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/opls.parameter ADDED
@@ -0,0 +1,1108 @@
1
+ remarks 08-26-96
2
+ remarks X-PLOR PARAMETER FILE FOR OPLS FORCE FIELD
3
+ remarks OPLS NONBONDED AND TORSIONAL PARMS USED WITH AMBER BONDED AND VALENCE
4
+ remarks PARMS
5
+ remarks ATOM TYPES COMPATIBLE WITH AMBER TYPES
6
+ remarks UNITED-ATOM REPRESENTATION for ALIPHATIC RESIDUES
7
+ remarks ALL-ATOM REPRESENTATION for AROMATIC RESIDUES
8
+ set echo=off end
9
+ set message=off end
10
+ ! Ebond = Sum [k(r-r0)**2]
11
+ ! -------------------------------------------------
12
+ BONDs N H 434. 1.01
13
+ BONDs N Ha 434. 1.00
14
+ BONDs N Hb 434. 1.01
15
+ BONDs N C 490. 1.335
16
+ BONDs N C1 490. 1.350
17
+ BONDs N CH 337. 1.449
18
+ BONDs N CHp 337. 1.449
19
+ BONDs N C2 337. 1.449
20
+ BONDs N C2p 337. 1.449
21
+ BONDs N C3 337. 1.449
22
+ BONDs N C3b 337. 1.449
23
+ BONDs N C0 337. 1.449
24
+ ! -------------------------------------------------
25
+ BONDs N2 H3 434. 1.01
26
+ BONDs N2 C2a 337. 1.463
27
+ BONDs N2 CAa 481. 1.340
28
+ ! -------------------------------------------------
29
+ BONDs N3 H3 434. 1.01
30
+ BONDs N3 CH 367. 1.471
31
+ BONDs N3 C2 367. 1.471
32
+ BONDs N3 C2a 367. 1.471
33
+ ! -------------------------------------------------
34
+ BONDs NA H 434. 1.01
35
+ BONDs NA CA 422. 1.385
36
+ BONDs NA CC 422. 1.385
37
+ ! -------------------------------------------------
38
+ BONDs NB CA 488. 1.335
39
+ ! -------------------------------------------------
40
+ BONDs OH HO 553. 0.960
41
+ BONDs OH CAb 450. 1.364
42
+ BONDs OH CHa 386. 1.425
43
+ BONDs OH C2a 386. 1.425
44
+ BONDs OH CT 320. 1.410
45
+ ! -------------------------------------------------
46
+ BONDs OW HW 529.60 0.9572
47
+ BONDs HW HW 38.25 1.5174
48
+ ! -------------------------------------------------
49
+ BONDs OS C 214. 1.327
50
+ BONDs OS C3 320. 1.425
51
+ BONDs OS C3b 320. 1.425
52
+ ! -------------------------------------------------
53
+ BONDs S O4 400. 1.49
54
+ BONDs S C2 222. 1.81
55
+ BONDs S C3b 222. 1.81
56
+ BONDs S S 166. 2.038
57
+ ! -------------------------------------------------
58
+ BONDs SH HS 274. 1.336
59
+ BONDs SH C2a 222. 1.81
60
+ ! -------------------------------------------------
61
+ BONDs C O 570. 1.229
62
+ BONDs C O2 656. 1.25
63
+ BONDs C CH 317. 1.522
64
+ BONDs C CHp 317. 1.522
65
+ BONDs C C2 317. 1.522
66
+ BONDs C C2a 317. 1.522
67
+ BONDs C C3 317. 1.522
68
+ BONDs C C0 317. 1.522
69
+ ! -------------------------------------------------
70
+ BONDs C1 O 570. 1.265
71
+ ! -------------------------------------------------
72
+ BONDs CH CHa 260. 1.526
73
+ BONDs CH C2 260. 1.526
74
+ BONDs CH C2a 260. 1.526
75
+ BONDs CH C3 260. 1.526
76
+ ! -------------------------------------------------
77
+ BONDs CHa C2p 260. 1.526
78
+ BONDs CHa C2a 260. 1.526
79
+ BONDs CHa C3 260. 1.526
80
+ ! -------------------------------------------------
81
+ BONDs C2a C2 260. 1.526
82
+ BONDs C2a C2a 260. 1.526
83
+ BONDs C2a C3a 260. 1.526
84
+ BONDs C2a C2p 260. 1.526
85
+ BONDs C2a CHp 260. 1.526
86
+ ! -------------------------------------------------
87
+ BONDs C3c C0 260. 1.526
88
+ ! -------------------------------------------------
89
+ BONDs CA HC 340. 1.08
90
+ BONDs CA CAb 469. 1.40
91
+ BONDs CA C2 317. 1.51
92
+ BONDs CA CA 469. 1.40
93
+ BONDs CA CB 388. 1.459
94
+ BONDs CA CC 469. 1.40
95
+ ! -------------------------------------------------
96
+ BONDs CB CC 469. 1.40
97
+ ! -------------------------------------------------
98
+ BONDs CT HCa 340. 1.09
99
+ BONDs CT CTf 268. 1.529
100
+ ! -------------------------------------------------
101
+ BONDs CTf F 367. 1.332
102
+
103
+ ! Eangle = Sum [k(t-t0)**2]
104
+ ! -------------------------------------------------
105
+ ANGLe H N H 35. 120.0
106
+ ANGLe Ha N Ha 35. 120.0
107
+ ANGLe Hb N Hb 35. 120.0
108
+ ANGLe C N H 35. 119.8
109
+ ANGLe C N Ha 35. 119.8
110
+ ANGLe C N Hb 35. 119.8
111
+ ANGLe C1 N Ha 35. 120.9
112
+ ANGLe H N CH 38. 118.4
113
+ ANGLe H N C2 38. 118.4
114
+ ANGLe H N C3 38. 118.4
115
+ ANGLe H N C3b 38. 118.4
116
+ ANGLe H N C0 38. 118.4
117
+ ANGLe H3 N H3 35. 120.0
118
+
119
+ ANGLe C N CH 70. 116.6
120
+ ANGLe C N CHp 70. 116.6
121
+ ANGLe C N C2 70. 116.6
122
+ ANGLe C N C2p 70. 116.6
123
+ ANGLe C N C3 70. 116.6
124
+ ANGLe C N C3b 70. 116.6
125
+ ANGLe C N C0 70. 116.6
126
+
127
+ ANGLe C2p N CHp 50. 118.0
128
+ ! -------------------------------------------------
129
+ ANGLe H3 N2 H3 35. 120.0
130
+ ANGLe C2a N2 H3 35. 118.4
131
+ ANGLe CAa N2 H3 35. 120.0
132
+ ANGLe CAa N2 C2a 50. 123.2
133
+ ! -------------------------------------------------
134
+ ANGLe H3 N3 H3 35. 109.5
135
