-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathpara.inp
337 lines (337 loc) · 16.7 KB
/
para.inp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
!Carbon Dioxide
CST OST 937.96 1.1600 ! JES
!Heme to Sulfate (PSUL) link
SS FE 250.0 2.3200 !force constant a guess
!equilbrium bond length optimized to reproduce
!CSD survey values of
!2.341pm0.01 (mean, standard error)
!adm jr., 7/01
C C 600.000 1.3350 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
CA CA 305.000 1.3750 ! ALLOW ARO
! benzene, JES 8/25/89
CE1 CE1 440.000 1.3400 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CE2 500.000 1.3420 !
! for propene, yin/adm jr., 12/95
CE1 CT2 365.000 1.5020 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CT3 383.000 1.5040 !
! for butene, yin/adm jr., 12/95
CE2 CE2 510.000 1.3300 !
! for ethene, yin/adm jr., 12/95
CP1 C 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CC 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CD 200.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 222.500 1.5270 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPB CE1 450.000 1.3800 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPA 299.800 1.4432 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB CPB 340.700 1.3464 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH1 CPH1 410.000 1.3600 ! ALLOW ARO
! histidine, adm jr., 6/27/90
CPM CPA 360.000 1.3716 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT CA 305.000 1.3680 ! ALLOW ARO
! adm jr., 12/30/91, for jwk
CPT CPT 360.000 1.4000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT1 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT1 222.500 1.5000 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT2 CA 230.000 1.4900 ! ALLOW ALI ARO
! phe,tyr, JES 8/25/89
CT2 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT2 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT3 CA 230.000 1.4900 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
CT3 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT3 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT3 CS 190.000 1.5310 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
CT3 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 222.500 1.5280 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT3 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CY CA 350.000 1.3650 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CY CPT 350.000 1.4400 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CT2 230.000 1.5100 ! ALLOW ARO
!JWK Kb from alkane freq.. b0 from TRP crystal
FE CM 258.000 1.9000 ! ALLOW HEM
! Heme (6-liganded): CO ligand (KK 05/13/91)
FE CPM 0.000 3.3814 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
H CD 330.000 1.1100 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
!HA C 330.000 1.1000 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
HA CA 340.000 1.0830 ! ALLOW ARO
! trp, adm jr., 10/02/89
HA CC 317.130 1.1000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
HA CP2 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CPM 367.600 1.0900 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT1 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 322.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CY 330.000 1.0800 ! ALLOW ARO
! JWK 05/14/91 new r0 from indole
HE1 CE1 360.500 1.1000 !
! for propene, yin/adm jr., 12/95
HE2 CE2 365.000 1.1000 !
! for ethene, yin/adm jr., 12/95
HB CP1 330.000 1.0800 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CT1 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT3 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HP CA 340.000 1.0800 ! ALLOW ARO
! phe,tyr JES 8/25/89
HP CY 350.000 1.0800 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HR1 CPH1 375.000 1.0830 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH2 340.000 1.0900 ! ALLOW ARO
! his, adm jr., 6/28/29
HR2 CPH2 333.000 1.0700 ! ALLOW ARO
! his, adm jr., 6/27/90
HR3 CPH1 365.000 1.0830 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HT HT 0.000 1.5139 ! ALLOW WAT
! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 320.000 1.4340 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 320.000 1.4550 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO
! 403.0->463.0, 1.305->1.365 guanidinium (KK)
NC2 CT2 261.000 1.4900 ! ALLOW ALI POL
! arg, (DS)
NC2 CT3 261.000 1.4900 ! ALLOW ALI POL
! methylguanidinium, adm jr., 3/26/92
NC2 HC 455.000 1.0000 ! ALLOW POL
! 405.0->455.0 GUANIDINIUM (KK)
NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO
! (DS)
NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
NH2 CT2 240.000 1.4550
! from NH2 CT3, neutral glycine, adm jr.
NH2 CT3 240.000 1.4550 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH2 H 480.000 1.0000 ! ALLOW POL
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 HC 460.000 1.0000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH3 CT1 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT2 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT3 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 HC 403.000 1.0400 ! ALLOW POL
! new stretch and bend; methylammonium (KK 03/10/92)
NP CP1 320.000 1.4850 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 320.000 1.5020 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP HC 460.000 1.0060 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NPH CPA 377.200 1.3757 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH FE 270.200 1.9580 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 CPH2 400.000 1.3600 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 H 466.000 1.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH2 400.000 1.3200 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 FE 65.000 2.2000 ! ALLOW HEM
! Heme (6-liganded): His ligand (KK 05/13/91)
NR3 CPH1 380.000 1.3700 ! ALLOW ARO
! his, adm jr., 6/28/90
NR3 CPH2 380.000 1.3200 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 H 453.000 1.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
NY CA 270.000 1.3700 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY CPT 270.000 1.3750 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY H 465.000 0.9760 ! ALLOW ARO
! indole JWK 08/28/89
O C 620.000 1.2300 ! ALLOW PEP POL ARO
! Peptide geometry, condensed phase (LK)
O CC 650.000 1.2300 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
OB CC 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr., 10/17/90, acetic acid vibrations and geom.
