+ CA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO
1072
+ ! JWK 09/05/89
1073
+ CA NY CPT CA 3.0000 2 180.00 ! ALLOW ARO
1074
+ ! JWK 05/14/91 fit to indole
1075
+ CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP
1076
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1077
+ CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
1078
+ ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
1079
+ CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
1080
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
1081
+ CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
1082
+ ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c
1083
+ CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP
1084
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1085
+ CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
1086
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
1087
+ CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
1088
+ ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c
1089
+ CE1 CE1 CT3 HA 0.0300 3 0.00 !
1090
+ ! for butene, yin/adm jr., 12/95
1091
+ CE2 CE1 CT2 CT3 0.5000 1 180.00 !
1092
+ ! 1-butene, adm jr., 2/00 update
1093
+ CE2 CE1 CT2 CT3 1.3000 3 180.00 !
1094
+ ! 1-butene, adm jr., 2/00 update
1095
+ CE2 CE1 CT2 HA 0.1200 3 0.00 !
1096
+ ! for butene, yin/adm jr., 12/95
1097
+ CE2 CE1 CT3 HA 0.0500 3 180.00 !
1098
+ ! for propene, yin/adm jr., 12/95
1099
+ CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO
1100
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1101
+ CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO
1102
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1103
+ CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP
1104
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1105
+ CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP
1106
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1107
+ CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO
1108
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1109
+ CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO
1110
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1111
+ CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO
1112
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1113
+ CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO
1114
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1115
+ CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO
1116
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1117
+ CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO
1118
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1119
+ CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO
1120
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1121
+ CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO
1122
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1123
+ CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO
1124
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1125
+ CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP
1126
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1127
+ CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO
1128
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1129
+ CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO
1130
+ ! his, ADM JR., 7/20/89
1131
+ CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO
1132
+ ! his, ADM JR., 7/20/89
1133
+ CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO
1134
+ ! his, ADM JR., 7/20/89
1135
+ CPT CA CA CA 3.1000 2 180.00 ! ALLOW ARO
1136
+ ! JWK 05/14/91 fit to indole
1137
+ CPT CPT CA CA 3.1000 2 180.00 ! ALLOW ARO
1138
+ ! JWK 05/14/91 fit to indole
1139
+ CPT CPT CY CA 4.0000 2 180.00 ! ALLOW ARO
1140
+ ! JWK 05/14/91 fit to indole
1141
+ CPT CPT NY CA 5.0000 2 180.00 ! ALLOW ARO
1142
+ ! JWK 05/14/91 fit to indole
1143
+ CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO
1144
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1145
+ CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO
1146
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1147
+ CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO
1148
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1149
+ CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO
1150
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1151
+ CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP
1152
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
1153
+ CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
1154
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1155
+ CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
1156
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
1157
+ CT1 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI
1158
+ ! ethylbenzene ethyl rotation, adm jr. 3/7/92
1159
+ CT1 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO
1160
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
1161
+ CT1 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO
1162
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
1163
+ CT1 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
1164
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
1165
+ CT1 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO
1166
+ ! from ethylbenzene, adm jr., 3/7/92
1167
+ CT1 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO
1168
+ ! from ethylbenzene, adm jr., 3/7/92
1169
+ CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
1170
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1171
+ CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
1172
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1173
+ CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO
1174
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1175
+ CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO
1176
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1177
+ CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO
1178
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1179
+ CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO
1180
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1181
+ CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP
1182
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
1183
+ CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
1184
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1185
+ CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP
1186
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
1187
+ CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP
1188
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1189
+ CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP
1190
+ ! from CT2 C NH1 CT2, adm jr. 10/21/96
1191
+ CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP
1192
+ ! from CT2 C NH1 CT2, adm jr. 10/21/96
1193
+ CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO
1194
+ ! JES 8/25/89 toluene and ethylbenzene
1195
+ CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
1196
+ ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2
1197
+ CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO
1198
+ ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2
1199
+ CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO
1200
+ ! his, adm jr., 6/27/90
1201
+ CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
1202
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
1203
+ CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO
1204
+ ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89
1205
+ CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI
1206
+ ! alkane update, adm jr., 3/2/92, butane trans/gauche
1207
+ CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP
1208
+ ! from CT2 CT1 NH1 C, for lactams, adm jr.
1209
+ CT2 CY CPT CA 3.0000 2 180.00 ! ALLOW ARO
1210
+ ! JWK
1211
+ CT2 CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO
1212
+ !JWK
1213
+ CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
1214
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1215
+ CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
1216
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1217
+ CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP
1218
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
1219
+ CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
1220
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1221
+ CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION
1222
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
1223
+ CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION
1224
+ ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL)
1225
+ CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION
1226
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
1227
+ CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO
1228
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1229
+ CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO
1230
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1231
+ CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO
1232
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1233
+ CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO
1234
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1235
+ CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP
1236
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
1237
+ CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
1238
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1239
+ CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP
1240
+ ! for acetylated GLY N-terminus, adm jr.
1241
+ CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP
1242
+ ! for acetylated GLY N-terminus, adm jr.
1243
+ CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP
1244
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
1245
+ CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP
1246
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1247
+ CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO
1248
+ ! toluene, adm jr., 3/7/92
1249
+ CT3 CE1 CE2 HE2 5.2000 2 180.00 !