+ ANGLe CH N3 H3 35. 109.5
136
+ ANGLe C2 N3 H3 35. 109.5
137
+ ANGLe C2a N3 H3 35. 109.5
138
+ ANGLe C0 N3 H3 35. 109.5
139
+ ! -------------------------------------------------
140
+ ANGLe H NA CA 35. 126.35
141
+ ANGLe CA NA CA 70. 107.3
142
+ ANGLe H NA CC 35. 124.2
143
+ ANGLe CA NA CC 70. 111.6
144
+ ! -------------------------------------------------
145
+ ANGLe CA NB CA 70. 105.3
146
+ ! -------------------------------------------------
147
+ ANGLe HW OW HW 34.05 104.52
148
+ ANGLe OW HW HW 0.00 37.74
149
+ ! -------------------------------------------------
150
+ ANGLe CAb OH HO 35. 113.0
151
+ ANGLe CHa OH HO 55. 108.5
152
+ ANGLe C2a OH HO 55. 108.5
153
+ ANGLe CT OH HO 55. 108.5
154
+ ! -------------------------------------------------
155
+ ANGLe C OS C3 83. 116.9
156
+ ANGLe C OS C3b 83. 116.9
157
+ ! -------------------------------------------------
158
+ ANGLe C2 S C3b 62. 98.9
159
+ ANGLe C2 S S 68. 103.7
160
+ ANGLe O4 S O4 85. 109.5
161
+ ! -------------------------------------------------
162
+ ANGLe C2a SH HS 44. 96.0
163
+ ! -------------------------------------------------
164
+ ANGLe O C N 80. 122.9
165
+ ANGLe N C N 70. 114.2
166
+ ANGLe CH C N 70. 116.6
167
+ ANGLe CHp C N 70. 116.6
168
+ ANGLe C2 C N 70. 116.6
169
+ ANGLe C2a C N 70. 116.6
170
+ ANGLe C3 C N 70. 116.6
171
+ ANGLe C0 C N 70. 116.6
172
+
173
+ ANGLe CH C O 80. 120.4
174
+ ANGLe CHp C O 80. 120.4
175
+ ANGLe C2 C O 80. 120.4
176
+ ANGLe C2a C O 80. 120.4
177
+ ANGLe C3 C O 80. 120.4
178
+ ANGLe C0 C O 80. 120.4
179
+
180
+ ANGLe O2 C O2 80. 126.0
181
+ ANGLe CH C O2 65. 117.0
182
+ ANGLe CHp C O2 65. 117.0
183
+ ANGLe C2 C O2 70. 117.0
184
+ ANGLe C2a C O2 70. 117.0
185
+ ANGLe C0 C O2 70. 117.0
186
+
187
+ ANGLe O C OS 83. 123.4
188
+ ANGLe CH C OS 81. 111.4
189
+ ANGLe CHp C OS 81. 111.4
190
+ ANGLe C2 C OS 81. 111.4
191
+ ANGLe C0 C OS 81. 111.4
192
+ ! -------------------------------------------------
193
+ ANGLe O C1 N 80. 121.4
194
+ ANGLe N C1 N 70. 117.2
195
+ ! -------------------------------------------------
196
+ ANGLe CA CAb OH 70. 120.0
197
+ ANGLe CA CAb CA 85. 120.0
198
+ ! -------------------------------------------------
199
+ ANGLe C CH N 50. 110.1
200
+ ANGLe CHa CH N 65. 109.7
201
+ ANGLe C2 CH N 65. 109.7
202
+ ANGLe C2a CH N 65. 109.7
203
+ ANGLe C3 CH N 65. 109.5
204
+
205
+ ANGLe C CH N3 65. 111.2
206
+ ANGLe CHa CH N3 65. 111.2
207
+ ANGLe C2 CH N3 65. 111.2
208
+ ANGLe C2a CH N3 65. 111.2
209
+ ANGLe C3 CH N3 65. 111.2
210
+
211
+ ANGLe CHa CH C 50. 111.1
212
+ ANGLe C2 CH C 50. 111.1
213
+ ANGLe C2a CH C 50. 111.1
214
+ ANGLe C3 CH C 50. 111.1
215
+ ! -------------------------------------------------
216
+ ANGLe CH CHa OH 80. 109.5
217
+ ANGLe C2a CHa OH 80. 109.5
218
+ ANGLe C2p CHa OH 80. 109.5
219
+ ANGLe C3 CHa OH 80. 109.5
220
+
221
+ ANGLe C3 CHa CH 63. 111.5
222
+
223
+ ANGLe CH CHa C2a 63. 111.5
224
+ ANGLe C2a CHa C2a 63. 111.5
225
+ ANGLe C2p CHa C2a 63. 111.5
226
+ ANGLe C3 CHa C2a 63. 111.5
227
+
228
+ ANGLe C3 CHa C3 63. 111.5
229
+ ! -------------------------------------------------
230
+ ANGLe C CHp N 50. 110.1
231
+
232
+ ANGLe C2a CHp N 65. 109.7
233
+ ANGLe C2a CHp C 50. 111.1
234
+ ! -------------------------------------------------
235
+ ANGLe C C2 N 65. 110.3
236
+ ANGLe C C2 N3 65. 111.2
237
+
238
+ ANGLe CA C2 CH 50. 114.0
239
+
240
+ ANGLe CH C2 S 65. 114.7
241
+ ANGLe C2a C2 S 65. 114.7
242
+ ! -------------------------------------------------
243
+ ANGLe C2a C2a N2 80. 111.2
244
+
245
+ ANGLe CHa C2a N3 80. 111.2
246
+ ANGLe C2a C2a N3 80. 111.2
247
+
248
+ ANGLe CH C2a OH 80. 109.5
249
+
250
+ ANGLe CH C2a SH 50. 108.6
251
+
252
+ ANGLe C C2a CH 63. 112.4
253
+ ANGLe CHa C2a CH 63. 112.4
254
+ ANGLe CHa C2a CHp 63. 112.4
255
+ ANGLe C2 C2a CH 63. 112.4
256
+ ANGLe C2a C2a CH 63. 112.4
257
+ ANGLe C2a C2a CHp 63. 112.4
258
+ ANGLe C2a C2a CHa 63. 112.4
259
+ ANGLe C3a C2a CHa 63. 112.4
260
+
261
+ ANGLe C C2a C2a 63. 112.4
262
+ ANGLe C2a C2a C2a 63. 112.4
263
+ ANGLe C2p C2a C2a 63. 112.4
264
+ ! -------------------------------------------------
265
+ ANGLe CHa C2p N 80. 111.2
266
+ ANGLe C2a C2p N 80. 111.2
267
+ ! -------------------------------------------------
268
+ ANGLe N C0 C 63. 110.1
269
+ ANGLe N3 C0 C 80. 111.2
270
+ ANGLe N C0 C3c 80. 109.7
271
+ ANGLe C C0 C3c 63. 111.1
272
+ ANGLe C3c C0 C3c 40. 109.5
273
+ ! -------------------------------------------------
274
+ ANGLe CTf CT OH 50. 109.5
275
+ ANGLe HCa CT OH 35. 109.5
276
+
277
+ ANGLe CTf CT HCa 37.5 110.7
278
+ ANGLe HCa CT HCa 33. 107.8
279
+ ! -------------------------------------------------
280
+ ANGLe CT CTf F 50. 109.5
281
+ ANGLe F CTf F 77. 109.1
282