OB CD 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 8/27/91, phenoxide
OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 7/23/91, acetic acid
OC CT2 450.000 1.3300 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT3 450.000 1.3300 ! ALLOW ALC
! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
OH1 CA 334.300 1.4110 ! ALLOW ARO ALC
! MeOH, EMB 10/10/89,
OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC
! adm jr. 5/02/91, acetic acid pure solvent
OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 H 545.000 0.9600 ! ALLOW ALC ARO
! EMB 11/21/89 methanol vib fit
OM CM 1115.000 1.1280 ! ALLOW HEM
! Heme (6-liganded): CO ligand (KK 05/13/91)
OM FE 250.000 1.8000 ! ALLOW HEM
! Heme (6-liganded): O2 ligand (KK 05/13/91)
OM OM 600.000 1.2300 ! ALLOW HEM
! Heme (6-liganded): O2 ligand (KK 05/13/91)
OS CD 150.000 1.3340 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
OS CT3 340.000 1.4300 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OT HT 450.000 0.9572 ! ALLOW WAT
! FROM TIPS3P GEOM
S CT2 198.000 1.8180 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S CT3 240.000 1.8160 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S HS 275.000 1.3250 ! ALLOW SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
SM CT2 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SM CT3 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SM SM 173.000 2.0290 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SS CS 205.000 1.8360 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
!lipid section
CTL3 CL 200.0 1.522 ! methyl acetate
CTL2 CL 200.0 1.522 ! methyl acetate
CTL1 CL 200.0 1.522 ! methyl acetate
OBL CL 750.0 1.220 ! methyl acetate
OCL CL 525.0 1.260 ! acetate, protein
OSL CL 150.0 1.334 ! methyl acetate
OHL CL 230.0 1.40 ! methyl acetate
HOL OHL 545.0 0.960 ! acetic acid
CTL1 HAL1 309.00 1.111 ! alkanes, 3/92
CTL2 HAL2 309.00 1.111 ! alkanes, 4/98
CTL3 HAL3 322.00 1.111 ! alkanes, 4/98
CTL3 OSL 340.0 1.43 ! phosphate
CTL2 OSL 340.0 1.43 ! phosphate
CTL1 OSL 340.0 1.43 ! phosphate
OSL PL 270.0 1.60 ! phosphate
O2L PL 580.0 1.48 ! phosphate
OHL PL 237.0 1.59 ! phosphate
NH3L HCL 410.0 1.04 ! ethanolamine
NH3L CTL2 261.0 1.51 ! ethanolamine
NTL CTL2 215.00 1.51 ! tetramethylammonium
NTL CTL5 215.00 1.51 ! tetramethylammonium
CTL5 HL 300.00 1.08 ! tetramethylammonium
CTL2 HL 300.00 1.08 ! tetramethylammonium
CTL1 CTL1 222.500 1.500 ! alkanes, 3/92
CTL1 CTL2 222.500 1.538 ! alkanes, 3/92
CTL1 CTL3 222.500 1.538 ! alkanes, 3/92
CTL2 CTL2 222.500 1.530 ! alkanes, 3/92
CTL2 CTL3 222.500 1.528 ! alkanes, 3/92
CTL3 CTL3 222.500 1.530 ! alkanes, 3/92
OHL CTL1 428.0 1.420 ! glycerol
OHL CTL2 428.0 1.420 ! glycerol
OHL CTL3 428.0 1.420 ! glycerol
SL O2L 540.0 1.448 ! methylsulfate
SL OSL 250.0 1.575 ! methylsulfate
!HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM)
!HT OT 450.0 0.9572 ! from TIPS3P geometry
CEL2 CEL2 510.000 1.330 ! ethene yin,adm jr., 12/95
HEL2 CEL2 365.000 1.100 ! propene; from ethene, yin,adm jr., 12/95
CEL1 CTL3 383.000 1.504 ! butene, yin,adm jr., 12/95
CEL1 CEL2 500.000 1.342 ! propene, yin,adm jr., 12/95
HEL1 CEL1 360.500 1.100 ! propene, yin,adm jr., 12/95
CEL1 CTL2 365.000 1.502 ! butene; from propene, yin,adm jr., 12/95
CEL1 CEL1 440.000 1.340 ! butene, yin,adm jr., 12/95