1250
+ ! for propene, yin/adm jr., 12/95
1251
+ CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
1252
+ ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2
1253
+ CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
1254
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
1255
+ CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI
1256
+ ! ethylbenzene ethyl rotation, adm jr. 3/7/92
1257
+ CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO
1258
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
1259
+ CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO
1260
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
1261
+ CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
1262
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
1263
+ CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI
1264
+ ! alkane update, adm jr., 3/2/92, butane trans/gauche
1265
+ CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI
1266
+ ! alkane update, adm jr., 3/2/92, butane trans/gauche
1267
+ CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO
1268
+ ! from ethylbenzene, adm jr., 3/7/92
1269
+ CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO
1270
+ ! from ethylbenzene, adm jr., 3/7/92
1271
+ CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION
1272
+ ! expt. MeEtS, 3/26/92 (FL)
1273
+ CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION
1274
+ ! DTN 8/24/90
1275
+ CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
1276
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1277
+ CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
1278
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1279
+ CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP
1280
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
1281
+ CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
1282
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1283
+ CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION
1284
+ ! expt. MeEtS, 3/26/92 (FL)
1285
+ CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION
1286
+ ! expt. MeEtS, 3/26/92 (FL)
1287
+ CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION
1288
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
1289
+ CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION
1290
+ ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL)
1291
+ CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION
1292
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
1293
+ CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO
1294
+ ! JWK 05/14/91 fit to indole
1295
+ CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO
1296
+ ! JWK 05/14/91 fit to indole
1297
+ CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO
1298
+ ! JWK 05/14/91 fit to indole
1299
+ H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
1300
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1301
+ H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
1302
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1303
+ H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP
1304
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1305
+ H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP
1306
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1307
+ H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP
1308
+ ! Alanine Dipeptide ab initio calc's (LK)
1309
+ H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL
1310
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
1311
+ H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL
1312
+ ! adm jr. 5/02/91, acetic acid pure solvent
1313
+ H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP
1314
+ ! Alanine Dipeptide ab initio calc's (LK)
1315
+ H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP
1316
+ ! Alanine Dipeptide ab initio calc's (LK)
1317
+ H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP
1318
+ ! Alanine Dipeptide ab initio calc's (LK)
1319
+ H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP
1320
+ ! Alanine Dipeptide ab initio calc's (LK)
1321
+ H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL
1322
+ ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
1323
+ H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL
1324
+ ! adm jr. 5/02/91, acetic acid pure solvent
1325
+ H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP
1326
+ ! from H NH1 CT2 CT3, for lactams, adm jr.
1327
+ H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP
1328
+ ! Alanine Dipeptide ab initio calc's (LK)
1329
+ H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
1330
+ ! adm jr. 4/10/91, acetamide update
1331
+ H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
1332
+ ! adm jr. 4/10/91, acetamide update
1333
+ H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
1334
+ ! adm jr. 4/10/91, acetamide update
1335
+ H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO
1336
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1337
+ H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO
1338
+ ! his, adm jr., 7/20/89
1339
+ H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO
1340
+ ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
1341
+ H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO
1342
+ ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
1343
+ H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO
1344
+ ! his, adm jr., 6/27/90
1345
+ H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
1346
+ ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
1347
+ H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
1348
+ ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
1349
+ H NY CA CY 0.8000 2 180.00 ! ALLOW ARO
1350
+ !adm jr., 12/30/91, for jwk
1351
+ H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO
1352
+ !adm jr., 12/30/91, for jwk
1353
+ H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO
1354
+ ! JWK 05/14/91 fit to indole
1355
+ H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC
1356
+ ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92
1357
+ H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC
1358
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1359
+ H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC
1360
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1361
+ H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC
1362
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1363
+ H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC
1364
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1365
+ H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC
1366
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1367
+ H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC
1368
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1369
+ H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC
1370
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1371
+ H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC
1372
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1373
+ H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC
1374
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1375
+ H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC
1376
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1377
+ H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC
1378
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1379
+ H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC
1380
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1381
+ H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC
1382
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1383
+ H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC
1384
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1385
+ H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC
1386
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
1387
+ HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO
1388
+ ! adm jr., 10/02/89
1389
+ HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO
1390
+ ! JWK 09/05/89
1391
+ HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO
1392
+ ! ADM JR., 10/02/89
1393
+ HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO
1394
+ ! TRP (JES)
1395
+ HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO
1396
+ ! JWK 09/05/89
1397
+ HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO
1398
+ ! JWK
1399
+ HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO
1400
+ ! JWK
1401
+ HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO
1402
+ ! JWK 09/05/89
1403
+ HA CA NY H 1.0000 2 180.00 ! ALLOW ARO
1404
+ ! JWK 09/05/89
1405
+ HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL
1406
+ ! adm jr. 4/10/91, acetamide update
1407
+ HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP
1408
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1409
+ HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO
1410
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1411
+ HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO
1412
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1413
+ HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
1414
+ ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
1415
+ HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
1416
+ ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
1417
+ HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO
1418
+ ! JWK
1419
+ HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO
1420
+ ! JWK
1421
+ HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP
1422
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
1423
+ HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP
1424
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
1425
+ HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION
1426
+ ! DTN 8/24/90
1427
+ HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
1428
+ ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
1429
+ HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL
1430
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
1431
+ HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
1432
+ ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
1433
+ HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP
1434
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
1435
+ HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP
1436
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
1437
+ HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION
1438
+ ! DTN 8/24/90
1439
+ HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO
1440
+ ! JWK 09/05/89
1441
+ HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO
1442
+ ! JWK 09/05/89
1443
+ HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO
1444
+ ! JWK 09/05/89
1445
+ HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO
1446
+ ! JWK 09/05/89
1447
+ HE1 CE1 CE1 HE1 1.0000 2 180.00 !
1448
+ ! 2-butene, adm jr., 8/98 update
1449
+ CT3 CE1 CE1 HE1 1.0000 2 180.00 !