+ ! -------------------------------------------------
283
+ ANGLe NA CA NA 70. 110.75
284
+ ANGLe NA CA NB 70. 111.6
285
+ ANGLe NA CA C2 70. 122.2
286
+ ANGLe NA CA CA 70. 108.75
287
+ ANGLe NA CA HC 35. 120.0
288
+
289
+ ANGLe NB CA C2 70. 121.05
290
+ ANGLe NB CA CA 70. 109.9
291
+ ANGLe NB CA HC 35. 119.1
292
+
293
+ ANGLe CAb CA CA 85. 120.0
294
+ ANGLe CAb CA HC 35. 120.0
295
+
296
+ ANGLe CA CA C2 70. 120.0
297
+ ANGLe CA CA CA 85. 120.0
298
+ ANGLe CA CA HC 35. 120.0
299
+
300
+ ANGLe CB CA C2 70. 128.6
301
+ ANGLe CB CA CA 85. 120.0
302
+ ANGLe CB CA HC 35. 120.0
303
+
304
+ ANGLe CC CA CA 85. 120.0
305
+ ANGLe CC CA HC 35. 120.0
306
+ ! -------------------------------------------------
307
+ ANGLe N2 CAa N2 70. 120.0
308
+ ! -------------------------------------------------
309
+ ANGLe CA CB CA 85. 134.9
310
+ ANGLe CA CB CC 85. 116.2
311
+ ! -------------------------------------------------
312
+ ANGLe CA CC NA 70. 132.8
313
+ ANGLe CB CC NA 70. 104.4
314
+ ANGLe CB CC CA 85. 122.7
315
+ ! -------------------------------------------------
316
+
317
+ ! Edihedral = Sum {k[1+cos(np+f)]}, n>0
318
+ ! Sum [k(p-f)**2], n=0
319
+ ! note: k=V/2 in OPLS-speak
320
+ ! ------------------BEGIN BACKBONE-----------------
321
+ ! ------------------------PHI----------------------
322
+ ! ----------------------OPLS#70--------------------
323
+ DIHEdral C C2 N C MULTIPLE= 2 -0.23583 1 0.
324
+ 0.05792 2 180.
325
+ ! ----------------------OPLS#47--------------------
326
+ DIHEdral C CH N C MULTIPLE= 2 -1.1872 1 0.
327
+ 0.3792 2 180.
328
+ DIHEdral C CHp N C MULTIPLE= 2 -1.1872 1 0.
329
+ 0.3792 2 180.
330
+ ! -----------------------PHI-H---------------------
331
+ ! ---------------------ZEROVALUE-------------------
332
+ DIHEdral C C2 N H 0.0001 2 180.
333
+ DIHEdral C CH N H 0.0001 2 180.
334
+ ! ----------------------OPLS#76--------------------
335
+ DIHEdral C CHp N C2p MULTIPLE= 3 -0.9439 1 0.
336
+ 6.3210 2 180.
337
+ -1.2028 3 0.
338
+ ! -----------------------PHI-C---------------------
339
+ ! ----------------------OPLS#48--------------------
340
+ DIHEdral C3 CH N C MULTIPLE= 2 -1.4773 1 0.
341
+ 0.3821 2 180.
342
+ DIHEdral C2a CH N C MULTIPLE= 2 -1.4773 1 0.
343
+ 0.3821 2 180.
344
+ DIHEdral C2 CH N C MULTIPLE= 2 -1.4773 1 0.
345
+ 0.3821 2 180.
346
+ DIHEdral CHa CH N C MULTIPLE= 2 -1.4773 1 0.
347
+ 0.3821 2 180.
348
+ DIHEdral C2a CHp N C MULTIPLE= 2 -1.4773 1 0.
349
+ 0.3821 2 180.
350
+ ! ----------------------PHI-C-H--------------------
351
+ ! ---------------------ZEROVALUE-------------------
352
+ DIHEdral CHa CH N H 0.0001 2 180.
353
+ DIHEdral C2 CH N H 0.0001 2 180.
354
+ DIHEdral C2a CH N H 0.0001 2 180.
355
+ DIHEdral C3 CH N H 0.0001 2 180.
356
+ ! ----------------------OPLS#78--------------------
357
+ DIHEdral C2a CHp N C2p MULTIPLE= 3 -4.9230 1 0.
358
+ 6.0940 2 180.
359
+ 1.8318 3 0.
360
+ ! ------------------------PSI----------------------
361
+ ! ----------------------OPLS#71--------------------
362
+ DIHEdral N C C2 N MULTIPLE= 2 0.70360 2 180.
363
+ 0.17244 3 0.
364
+ ! ----------------------OPLS#49--------------------
365
+ DIHEdral N C CH N MULTIPLE= 2 1.2916 2 180.
366
+ -0.3164 3 0.
367
+ DIHEdral N C CHp N MULTIPLE= 2 1.2916 2 180.
368
+ -0.3164 3 0.
369
+ ! -----------------------PSI-O---------------------
370
+ ! ---------------------ZEROVALUE-------------------
371
+ DIHEdral O C C2 N 0.0001 2 180.
372
+ DIHEdral O C CH N 0.0001 2 180.
373
+ DIHEdral O C CHp N 0.0001 2 180.
374
+ ! -----------------------PSI-C---------------------
375
+ ! ----------------------OPLS#50--------------------
376
+ DIHEdral N C CH C3 MULTIPLE= 3 -1.0910 1 0.
377
+ 2.5694 2 180.
378
+ 0.1864 3 0.
379
+ DIHEdral N C CH C2a MULTIPLE= 3 -1.0910 1 0.
380
+ 2.5694 2 180.
381
+ 0.1864 3 0.
382
+ DIHEdral N C CH C2 MULTIPLE= 3 -1.0910 1 0.
383
+ 2.5694 2 180.
384
+ 0.1864 3 0.
385
+ DIHEdral N C CH CHa MULTIPLE= 3 -1.0910 1 0.
386
+ 2.5694 2 180.
387
+ 0.1864 3 0.
388
+ DIHEdral N C CHp C2a MULTIPLE= 3 -1.0910 1 0.
389
+ 2.5694 2 180.
390
+ 0.1864 3 0.
391
+ ! ----------------------PSI-C-O--------------------
392
+ ! ---------------------ZEROVALUE-------------------
393
+ DIHEdral O C CH CHa 0.0001 2 180.
394
+ DIHEdral O C CH C2 0.0001 2 180.
395
+ DIHEdral O C CH C2a 0.0001 2 180.
396
+ DIHEdral O C CH C3 0.0001 2 180.
397
+ DIHEdral O C CHp C2a 0.0001 2 180.
398
+ ! -----------------------OMEGA---------------------
399
+ ! ----------------------OPLS#75--------------------
400
+ DIHEdral C2 N C C2 MULTIPLE= 2 0.4550 1 0.
401
+ 11.6530 2 180.
402
+ DIHEdral CH N C C2 MULTIPLE= 2 0.4550 1 0.
403
+ 11.6530 2 180.
404
+ DIHEdral C2 N C CH MULTIPLE= 2 0.4550 1 0.