1450
+ ! 2-butene, adm jr., 8/98 update
1451
+ HE1 CE1 CE2 HE2 5.2000 2 180.00 !
1452
+ ! for propene, yin/adm jr., 12/95
1453
+ HE1 CE1 CT2 HA 0.0000 3 0.00
1454
+ ! butene, adm jr., 2/00 update
1455
+ HE1 CE1 CT2 CT3 0.1200 3 0.00 !
1456
+ ! for butene, yin/adm jr., 12/95
1457
+ HE1 CE1 CT3 HA 0.0000 3 0.00
1458
+ ! butene, adm jr., 2/00 update
1459
+ HE2 CE2 CE1 CT2 5.2000 2 180.00 !
1460
+ ! for butene, yin/adm jr., 12/95
1461
+ HE2 CE2 CE1 CPB 5.2000 2 180.00 !
1462
+ ! for vinyl, from butene, yin/adm jr., 12/95
1463
+ HB CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP
1464
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1465
+ HB CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO
1466
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1467
+ HB CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO
1468
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1469
+ HB CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP
1470
+ ! Alanine Dipeptide ab initio calc's (LK)
1471
+ HB CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP
1472
+ ! Alanine Dipeptide ab initio calc's (LK)
1473
+ HB CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP
1474
+ ! Alanine Dipeptide ab initio calc's (LK)
1475
+ HB CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP
1476
+ ! Alanine Dipeptide ab initio calc's (LK)
1477
+ HB CT3 NH1 C 0.0000 1 0.00 ! ALLOW PEP
1478
+ ! Alanine Dipeptide ab initio calc's (LK)
1479
+ HB CT3 NH1 H 0.0000 1 0.00 ! ALLOW PEP
1480
+ ! Alanine Dipeptide ab initio calc's (LK)
1481
+ HC NH2 CT2 CT2 0.1100 3 0.00
1482
+ !from X CT3 NH2 X, neutral lysine
1483
+ HC NH2 CT2 HA 0.1100 3 0.00
1484
+ !from X CT3 NH2 X, neutral lysine
1485
+ HC NH2 CT2 HB 0.1100 3 0.00
1486
+ !from X CT3 NH2 X, neutral glycine, adm jr.
1487
+ HC NH2 CT2 CD 0.1100 3 0.00
1488
+ !from X CT3 NH2 X, neutral glycine, adm jr.
1489
+ HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO
1490
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1491
+ HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO
1492
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1493
+ HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP
1494
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1495
+ HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO
1496
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1497
+ HC NP CP1 HB 0.0800 3 0.00 ! ALLOW PRO
1498
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1499
+ HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO
1500
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1501
+ HC NP CP3 HA 0.0800 3 0.00 ! ALLOW PRO
1502
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1503
+ HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO
1504
+ ! JES 8/25/89 benzene
1505
+ HP CA CA CPT 3.0000 2 180.00 ! ALLOW ARO
1506
+ ! JWK 05/14/91 fit to indole
1507
+ HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO
1508
+ ! JES 8/25/89 toluene and ethylbenzene
1509
+ HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO
1510
+ ! toluene, adm jr., 3/7/92
1511
+ HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO
1512
+ ! JES 8/25/89 benzene
1513
+ HP CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO
1514
+ ! JWK indole 05/14/91
1515
+ HP CA CPT CY 3.0000 2 180.00 ! ALLOW ARO
1516
+ ! JWK 05/14/91 fit to indole
1517
+ HP CA CY CPT 2.0000 2 180.00 ! ALLOW ARO
1518
+ !adm jr., 12/30/91, for jwk
1519
+ HP CA CY CT2 1.2000 2 180.00 ! ALLOW ARO
1520
+ ! JWK indole 05/14/91
1521
+ HP CA NY CPT 2.0000 2 180.00 ! ALLOW ARO
1522
+ !adm jr., 12/30/91, for jwk
1523
+ HP CA NY H 0.4000 2 180.00 ! ALLOW ARO
1524
+ ! JWK 05/14/91 fit to indole
1525
+ HP CY CA HP 1.0000 2 180.00 ! ALLOW ARO
1526
+ ! JWK 05/14/91 fit to indole
1527
+ HP CY CPT CA 2.8000 2 180.00 ! ALLOW ARO
1528
+ ! JWK 05/14/91 fit to indole
1529
+ HP CY CPT CPT 2.8000 2 180.00 ! ALLOW ARO
1530
+ ! JWK 05/14/91 fit to indole
1531
+ HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO
1532
+ ! his, adm jr., 6/27/90
1533
+ HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO
1534
+ ! his, adm jr., 6/27/90
1535
+ HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO
1536
+ ! his, adm jr., 6/27/90, his
1537
+ HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO
1538
+ ! his, adm jr., 6/27/90
1539
+ HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO
1540
+ ! his, adm jr., 6/27/90
1541
+ HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO
1542
+ ! his, adm jr., 6/27/90
1543
+ HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO
1544
+ ! his, adm jr., 6/27/90
1545
+ HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO
1546
+ ! his, adm jr., 6/27/90
1547
+ HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO
1548
+ ! his, adm jr., 6/27/90
1549
+ HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO
1550
+ ! his, adm jr., 6/27/90, YES, 0.0
1551
+ HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO
1552
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
1553
+ HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO
1554
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
1555
+ HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO
1556
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
1557
+ HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
1558
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
1559
+ HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO
1560
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
1561
+ HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO
1562
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
1563
+ HS S CT2 CT1 0.2400 1 0.00 ! ALLOW ALI SUL ION
1564
+ ! methanethiol pure solvent, adm jr., 6/22/92
1565
+ HS S CT2 CT1 0.1500 2 0.00 ! ALLOW ALI SUL ION
1566
+ ! methanethiol pure solvent, adm jr., 6/22/92
1567
+ HS S CT2 CT1 0.2700 3 0.00 ! ALLOW ALI SUL ION
1568
+ ! methanethiol pure solvent, adm jr., 6/22/92
1569
+ HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION
1570
+ ! ethanethiol C-C-S-H surface, adm jr., 4/18/93
1571
+ HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION
1572
+ ! ethanethiol C-C-S-H surface, adm jr., 4/18/93
1573
+ HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION
1574
+ ! ethanethiol C-C-S-H surface, adm jr., 4/18/93
1575
+ HS S CT2 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION
1576
+ ! methanethiol pure solvent, adm jr., 6/22/92
1577
+ HS S CT3 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION
1578
+ ! methanethiol pure solvent, adm jr., 6/22/92
1579
+ N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO
1580
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1581
+ N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
1582
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1583
+ N C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO
1584
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1585
+ N C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
1586
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1587
+ N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO
1588
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1589
+ N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
1590
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1591
+ N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO
1592
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1593
+ N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO
1594
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1595
+ N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO
1596
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1597
+ N C CT1 HB 0.0000 1 0.00 ! ALLOW PEP PRO
1598
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1599
+ N C CT2 HB 0.0000 1 0.00 ! ALLOW PEP PRO
1600
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1601
+ N C CT3 HA 0.0000 1 0.00 ! ALLOW PEP PRO
1602
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1603
+ N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
1604
+ ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
1605
+ NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO
1606
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1607
+ NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
1608
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1609
+ NH1 C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO
1610
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1611
+ NH1 C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
1612
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1613
+ NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO
1614
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1615
+ NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
1616
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1617
+ NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP
1618
+ ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
1619
+ NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP
1620
+ ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
1621
+ NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP
1622
+ ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
1623
+ NH1 C CT1 HB 0.0000 1 0.00 ! ALLOW PEP
1624
+ ! Alanine Dipeptide ab initio calc's (LK)
1625
+ NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP
1626
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
1627
+ NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP
1628
+ ! from NH1 C CT1 CT2, for lactams, adm jr.
1629
+ NH1 C CT2 HA 0.0000 3 0.00 ! ALLOW PEP
1630
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
1631
+ NH1 C CT2 HB 0.0000 1 0.00 ! ALLOW PEP
1632
+ ! Alanine Dipeptide ab initio calc's (LK)
1633
+ NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP
1634
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
1635
+ NH1 C CT3 HA 0.0000 3 0.00 ! ALLOW PEP
1636
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
1637
+ NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO
1638
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1639
+ NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO
1640
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1641
+ NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO
1642
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1643
+ NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
1644
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1645
+ NH2 CC CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO
1646
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1647
+ NH2 CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
1648
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1649
+ NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO
1650
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1651
+ NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
1652
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1653
+ NH2 CC CT2 HA 0.0000 3 180.00 ! ALLOW POL
1654
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
1655
+ NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO
1656
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1657
+ NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO
1658
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
1659
+ NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO
1660
+ ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
1661
+ NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO
1662
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1663
+ NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO
1664
+ ! adm jr. 3/24/92, for PRES GLYP
1665
+ NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO
1666
+ ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
1667
+ NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO
1668
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1669
+ NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO
1670
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1671
+ NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO
1672
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1673
+ NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
1674
+ ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA
1675
+ NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
1676
+ ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA
1677
+ NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO
1678
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
1679
+ NR1 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
1680
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1681
+ NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
1682
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1683
+ NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
1684
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1685
+ NR1 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
1686
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1687
+ NR1 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
1688
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1689
+ NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO
1690
+ ! his, ADM JR., 7/20/89
1691
+ NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
1692
+ ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA
1693
+ NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
1694
+ ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA
1695
+ NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO
1696
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
1697
+ NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO
1698
+ ! his, ADM JR., 7/20/89
1699
+ NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
1700
+ ! HIS CB-CG TORSION,
1701
+ NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
1702
+ ! HIS CB-CG TORSION,
1703
+ NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
1704
+ ! HIS CB-CG TORSION,
1705
+ NR2 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
1706
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1707
+ NR2 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
1708
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1709
+ NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO
1710
+ ! his, ADM JR., 7/20/89
1711
+ NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO
1712
+ ! his, ADM JR., 7/20/89
1713
+ NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO
1714
+ ! his, adm jr., 6/27/90
1715
+ NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO
1716
+ ! his, adm jr., 6/27/90
1717
+ NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO
1718
+ ! his, adm jr., 6/27/90
1719
+ NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO
1720
+ ! his, adm jr., 6/27/90
1721
+ NR3 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
1722
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1723
+ NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
1724
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1725
+ NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
1726
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1727
+ NR3 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
1728
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1729
+ NR3 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
1730
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
1731
+ NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO
1732
+ ! his, ADM JR., 7/20/89
1733
+ NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO
1734
+ ! his, adm jr., 6/27/90
1735
+ NY CA CY CPT 4.0000 2 180.00 ! ALLOW ARO
1736
+ ! JWK 05/14/91 fit to indole
1737
+ NY CA CY CT2 3.5000 2 180.00 ! ALLOW ARO
1738
+ ! JWK
1739
+ NY CA CY HA 3.5000 2 180.00 ! ALLOW ARO
1740
+ ! JWK 09/05/89
1741
+ NY CA CY HP 3.5000 2 180.00 ! ALLOW ARO
1742
+ ! JWK indole 05/14/91
1743
+ NY CPT CA CA 2.8000 2 180.00 ! ALLOW ARO
1744
+ ! JWK 05/14/91 fit to indole
1745
+ NY CPT CA HA 4.0000 2 180.00 ! ALLOW ARO
1746
+ ! JWK 09/05/89
1747
+ NY CPT CA HP 3.0000 2 180.00 ! ALLOW ARO
1748
+ ! JWK 05/14/91 fit to indole
1749
+ NY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO
1750
+ ! JWK 05/14/91 fit to indole
1751
+ NY CPT CPT CY 5.0000 2 180.00 ! ALLOW ARO
1752
+ ! JWK 05/14/91 fit to indole
1753
+ O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO
1754
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1755
+ O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
1756
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1757
+ O C CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO
1758
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1759
+ O C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
1760
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1761
+ O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
1762
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1763
+ O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP
1764
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
1765
+ O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP
1766
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
1767
+ O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP
1768
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
1769
+ O C CT1 HB 0.0000 1 0.00 ! ALLOW PEP
1770
+ ! Alanine Dipeptide ab initio calc's (LK)
1771
+ O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP
1772
+ ! Alanine Dipeptide ab initio calc's (LK)
1773
+ O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO
1774
+ ! Backbone parameter set made complete RLD 8/8/90
1775
+ O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP
1776
+ ! from O C CT1 CT2, for lactams, adm jr.