405
+ 11.6530 2 180.
406
+ DIHEdral CH N C CH MULTIPLE= 2 0.4550 1 0.
407
+ 11.6530 2 180.
408
+ DIHEdral C2 N C CHp MULTIPLE= 2 0.4550 1 0.
409
+ 11.6530 2 180.
410
+ DIHEdral CH N C CHp MULTIPLE= 2 0.4550 1 0.
411
+ 11.6530 2 180.
412
+ ! ----------------------OPLS#74--------------------
413
+ DIHEdral CHp N C C2 8.3775 2 180.
414
+ DIHEdral CHp N C CH 8.3775 2 180.
415
+ DIHEdral CHp N C CHp 8.3775 2 180.
416
+ ! ----------------OMEGA-O-&-H-OMEGA-O--------------
417
+ ! ---------------------ZEROVALUE-------------------
418
+ DIHEdral H N C O 0.0001 2 180.
419
+ DIHEdral CH N C O 0.0001 2 180.
420
+ DIHEdral CHp N C O 0.0001 2 180.
421
+ DIHEdral C2 N C O 0.0001 2 180.
422
+ DIHEdral C2p N C O 0.0001 2 180.
423
+ DIHEdral C3b N C O 0.0001 2 180.
424
+ ! ----------------------H-OMEGA--------------------
425
+ ! ---------------------ZEROVALUE-------------------
426
+ DIHEdral H N C CH 0.0001 2 180.
427
+ DIHEdral H N C CHp 0.0001 2 180.
428
+ DIHEdral H N C C2 0.0001 2 180.
429
+ DIHEdral H N C C3 0.0001 2 180.
430
+ ! ----------------------OPLS#74--------------------
431
+ DIHEdral C2p N C C2 8.3775 2 180.
432
+ DIHEdral C2p N C CH 8.3775 2 180.
433
+ DIHEdral C2p N C CHp 8.3775 2 180.
434
+ ! -------------------END BACKBONE-----------------
435
+ ! ------------------BEGIN SIDECHAIN----------------
436
+ ! ---------------------X-CH-CH-X-------------------
437
+ ! ----------------------OPLS#59--------------------
438
+ DIHEdral C3 CHa CH N MULTIPLE= 3 -2.9104 1 0.
439
+ 1.3339 2 180.
440
+ 0.3502 3 0.
441
+ DIHEdral C3 CHa CH C MULTIPLE= 3 -2.9104 1 0.
442
+ 1.3339 2 180.
443
+ 0.3502 3 0.
444
+ DIHEdral C2a CHa CH N MULTIPLE= 3 -2.9104 1 0.
445
+ 1.3339 2 180.
446
+ 0.3502 3 0.
447
+ DIHEdral C2a CHa CH C MULTIPLE= 3 -2.9104 1 0.
448
+ 1.3339 2 180.
449
+ 0.3502 3 0.
450
+ ! ----------------------OPLS#65--------------------
451
+ DIHEdral OH CHa CH N MULTIPLE= 3 0.178 1 0.
452
+ -0.053 2 180.
453
+ 0.765 3 0.
454
+ DIHEdral OH CHa CH C MULTIPLE= 3 0.178 1 0.
455
+ -0.053 2 180.
456
+ 0.765 3 0.
457
+ ! ---------------------X-CH-OH-X-------------------
458
+ ! ----------------------OPLS#82--------------------
459
+ DIHEdral C3 CHa OH HO MULTIPLE= 3 0.133 1 0.
460
+ -0.1549 2 180.
461
+ 0.3800 3 0.
462
+ DIHEdral C2a CHa OH HO MULTIPLE= 3 0.133 1 0.
463
+ -0.1549 2 180.
464
+ 0.3800 3 0.
465
+ DIHEdral C2 CHa OH HO MULTIPLE= 3 0.133 1 0.
466
+ -0.1549 2 180.
467
+ 0.3800 3 0.
468
+ DIHEdral C2p CHa OH HO MULTIPLE= 3 0.133 1 0.
469
+ -0.1549 2 180.
470
+ 0.3800 3 0.
471
+ DIHEdral CH CHa OH HO MULTIPLE= 3 0.133 1 0.
472
+ -0.1549 2 180.
473
+ 0.3800 3 0.
474
+ ! ---------------------X-C2-C2-X-------------------
475
+ ! ----------------------OPLS#73--------------------
476
+ DIHEdral C2a C2a C2a C2a MULTIPLE= 3 -2.0198 1 0.
477
+ 0.6130 2 180.
478
+ 1.7818 3 0.
479
+ DIHEdral C2a C2a C2a CH MULTIPLE= 3 -2.0198 1 0.
480
+ 0.6130 2 180.
481
+ 1.7818 3 0.
482
+ DIHEdral C2 C2a C2a CH MULTIPLE= 3 -2.0198 1 0.
483
+ 0.6130 2 180.
484
+ 1.7818 3 0.
485
+ DIHEdral C2p C2a C2a CHp MULTIPLE= 3 -2.0198 1 0.
486
+ 0.6130 2 180.
487
+ 1.7818 3 0.
488
+ DIHEdral CHa C2a C2a CH MULTIPLE= 3 -2.0198 1 0.
489
+ 0.6130 2 180.
490
+ 1.7818 3 0.
491
+ DIHEdral C C2a C2a CH MULTIPLE= 3 -2.0198 1 0.
492
+ 0.6130 2 180.
493
+ 1.7818 3 0.
494
+ DIHEdral C2a C2a C2 N MULTIPLE= 3 -2.0198 1 0.
495
+ 0.6130 2 180.
496
+ 1.7818 3 0.
497
+ DIHEdral C2a C2a C2p N MULTIPLE= 3 -2.0198 1 0.
498
+ 0.6130 2 180.
499
+ 1.7818 3 0.
500
+ ! ----------------------OPLS#68--------------------
501
+ DIHEdral C2a C2a C2a N2 MULTIPLE= 3 -1.0614 1 0.
502
+ 0.4415 2 180.
503
+ 1.8092 3 0.
504
+ DIHEdral C2a C2a C2a N3 MULTIPLE= 3 -1.0614 1 0.
505
+ 0.4415 2 180.
506
+ 1.8092 3 0.
507
+ ! ----------------------OPLS#66--------------------
508
+ DIHEdral S C2 C2a CH MULTIPLE= 3 -1.6162 1 0.
509
+ 1.1873 2 180.
510
+ 1.1100 3 0.
511
+ ! ---------------------X-C2-CH-X-------------------
512
+ ! ----------------------OPLS#58--------------------
513
+ DIHEdral C2a C2a CH N MULTIPLE= 3 -1.7744 1 0.
514
+ 0.6740 2 180.
515
+ -0.8520 3 180.
516
+ DIHEdral C2a C2a CHp N MULTIPLE= 3 -1.7744 1 0.
517
+ 0.6740 2 180.
518
+ -0.8520 3 180.
519
+ DIHEdral C2 C2a CH N MULTIPLE= 3 -1.7744 1 0.
520
+ 0.6740 2 180.
521
+ -0.8520 3 180.
522
+ DIHEdral CHa C2a CH N MULTIPLE= 3 -1.7744 1 0.
523
+ 0.6740 2 180.
524
+ -0.8520 3 180.
525
+ DIHEdral CHa C2a CHp N MULTIPLE= 3 -1.7744 1 0.
526
+ 0.6740 2 180.
527
+ -0.8520 3 180.
528
+ DIHEdral CA C2a CH N MULTIPLE= 3 -1.7744 1 0.
529
+ 0.6740 2 180.
530
+ -0.8520 3 180.
531
+ DIHEdral CA C2 CH N MULTIPLE= 3 -1.7744 1 0.
532
+ 0.6740 2 180.
533
+ -0.8520 3 180.
534
+ DIHEdral C C2a CH N MULTIPLE= 3 -1.7744 1 0.
535
+ 0.6740 2 180.
536
+ -0.8520 3 180.
537
+ DIHEdral C2a C2a CH C MULTIPLE= 3 -1.7744 1 0.
538
+ 0.6740 2 180.
539
+ -0.8520 3 180.
540
+ DIHEdral C2a C2a CHp C MULTIPLE= 3 -1.7744 1 0.
541
+ 0.6740 2 180.
542
+ -0.8520 3 180.
543
+ DIHEdral C2 C2a CH C MULTIPLE= 3 -1.7744 1 0.
544
+ 0.6740 2 180.
545
+ -0.8520 3 180.
546
+ DIHEdral CHa C2a CH C MULTIPLE= 3 -1.7744 1 0.
547
+ 0.6740 2 180.
548
+ -0.8520 3 180.
549
+ DIHEdral CHa C2a CHp C MULTIPLE= 3 -1.7744 1 0.
550
+ 0.6740 2 180.
551
+ -0.8520 3 180.
552
+ DIHEdral CA C2a CH C MULTIPLE= 3 -1.7744 1 0.
553
+ 0.6740 2 180.
554
+ -0.8520 3 180.
555
+ DIHEdral CA C2 CH C MULTIPLE= 3 -1.7744 1 0.
556
+ 0.6740 2 180.
557
+ -0.8520 3 180.
558
+ DIHEdral C C2a CH C MULTIPLE= 3 -1.7744 1 0.
559
+ 0.6740 2 180.
560
+ -0.8520 3 180.
561
+ DIHEdral C3a C2a CHa C3 MULTIPLE= 3 -1.7744 1 0.
562
+ 0.6740 2 180.
563
+ -0.8520 3 180.
564
+ DIHEdral C2a C2a CHa C2a MULTIPLE= 3 -1.7744 1 0.
565
+ 0.6740 2 180.
566
+ -0.8520 3 180.
567
+ DIHEdral C3a C2a CHa CH MULTIPLE= 3 -1.7744 1 0.
568
+ 0.6740 2 180.
569
+ -0.8520 3 180.
570
+ DIHEdral C3a C2a CHa C3 MULTIPLE= 3 -1.7744 1 0.
571
+ 0.6740 2 180.
572
+ -0.8520 3 180.
573
+ DIHEdral CH C2a CHa C3 MULTIPLE= 3 -1.7744 1 0.
574
+ 0.6740 2 180.
575
+ -0.8520 3 180.
576
+ ! ----------------------OPLS#65--------------------
577
+ DIHEdral C2a C2a CHa OH MULTIPLE= 3 0.178 1 0.
578
+ -0.053 2 180.
579
+ 0.765 3 0.
580
+ DIHEdral CH C2a CHa OH MULTIPLE= 3 0.178 1 0.
581
+ -0.053 2 180.
582
+ 0.765 3 0.
583
+ DIHEdral CHp C2a CHa OH MULTIPLE= 3 0.178 1 0.
584
+ -0.053 2 180.
585
+ 0.765 3 0.
586
+ DIHEdral N3 C2a CHa OH MULTIPLE= 3 0.178 1 0.
587
+ -0.053 2 180.
588
+ 0.765 3 0.
589
+ DIHEdral N C2 CHa OH MULTIPLE= 3 0.178 1 0.
590
+ -0.053 2 180.
591
+ 0.765 3 0.
592
+ DIHEdral N C2p CHa OH MULTIPLE= 3 0.178 1 0.
593
+ -0.053 2 180.
594
+ 0.765 3 0.
595
+ DIHEdral OH C2a CH N MULTIPLE= 3 0.178 1 0.
596
+ -0.053 2 180.
597
+ 0.765 3 0.
598
+ DIHEdral OH C2a CH C MULTIPLE= 3 0.178 1 0.
599
+ -0.053 2 180.
600
+ 0.765 3 0.
601
+ ! ----------------------OPLS#66--------------------
602
+ DIHEdral SH C2a CH N MULTIPLE= 3 -1.6162 1 0.
603
+ 1.1874 2 180.
604
+ 1.1100 3 0.
605
+ DIHEdral SH C2a CH C MULTIPLE= 3 -1.6162 1 0.
606
+ 1.1874 2 180.
607
+ 1.1100 3 0.
608
+ DIHEdral S C2 CH N MULTIPLE= 3 -1.6162 1 0.
609
+ 1.1874 2 180.
610
+ 1.1100 3 0.
611
+ DIHEdral S C2 CH C MULTIPLE= 3 -1.6162 1 0.
612
+ 1.1874 2 180.
613
+ 1.1100 3 0.
614
+ ! ----------------------OPLS#68--------------------
615
+ DIHEdral N3 C2a CHa C2a MULTIPLE= 3 -1.0614 1 0.
616
+ 0.4415 2 180.
617
+ 1.8092 3 0.
618
+ ! ----------------------OPLS#73--------------------
619
+ DIHEdral CH C2a CHa C2 MULTIPLE= 3 -2.0198 1 0.
620
+ 0.6133 2 180.
621
+ 1.7816 3 0.
622
+ DIHEdral CHp C2a CHa C2p MULTIPLE= 3 -2.0198 1 0.
623
+ 0.6133 2 180.
624
+ 1.7816 3 0.
625
+ DIHEdral N C2 CHa C2a MULTIPLE= 3 -2.0198 1 0.
626
+ 0.6133 2 180.
627
+ 1.7816 3 0.
628
+ DIHEdral N C2p CHa C2a MULTIPLE= 3 -2.0198 1 0.
629
+ 0.6133 2 180.
630
+ 1.7816 3 0.
631
+ ! ---------------------X-C2-CA-X-------------------
632
+ ! ----------------------OPLS#60--------------------
633
+ DIHEdral CH C2a CA CA MULTIPLE= 3 -3.8976 1 0.
634
+ 0.6723 2 180.
635
+ -0.8582 3 0.
636
+ DIHEdral CH C2 CA CA MULTIPLE= 3 -3.8976 1 0.
637
+ 0.6723 2 180.
638
+ -0.8582 3 0.
639
+ DIHEdral CH C2a CA CB MULTIPLE= 3 -3.8976 1 0.
640
+ 0.6723 2 180.
641
+ -0.8582 3 0.
642
+ DIHEdral CH C2 CA CB MULTIPLE= 3 -3.8976 1 0.