1777
+ O C CT2 HA 0.0000 3 180.00 ! ALLOW POL
1778
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
1779
+ O C CT2 HB 0.0000 1 0.00 ! ALLOW PEP
1780
+ ! Alanine Dipeptide ab initio calc's (LK)
1781
+ O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP
1782
+ ! Alanine Dipeptide ab initio calc's (LK)
1783
+ O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO
1784
+ ! Backbone parameter set made complete RLD 8/8/90
1785
+ O C CT3 HA 0.0000 3 180.00 ! ALLOW POL
1786
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
1787
+ O C N CP1 2.7500 2 180.00 ! ALLOW PRO
1788
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1789
+ O C N CP1 0.3000 4 0.00 ! ALLOW PRO
1790
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1791
+ O C N CP3 2.7500 2 180.00 ! ALLOW PRO
1792
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1793
+ O C N CP3 0.3000 4 0.00 ! ALLOW PRO
1794
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1795
+ O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
1796
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1797
+ O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP
1798
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1799
+ O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP
1800
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1801
+ O C NH1 H 2.5000 2 180.00 ! ALLOW PEP
1802
+ ! Gives appropriate NMA cis/trans barrier. (LK)
1803
+ O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO
1804
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1805
+ O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
1806
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1807
+ O CC CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO
1808
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1809
+ O CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
1810
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1811
+ O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
1812
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1813
+ O CC CT2 HA 0.0000 3 180.00 ! ALLOW POL
1814
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
1815
+ O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
1816
+ ! adm jr. 4/10/91, acetamide update
1817
+ OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL
1818
+ ! adm jr. 3/19/92, from lipid methyl acetate
1819
+ OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL
1820
+ ! adm jr. 3/19/92, from lipid methyl acetate
1821
+ OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL
1822
+ ! adm jr. 3/19/92, from lipid methyl acetate
1823
+ OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL
1824
+ ! adm jr. 3/19/92, from lipid methyl acetate
1825
+ OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO
1826
+ ! adm jr. 8/27/91, phenoxide
1827
+ OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO
1828
+ ! adm jr. 8/27/91, phenoxide
1829
+ OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL
1830
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1831
+ OC CC CP1 HB 0.1600 3 0.00 ! ALLOW PEP PRO POL
1832
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1833
+ OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL
1834
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1835
+ OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL
1836
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1837
+ OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO
1838
+ ! adm jr. 4/17/94, zwitterionic glycine
1839
+ OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO
1840
+ ! adm jr. 4/17/94, zwitterionic glycine
1841
+ OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO
1842
+ ! JES 8/25/89 phenol
1843
+ OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO
1844
+ ! JES 8/25/89 phenol
1845
+ S CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION
1846
+ ! DTN 8/24/90
1847
+ SM CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION
1848
+ ! DTN 8/24/90
1849
+ SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI
1850
+ ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90
1851
+ SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI
1852
+ ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90
1853
+ SM SM CT2 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION
1854
+ ! expt. dimethyldisulfide, 3/26/92 (FL)
1855
+ SM SM CT3 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION
1856
+ ! expt. dimethyldisulfide, 3/26/92 (FL)
1857
+ SS CS CT3 HA 0.1500 3 0.00 ! ALLOW SUL
1858
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
1859
+ !X C C X 4.0000 2 180.00 ! ALLOW HEM
1860
+ ! Heme (6-liganded): substituents (KK 05/13/91)
1861
+ X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO
1862
+ ! 9.0->2.25 GUANIDINIUM (KK)
1863
+ X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC
1864
+ ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier
1865
+ X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL
1866
+ ! adm jr. 3/19/92, from lipid methyl acetate
1867
+ X CE1 CE1 X 0.1500 1 0.00
1868
+ ! 2-butene, adm jr., 2/00 update
1869
+ X CE1 CE1 X 8.5000 2 180.00
1870
+ ! 2-butene, adm jr., 2/00 update
1871
+ X CE2 CE2 X 4.9000 2 180.00 !