643
+ 0.6723 2 180.
644
+ -0.8582 3 0.
645
+ DIHEdral CH C2a CA NA MULTIPLE= 3 -3.8976 1 0.
646
+ 0.6723 2 180.
647
+ -0.8582 3 0.
648
+ DIHEdral CH C2 CA NA MULTIPLE= 3 -3.8976 1 0.
649
+ 0.6723 2 180.
650
+ -0.8582 3 0.
651
+ DIHEdral CH C2a CA NB MULTIPLE= 3 -3.8976 1 0.
652
+ 0.6723 2 180.
653
+ -0.8582 3 0.
654
+ DIHEdral CH C2 CA NB MULTIPLE= 3 -3.8976 1 0.
655
+ 0.6723 2 180.
656
+ -0.8582 3 0.
657
+ ! ---------------------X-C2-C--X-------------------
658
+ ! ----------------------OPLS#62--------------------
659
+ DIHEdral C2a C2a C O2 MULTIPLE= 3 -3.8605 1 0.
660
+ 0.8308 2 180.
661
+ -0.9303 3 0.
662
+ DIHEdral CH C2a C O2 MULTIPLE= 3 -3.8605 1 0.
663
+ 0.8308 2 180.
664
+ -0.9303 3 0.
665
+ ! ----------------------OPLS#64--------------------
666
+ DIHEdral C2a C2a C N MULTIPLE= 2 0.2772 1 0.
667
+ 1.0940 2 180.
668
+ DIHEdral CH C2a C N MULTIPLE= 2 0.2772 1 0.
669
+ 1.0940 2 180.
670
+ ! ---------------------ZEROVALUE-------------------
671
+ DIHEdral C2a C2a C O 0.0001 2 180.
672
+ DIHEdral CH C2a C O 0.0001 2 180.
673
+ ! ---------------------X-C2-N--X-------------------
674
+ ! ----------------------OPLS#80--------------------
675
+ DIHEdral C2a C2 N CH MULTIPLE= 3 -0.6905 1 0.
676
+ -1.6802 2 0.
677
+ 1.2631 3 0.
678
+ DIHEdral C2a C2p N CHp MULTIPLE= 3 -0.6905 1 0.
679
+ -1.6802 2 0.
680
+ 1.2631 3 0.
681
+ DIHEdral CHa C2 N CH MULTIPLE= 3 -0.6905 1 0.
682
+ -1.6802 2 0.
683
+ 1.2631 3 0.
684
+ DIHEdral CHa C2p N CHp MULTIPLE= 3 -0.6905 1 0.
685
+ -1.6802 2 0.
686
+ 1.2631 3 0.
687
+ ! ----------------------OPLS#79--------------------
688
+ DIHEdral C2a C2 N C MULTIPLE= 3 1.2321 1 0.
689
+ -0.1557 2 0.
690
+ 0.7170 3 0.
691
+ DIHEdral C2a C2p N C MULTIPLE= 3 1.2321 1 0.
692
+ -0.1557 2 0.
693
+ 0.7170 3 0.
694
+ DIHEdral CHa C2 N C MULTIPLE= 3 1.2321 1 0.
695
+ -0.1557 2 0.
696
+ 0.7170 3 0.
697
+ DIHEdral CHa C2p N C MULTIPLE= 3 1.2321 1 0.
698
+ -0.1557 2 0.
699
+ 0.7170 3 0.
700
+ ! ---------------------X-C2-N2-X-------------------
701
+ ! ----------------------OPLS#77--------------------
702
+ DIHEdral C2a C2a N2 CAa MULTIPLE= 3 0.1225 1 0.
703
+ 0.2788 2 180.
704
+ 0.4996 3 0.
705
+ ! ---------------------ZEROVALUE-------------------
706
+ DIHEdral C2a C2a N2 H3 0.0001 2 180.
707
+ ! ---------------------X-C2-N3-X-------------------
708
+ ! ----------------------OPLS#69--------------------
709
+ DIHEdral C2a C2a N3 H3 0.4379 3 0.
710
+ DIHEdral CHa C2a N3 H3 0.4379 3 0.
711
+ ! ---------------------X-C2-OH-X-------------------
712
+ ! ----------------------OPLS#81--------------------
713
+ DIHEdral CH C2a OH HO MULTIPLE= 3 0.2016 1 0.
714
+ -0.1250 2 180.
715
+ 0.7001 3 0.
716
+ ! ---------------------X-C2-SH-X-------------------
717
+ ! ----------------------OPLS#83--------------------
718
+ DIHEdral CH C2a SH HS MULTIPLE= 3 -0.0999 1 0.
719
+ -0.2364 2 180.
720
+ 0.7813 3 0.
721
+ ! ---------------------X-C2-S--X-------------------
722
+ ! ----------------------OPLS#84--------------------
723
+ DIHEdral C2a C2 S C3b MULTIPLE= 3 -0.6840 1 0.
724
+ 0.1050 2 180.
725
+ 0.9676 3 0.
726
+ ! ---------------------X-C--N--X-------------------
727
+ ! ----------------------OPLS#63--------------------
728
+ DIHEdral C2a C N Hb 2.4256 2 180.
729
+ DIHEdral O C N Hb 2.4256 2 180.
730
+ ! ---------------------X-C--OH-X-------------------
731
+ ! ----------------------OPLS#61--------------------
732
+ DIHEdral CA CAb OH HO MULTIPLE= 3 -0.4620 1 0.
733
+ 0.8377 2 180.
734
+ -3.7814 3 0.
735
+ ! ---------------------X-CA-CA-X-------------------
736
+ DIHEdral X CA CA X 1.3250 2 180.
737
+ DIHEdral X CA CAb X 1.3250 2 180.
738
+ ! ---------------------X-CA-CB-X-------------------
739
+ DIHEdral X CA CB X 1.3250 2 180.
740
+ ! ---------------------X-CA-CC-X-------------------
741
+ DIHEdral X CA CC X 1.3250 2 180.
742
+ DIHEdral X CB CC X 1.3250 2 180.
743
+ ! ---------------------X-CA-NA-X-------------------
744
+ DIHEdral X CA NA X 1.4000 2 180.
745
+ DIHEdral X CC NA X 1.4000 2 180.
746
+ ! ---------------------X-CA-NB-X-------------------
747
+ DIHEdral X CA NB X 2.4000 2 180.
748
+ ! ---------------------X-CA-N2-X-------------------
749
+ DIHEdral X CAa N2 X 1.8255 2 180.
750
+ ! -------------------END SIDECHAIN-----------------
751
+ ! ------------------SNAP-ON CHANGES----------------
752
+ ! -----------------N-TERMINAL ACETYL---------------
753
+ ! ----------------------OPLS#75--------------------
754
+ DIHEdral C2 N C C3 MULTIPLE= 2 0.4550 1 0.
755
+ 11.6530 2 180.
756
+ DIHEdral CH N C C3 MULTIPLE= 2 0.4550 1 0.
757
+ 11.6530 2 180.
758
+ ! ----------------------OPLS#74--------------------
759
+ DIHEdral CHp N C C3 8.3775 2 180.
760
+ DIHEdral C2p N C C3 8.3775 2 180.
761
+ ! -----------------C-TERMINAL METHYL---------------
762
+ ! ----------------------OPLS#75--------------------
763
+ DIHEdral C3b N C C2 MULTIPLE= 2 0.4550 1 0.
764
+ 11.6530 2 180.
765
+ DIHEdral C3b N C CH MULTIPLE= 2 0.4550 1 0.
766
+ 11.6530 2 180.
767
+ DIHEdral C3b N C CHp MULTIPLE= 2 0.4550 1 0.
768
+ 11.6530 2 180.
769
+ ! -----------------C-TERMINAL AMINO---------------
770
+ ! --------------------aaOPLS#85aa------------------
771
+ DIHEdral Ha N C C2 2.4423 2 180.
772
+ DIHEdral Ha N C CH 2.4423 2 180.
773
+ DIHEdral Ha N C CHp 2.4423 2 180.
774
+ DIHEdral Ha N C O 2.4423 2 180.
775
+ ! ----------------END SNAP-ON CHANGES--------------
776
+ ! -----------------------NH3-----------------------
777
+ ! ---------------THE MODIFIED BACKBONE-------------
778
+ ! ----------------------OPLS#71--------------------
779
+ DIHEdral N C C2 N3 MULTIPLE= 2 0.70360 2 180.
780
+ 0.17244 3 0.
781
+ ! ----------------------OPLS#49--------------------
782
+ DIHEdral N C CH N3 MULTIPLE= 2 1.2916 2 180.
783
+ -0.3164 3 0.
784
+ ! ---------------------ZEROVALUE-------------------
785
+ DIHEdral O C C2 N3 0.0001 2 180.
786
+ DIHEdral O C CH N3 0.0001 2 180.
787
+ DIHEdral C C2 N3 H3 0.0001 3 0.
788
+ DIHEdral C CH N3 H3 0.0001 3 0.
789
+ DIHEdral CHa CH N3 H3 0.0001 3 0.
790
+ DIHEdral CH2 CH N3 H3 0.0001 3 0.
791
+ DIHEdral C2a CH N3 H3 0.0001 3 0.
792
+ DIHEdral C3 CH N3 H3 0.0001 3 0.
793
+ ! ---------------THE MODIFIED SIDECHAIN------------
794
+ ! ----------------------OPLS#58--------------------
795
+ DIHEdral C2a C2a CH N3 MULTIPLE= 3 -1.7744 1 0.
796
+ 0.6740 2 180.
797
+ -0.8520 3 180.
798
+ DIHEdral C2 C2a CH N3 MULTIPLE= 3 -1.7744 1 0.
799
+ 0.6740 2 180.
800
+ -0.8520 3 180.
801
+ DIHEdral CHa C2a CH N3 MULTIPLE= 3 -1.7744 1 0.
802
+ 0.6740 2 180.
803
+ -0.8520 3 180.
804
+ DIHEdral CA C2 CH N3 MULTIPLE= 3 -1.7744 1 0.
805
+ 0.6740 2 180.
806
+ -0.8520 3 180.
807
+ DIHEdral C C2a CH N3 MULTIPLE= 3 -1.7744 1 0.
808
+ 0.6740 2 180.
809
+ -0.8520 3 180.
810
+ ! ----------------------OPLS#59--------------------
811
+ DIHEdral C3 CHa CH N3 MULTIPLE= 3 -2.9104 1 0.
812
+ 1.3339 2 180.
813
+ 0.3502 3 0.
814
+ DIHEdral C2a CHa CH N3 MULTIPLE= 3 -2.9104 1 0.
815
+ 1.3339 2 180.
816
+ 0.3502 3 0.
817
+ ! ----------------------OPLS#65--------------------
818
+ DIHEdral OH C2a CH N3 MULTIPLE= 3 0.178 1 0.
819
+ -0.053 2 180.
820
+ 0.765 3 0.
821
+ DIHEdral OH CHa CH N3 MULTIPLE= 3 0.178 1 0.
822
+ -0.053 2 180.
823
+ 0.765 3 0.
824
+ ! ----------------------OPLS#66--------------------
825
+ DIHEdral SH C2a CH N3 MULTIPLE= 3 -1.6162 1 0.
826
+ 1.1874 2 180.
827
+ 1.1100 3 0.
828
+ DIHEdral S C2 CH N3 MULTIPLE= 3 -1.6162 1 0.
829
+ 1.1874 2 180.
830
+ 1.1100 3 0.
831
+ ! ----------------------END NH3-------------------
832
+ ! ---------------------BEGIN CO2-------------------
833
+ ! ---------------------ZEROVALUE-------------------
834
+ DIHEdral O2 C C2 N 0.0001 2 180.
835
+ DIHEdral O2 C CH N 0.0001 2 180.
836
+ DIHEdral O2 C CH CHa 0.0001 2 180.
837
+ DIHEdral O2 C CH C2 0.0001 2 180.
838
+ DIHEdral O2 C CH C2a 0.0001 2 180.
839
+ DIHEdral O2 C CH C3 0.0001 2 180.
840
+ ! ----------------------END CO2-------------------
841
+ ! -------------------BEGIN DISULFIDE----------------
842
+ DIHEdral C2 S S C2 8.6700 2 0.
843
+ DIHEdral CH C2 S S 2.5000 3 0.
844
+ ! --------------------END DISULFIDE-----------------
845
+ ! -------------------BEGIN UREA-----------------
846
+ ! --------------------aaOPLS#85aa------------------
847
+ DIHEdral Ha N C1 N 2.4423 2 180.
848
+ DIHEdral Ha N C1 O 2.4423 2 180.
849
+ ! --------------------END UREA-----------------
850
+ ! -------------------BEGIN TFE-----------------
851
+ ! --------------------aaOPLS#90aa------------------
852
+ DIHEdral HO OH CT CTf MULTIPLE= 2 2.2390 1 0.
853
+ -1.0873 2 180.
854
+ ! --------------------aaOPLS#91aa------------------
855
+ DIHEdral HO OH CT HCa 0.2380 3 0.
856
+ ! --------------------aaOPLS#92aa------------------
857
+ DIHEdral F CTf CT HCa 0.1568 3 0.
858
+ ! --------------------aaOPLS#93aa------------------
859
+ DIHEdral F CTf CT OH 0.2701 3 0.
860
+ ! --------------------END TFE-----------------
861
+
862
+ ! Eimproper = Sum {k[1+cos(np+f)]}, n>0
863
+ ! Sum [k(p-f)**2], n=0
864
+ ! note: k=V/2 in OPLS-speak
865
+ !-------------------------HOLD THE PLANE----------------
866
+
867
+ ! to retain planarity about amide centers with zero-value dihedrals
868
+ IMPRoper C N C2 O 100.0000 0 0.
869
+ IMPRoper C N CH O 100.0000 0 0.
870
+ IMPRoper C N CHp O 100.0000 0 0.
871
+ IMPRoper C N C3 O 100.0000 0 0.
872
+
873
+ IMPRoper C N N O 100.0000 0 0.