1872
+ ! for ethene, yin/adm jr., 12/95
1873
+ X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO
1874
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1875
+ X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP
1876
+ ! changed to 0.0 RLD 5/19/92
1877
+ X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP
1878
+ ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
1879
+ X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO
1880
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1881
+ X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO
1882
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1883
+ X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO
1884
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
1885
+ X CPA CPB X 0.0000 2 0.00 ! ALLOW HEM
1886
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
1887
+ X CPA CPM X 0.0000 2 0.00 ! ALLOW HEM
1888
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
1889
+ X CPB CE1 X 3.0000 2 180.00 ! ALLOW HEM
1890
+ ! Heme (6-liganded): substituents (KK 05/13/91)
1891
+ X CPB CPB X 0.0000 2 0.00 ! ALLOW HEM
1892
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
1893
+ X CPB CT2 X 0.0000 6 0.00 ! ALLOW HEM
1894
+ ! Heme (6-liganded): substituents (KK 05/13/91)
1895
+ X CPB CT3 X 0.0000 6 0.00 ! ALLOW HEM
1896
+ ! Heme (6-liganded): substituents (KK 05/13/91)
1897
+ X CPT CPT X 0.0000 2 180.00 ! ALLOW ARO
1898
+ ! JWK indole 05/14/91
1899
+ X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP
1900
+ ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
1901
+ X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP
1902
+ ! adm jr. 3/19/92, from lipid methyl acetate
1903
+ X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI
1904
+ ! alkane update, adm jr., 3/2/92
1905
+ X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI
1906
+ ! alkane update, adm jr., 3/2/92
1907
+ X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI
1908
+ ! alkane update, adm jr., 3/2/92
1909
+ X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL
1910
+ ! 0.715->0.10 METHYLAMMONIUM (KK)
1911
+ X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
1912
+ ! EMB 11/21/89 methanol vib fit
1913
+ X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL
1914
+ ! adm jr. 3/19/92, from lipid methyl acetate
1915
+ X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO
1916
+ ! toluene, adm jr., 3/7/92
1917
+ X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP
1918
+ ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
1919
+ X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP
1920
+ ! adm jr. 3/19/92, from lipid methyl acetate
1921
+ X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI
1922
+ ! alkane update, adm jr., 3/2/92
1923
+ X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI
1924
+ ! rotation barrier in Ethane (SF)
1925
+ X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL
1926
+ ! methylguanidinium, adm jr., 3/26/92
1927
+ X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL
1928
+ ! 0.715->0.10 METHYLAMMONIUM (KK)
1929
+ X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
1930
+ ! EMB 11/21/89 methanol vib fit
1931
+ X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL
1932
+ ! adm jr. 3/19/92, from lipid methyl acetate
1933
+ X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO
1934
+ ! toluene, adm jr., 3/7/92
1935
+ X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP
1936
+ ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
1937
+ X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP
1938
+ ! adm jr. 3/19/92, from lipid methyl acetate
1939
+ X CT3 CT3 X 0.1550 3 0.00 ! ALLOW ALI
1940
+ ! alkane update, adm jr., 3/2/92
1941
+ X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL
1942
+ ! methylguanidinium, adm jr., 3/26/92
1943
+ X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL
1944
+ ! methylamine geom/freq, adm jr., 6/2/92
1945
+ X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL
1946
+ ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92
1947
+ X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
1948
+ ! EMB 11/21/89 methanol vib fit
1949
+ X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL
1950
+ ! adm jr. 3/19/92, from lipid methyl acetate
1951
+ X FE CM X 0.0500 4 0.00 ! ALLOW HEM
1952
+ ! Heme (6-liganded): ligands (KK 05/13/91)
1953
+ X FE NPH X 0.0000 2 0.00 ! ALLOW HEM
1954
+ ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
1955
+ X FE OM X 0.0000 4 0.00 ! ALLOW HEM
1956
+ ! Heme (6-liganded): ligands (KK 05/13/91)
1957
+ X NPH CPA X 0.0000 2 0.00 ! ALLOW HEM
1958
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
1959
+
1960
+ IMPROPER
1961
+ !
1962
+ !V(improper) = Kpsi(psi - psi0)**2
1963
+ !
1964
+ !Kpsi: kcal/mole/rad**2
1965
+ !psi0: degrees
1966
+ !note that the second column of numbers (0) is ignored
1967
+ !
1968
+ !atom types Kpsi psi0
1969
+ !
1970
+ CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM
1971
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
1972
+ CPB X X CE1 90.0000 0 0.0000 ! ALLOW HEM
1973
+ ! Heme (6-liganded): substituents (KK 05/13/91)
1974
+ CT2 X X CPB 90.0000 0 0.0000 ! ALLOW HEM
1975
+ ! Heme (6-liganded): substituents (KK 05/13/91)
1976
+ CT3 X X CPB 90.0000 0 0.0000 ! ALLOW HEM
1977
+ ! Heme (6-liganded): substituents (KK 05/13/91)
1978
+ !HA C C HA 20.0000 0 0.0000 ! ALLOW PEP POL ARO
1979
+ ! Heme vinyl substituent (KK, from propene (JCS))
1980
+ HA CPA CPA CPM 29.4000 0 0.0000 ! ALLOW HEM
1981
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
1982
+ !HA CPB C C 20.0000 0 0.0000 ! ALLOW HEM ARO
1983
+ ! Heme (6-liganded): substituents (KK 05/13/91)
1984
+ !HA HA C C 20.0000 0 180.0000 ! ALLOW PEP POL ARO
1985
+ ! Heme vinyl substituent (KK, from propene (JCS))
1986
+ HE2 HE2 CE2 CE2 3.0 0 0.00 !
1987
+ ! for ethene, yin/adm jr., 12/95
1988
+ HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO
1989
+ ! his, adm jr., 7/05/90
1990
+ HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO
1991
+ ! his, adm jr., 7/05/90
1992
+ HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
1993
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
1994
+ HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO
1995
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
1996
+ HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO
1997
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
1998
+ HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
1999
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
2000
+ HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
2001
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
2002
+ N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO
2003
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
2004
+ NC2 X X C 40.0000 0 0.0000 ! ALLOW PEP POL ARO
2005
+ ! 5.75->40.0 GUANIDINIUM (KK)
2006
+ NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO
2007
+ ! NMA Vibrational Modes (LK)
2008
+ NH2 X X H 4.0000 0 0.0000 ! ALLOW POL
2009
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
2010
+ NPH CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM
2011
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
2012
+ NPH CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM
2013
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
2014
+ NPH CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM
2015
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
2016
+ NPH CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM
2017
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
2018
+ NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO
2019
+ ! his, adm jr., 7/05/90
2020
+ NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO
2021
+ ! his, adm jr., 7/05/90
2022
+ NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO
2023
+ ! his, adm jr., 6/27/90
2024
+ NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO
2025
+ ! his, adm jr., 6/27/90
2026
+ NY CA CY CPT 100.0000 0 0.0000 ! ALLOW ARO
2027
+ !adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf.
2028
+ O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
2029
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
2030
+ O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
2031
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
2032
+ O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
2033
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
2034
+ O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
2035
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
2036
+ O HA NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
2037
+ ! adm jr., 5/13/91, formamide geometry and vibrations
2038
+ O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO
2039
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
2040
+ O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
2041
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
2042
+ O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL
2043
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
2044
+ O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
2045
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
2046
+ O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL
2047
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
2048
+ O NH2 HA CC 45.0000 0 0.0000 ! ALLOW PEP POL
2049
+ ! adm jr., 5/13/91, formamide geometry and vibrations
2050
+ O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO
2051
+ ! NMA Vibrational Modes (LK)
2052
+ OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL
2053
+ ! adm jr., 10/17/90, acetic acid vibrations
2054
+ OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
2055
+ ! 90.0->96.0 acetate, single impr (KK)
2056
+ CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
2057
+ ! 90.0->96.0 acetate, single impr (KK)
2058
+ CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
2059
+ ! 90.0->96.0 acetate, single impr (KK)
2060
+ CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
2061
+ ! 90.0->96.0 acetate, single impr (KK)
2062
+
2063
+ NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
2064
+ cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
2065
+ !adm jr., 5/08/91, suggested cutoff scheme
2066
+ !
2067
+ !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
2068
+ !
2069
+ !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
2070
+ !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
2071
+ !
2072
+ !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
2073
+ !
2074
+ !carbons
2075
+ C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO
2076
+ ! NMA pure solvent, adm jr., 3/3/93
2077
+ CA 0.000000 -0.070000 1.992400 ! ALLOW ARO
2078
+ ! benzene (JES)
2079
+ CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO
2080
+ ! adm jr. 3/3/92, acetic acid heat of solvation
2081
+ CD 0.000000 -0.070000 2.000000 ! ALLOW POL
2082
+ ! adm jr. 3/19/92, acetate a.i. and dH of solvation
2083
+ CE1 0.000000 -0.068000 2.090000 !
2084
+ ! for propene, yin/adm jr., 12/95
2085
+ CE2 0.000000 -0.064000 2.080000 !
2086
+ ! for ethene, yin/adm jr., 12/95
2087
+ CM 0.000000 -0.110000 2.100000 ! ALLOW HEM
2088
+ ! Heme (6-liganded): CO ligand carbon (KK 05/13/91)
2089
+ CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI
2090
+ ! alkane update, adm jr., 3/2/92
2091
+ CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
2092
+ ! alkane update, adm jr., 3/2/92
2093
+ CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
2094
+ ! alkane update, adm jr., 3/2/92
2095
+ CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM
2096
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
2097
+ CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM
2098
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
2099
+ CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO
2100
+ ! adm jr., 10/23/91, imidazole solvation and sublimation
2101
+ CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO
2102
+ ! adm jr., 10/23/91, imidazole solvation and sublimation
2103
+ CPM 0.000000 -0.090000 1.800000 ! ALLOW HEM
2104
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
2105
+ CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 ! ALLOW ARO
2106
+ ! benzene (JES)
2107
+ CS 0.000000 -0.110000 2.200000 ! ALLOW SUL
2108
+ ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
2109
+ CST 0.000000 -0.058000 1.563000 !
2110
+ ! carbon dioxide, JES
2111
+ CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI
2112
+ ! isobutane pure solvent properties, adm jr, 2/3/92
2113
+ CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
2114
+ ! propane pure solvent properties, adm jr, 2/3/92
2115
+ CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI
2116
+ ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
2117
+ CY 0.000000 -0.070000 1.992400 ! ALLOW ARO
2118
+ ! TRP, JWK 08/29/89
2119
+ !new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str)
2120
+ CT 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! from CT1x: needs work
2121
+ CT1x 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92: needs work
2122
+ CT2x 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
2123
+ CT3x 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
2124
+ ! hydrogens
2125
+ H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC
2126
+ ! same as TIP3P hydrogen, adm jr., 7/20/89
2127
+ HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
2128
+ ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
2129
+ HE1 0.000000 -0.031000 1.250000 !
2130
+ ! for propene, yin/adm jr., 12/95
2131
+ HE2 0.000000 -0.026000 1.260000 !
2132
+ ! for ethene, yin/adm jr., 12/95
2133
+ HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
2134
+ ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
2135
+ HC 0.000000 -0.046000 0.224500 ! ALLOW POL
2136
+ ! new, small polar Hydrogen, see also adm jr. JG 8/27/89
2137
+ HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO
2138
+ ! JES 8/25/89 values from Jorgensen fit to hydration energy
2139
+ HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO
2140
+ ! adm jr., 6/27/90, his
2141
+ HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO
2142
+ ! adm jr., 6/27/90, his
2143
+ HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO
2144
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
2145
+ HS 0.000000 -0.100000 0.450000 ! ALLOW SUL
2146
+ ! methanethiol pure solvent, adm jr., 6/22/92
2147
+ HT 0.000000 -0.046000 0.224500 ! ALLOW WAT
2148
+ !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete
2149
+ !new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str)
2150
+ HA1 0.0 -0.022 1.3200 ! alkane, 3/92
2151
+ HA2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98
2152
+ HA3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98
2153
+ !nitrogens
2154
+ N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO
2155
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
2156
+ NC2 0.000000 -0.200000 1.850000 ! ALLOW POL
2157
+ ! JG 8/27/89; note: NH1 in ARG was changed to NC2.
2158
+ NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO
2159
+ ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
2160
+ NH2 0.000000 -0.200000 1.850000 ! ALLOW POL
2161
+ ! adm jr.
2162
+ NH3 0.000000 -0.200000 1.850000 ! ALLOW POL
2163
+ ! adm jr.
2164
+ NP 0.000000 -0.200000 1.850000 ! ALLOW PRO
2165
+ ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90
2166
+ NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM
2167
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
2168
+ NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO
2169
+ ! His, adm jr., 9/4/89
2170
+ NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO
2171
+ ! His, adm jr., 9/4/89
2172
+ NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO
2173
+ ! His, adm jr., 9/4/89
2174
+ NY 0.000000 -0.200000 1.850000 ! ALLOW ARO
2175
+ ! trp, JWK
2176
+ ! oxygens
2177
+ O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL
2178
+ ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
2179
+ OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO
2180
+ ! adm jr., 10/17/90, acetic acid carbonyl O
2181
+ OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION
2182
+ ! JG 8/27/89
2183
+ OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO
2184
+ ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P)
2185
+ OM 0.000000 -0.120000 1.700000 ! ALLOW HEM
2186
+ ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91)
2187
+ OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO
2188
+ ! adm jr. 9/17/90, avoid O* wildcard
2189
+ OST 0.000000 -0.165000 1.692000 !
2190
+ ! carbon dioxide, JES
2191
+ OT 0.000000 -0.152100 1.768200 ! ALLOW WAT
2192
+ !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete
2193
+ ! sulfurs
2194
+ S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION
2195
+ ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent
2196
+ SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION
2197
+ ! adm jr., 3/3/92, dimethyldisulphide pure solvent
2198
+ SS 0.000000 -0.470000 2.200000 ! ALLOW SUL
2199
+ ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
2200
+ ! ions and miscellaneous types
2201
+ SOD 0.0 -0.0469 1.36375 ! sodium
2202
+ ! D. Beglovd and B. Roux, dA=-100.8 kcal/mol
2203
+ POT 0.0 -0.0870 1.76375 ! potassium
2204
+ ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol
2205
+ CLA 0.0 -0.150 2.27 ! chloride
2206
+ ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol
2207
+ CAL 0.0 -0.120 1.367 ! Calcium
2208
+ ! S. Marchand and B. Roux, dA = -384.8 kcal/mol
2209
+ !CAL 0.000000 -0.120000 1.710000 ! Calcium (BP) in proteins prior
2210
+ ! to 2003; not recommended due to need for NBFIX terms
2211
+ MG 0.0 -0.0150 1.18500 ! Magnesium
2212
+ ! B. Roux dA = -441.65
2213
+ CES 0.0 -0.1900 2.100
2214
+ ! Cesium, so far untested.
2215
+ ZN 0.000000 -0.250000 1.090000 ! ALLOW ION
2216
+ ! RHS March 18, 1990
2217
+ FE 0.010000 0.000000 0.650000 ! ALLOW HEM
2218
+ ! Heme (6-liganded): Iron atom (KK 05/13/91)
2219
+ HE 0.000000 -0.021270 1.4800 !
2220
+ ! helium, experimental pot. energy surface, adm jr., 12/95
2221
+ NE 0.000000 -0.086000 1.5300
2222
+ ! neon, semiempirical pot. energy surface, adm jr., 12/95
2223
+ CLAL 0.000000 -0.030000 1.908200 ! chlorine from Jorgensen/BOSS
2224
+ ! for choroacetaldehyde
2225
+ DUM 0.000000 -0.000000 0.000000 !
2226
+ ! dummy atom
2227
+ !pyridine series LJ parametes (see toppar_pyridines.str)
2228
+ CAP 0.000000 -0.070000 1.992400 !
2229
+ FA 0.000000 -0.12000 1.700000
2230
+ ! from 1,3-difluorobenzene pure solvent
2231
+ CN 0.000000 -0.200000 1.750000 ! cyanopyridine
2232
+ NC 0.000000 -0.600000 1.850000 ! cyanopyridine
2233
+ OCA 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! 3acp
2234
+ COA 0.000000 -0.110000 2.000000 ! 3acp
2235
+ !fluorinated alkanes LJ parameters (see toppar_fluoro_alkanes.str)
2236
+ CF1 0.000000 -0.060000 1.900000
2237
+ CF2 0.000000 -0.042000 2.050000
2238
+ CF3 0.000000 -0.020000 2.300000
2239
+ HF1 0.000000 -0.028000 1.3200
2240
+ HF2 0.000000 -0.030000 1.3000
2241
+ F1 0.0 -0.135 1.63
2242
+ F2 0.0 -0.105 1.63
2243
+ F3 0.0 -0.097 1.60
2244
+
2245
+
2246
+ HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
2247
+ ! READ PARAM APPEND CARD
2248
+ ! to append hbond parameters from the file: par_hbond.inp
2249
+
2250
+ END