874
+ IMPRoper C1 N N O 100.0000 0 0.
875
+
876
+ IMPRoper C N C2a O 100.0000 0 0.
877
+
878
+ IMPRoper N C2 C H 45.0000 0 0.
879
+ IMPRoper N CH C H 45.0000 0 0.
880
+ IMPRoper N C3b C H 45.0000 0 0.
881
+ ! to retain planarity about amide centers with zero-value dihedrals
882
+
883
+ IMPRoper C2 OS C O 15.0000 2 180.
884
+ IMPRoper CH OS C O 15.0000 2 180.
885
+ IMPRoper CHp OS C O 15.0000 2 180.
886
+ IMPRoper C2 O2 C O2 15.0000 2 180.
887
+ IMPRoper C2a O2 C O2 15.0000 2 180.
888
+ IMPRoper CH O2 C O2 15.0000 2 180.
889
+
890
+ IMPRoper C CHp N C2p 20.0000 2 180.
891
+ IMPRoper C H N H 20.0000 2 180.
892
+ IMPRoper C Ha N Ha 20.0000 2 180.
893
+ IMPRoper C1 Ha N Ha 20.0000 2 180.
894
+ IMPRoper C Hb N Hb 20.0000 2 180.
895
+
896
+ IMPRoper CHa CH N C 15.0000 3 180.
897
+ IMPRoper C2 CH N C 15.0000 3 180.
898
+ IMPRoper C2a CH N C 15.0000 3 180.
899
+ IMPRoper C3 CH N C 15.0000 3 180.
900
+ IMPRoper C2a CHp N C 15.0000 3 180.
901
+
902
+ IMPRoper CHa CH N3 C 15.0000 3 180.
903
+ IMPRoper C2 CH N3 C 15.0000 3 180.
904
+ IMPRoper C2a CH N3 C 15.0000 3 180.
905
+ IMPRoper C3 CH N3 C 15.0000 3 180.
906
+
907
+ IMPRoper C2a CH CHa C3 15.0000 3 180.
908
+ IMPRoper C3 CHa CH C3 15.0000 3 180.
909
+ IMPRoper C3 CHa C2a C3 15.0000 3 180.
910
+
911
+ IMPRoper N2 CAa N2 N2 20.0000 2 180.
912
+ ! permit usage of zero-value dihedral
913
+ IMPRoper N2 CAa C2a H3 45.0000 0 0.
914
+ ! permit usage of zero-value dihedral
915
+ IMPRoper H3 N2 CAa H3 20.0000 2 180.
916
+
917
+ IMPRoper OH CH CHa C3 15.0000 3 180.
918
+ IMPRoper OH CHa C2a C2a 15.0000 3 180.
919
+ IMPRoper OH CHa C2a C2p 15.0000 3 180.
920
+
921
+ IMPRoper H NA CA CA 15.0000 2 180.
922
+ IMPRoper H NA CC CA 15.0000 2 180.
923
+
924
+ IMPRoper CA CA C2 CA 15.5000 2 180.
925
+ IMPRoper CA CA CA C2 15.5000 2 180.
926
+ IMPRoper CA CA NA C2 15.5000 2 180.
927
+ IMPRoper CA CA NB C2 15.5000 2 180.
928
+ IMPRoper CB CA CA C2 15.5000 2 180.
929
+ IMPRoper CA CA CB C2 15.5000 2 180.
930
+ IMPRoper CA CB CA CC 15.5000 2 180.
931
+ IMPRoper CA CC CB NA 15.5000 2 180.
932
+
933
+ IMPRoper HC CA CA CA 15.0000 2 180.
934
+ IMPRoper HC CA CA CC 15.0000 2 180.
935
+ IMPRoper HC CA CB CA 15.0000 2 180.
936
+ IMPRoper HC CA NA CA 15.0000 2 180.
937
+ IMPRoper HC CA NB CA 15.0000 2 180.
938
+ IMPRoper HC CA NA NB 15.0000 2 180.
939
+ IMPRoper HC CA NB NA 15.0000 2 180.
940
+ IMPRoper HC CA NA NA 15.0000 2 180.
941
+ IMPRoper HC CA CA CAb 15.0000 2 180.
942
+ IMPRoper HC CA CAb CA 15.0000 2 180.
943
+ IMPRoper OH CAb CA CA 15.5000 2 180.
944
+
945
+ !------------------------------L-J----------------------
946
+
947
+ remarks MODIFY CUTOFF VALUES FOR PARTICULAR SYSTEM
948
+ remarks GROUP cutoff chosen for consistency with MCPRO
949
+ {
950
+ NBONds
951
+ GROUp
952
+ NBXMod=+5
953
+ E14Fac=0.5
954
+ CDIE EPS=1.0
955
+ TRUNcation
956
+ CUTNb=12.0
957
+ END
958
+ }
959
+ NONBonded H 0.000 0.000 0.000 0.000
960
+ NONBonded Ha 0.000 0.000 0.000 0.000
961
+ NONBonded Hb 0.000 0.000 0.000 0.000
962
+ NONBonded H3 0.000 0.000 0.000 0.000
963
+ NONBonded HC 0.030 2.420 0.015 2.420
964
+ NONBonded HCa 0.030 2.500 0.015 2.500
965
+ NONBonded HO 0.000 0.000 0.000 0.000
966
+ NONBonded HS 0.000 0.000 0.000 0.000
967
+ NONBonded HW 0.000 0.000 0.000 0.000
968
+
969
+ NONBonded C 0.105 3.750 0.052 3.750
970
+ NONBonded C1 0.105 3.750 0.052 3.750
971
+ NONBonded CAb 0.070 3.550 0.035 3.550
972
+ NONBonded C2 0.118 3.800 0.059 3.800
973
+ NONBonded C2a 0.118 3.905 0.059 3.905
974
+ NONBonded C2p 0.118 3.800 0.059 3.800
975
+ NONBonded C3 0.160 3.910 0.080 3.910
976
+ NONBonded C3a 0.175 3.905 0.088 3.905
977
+ NONBonded C3b 0.170 3.800 0.085 3.800
978
+ NONBonded C3c 0.145 3.960 0.145 3.960
979
+ NONBonded CA 0.070 3.550 0.035 3.550
980
+ NONBonded CAa 0.050 2.250 0.025 2.250
981
+ NONBonded CB 0.145 3.750 0.072 3.750
982
+ NONBonded CC 0.145 3.750 0.072 3.750
983
+ NONBonded CH 0.080 3.800 0.040 3.800
984
+ NONBonded CHa 0.080 3.850 0.040 3.850
985
+ NONBonded CHp 0.080 3.850 0.040 3.850
986
+ NONBonded C0 0.050 3.800 0.025 3.800
987
+ NONBonded CT 0.066 3.500 0.033 3.500
988
+ NONBonded CTf 0.062 3.250 0.031 3.250
989
+
990
+ NONBonded N 0.170 3.250 0.085 3.250
991
+ NONBonded N2 0.170 3.250 0.085 3.250
992
+ NONBonded N3 0.170 3.250 0.085 3.250
993
+ NONBonded NA 0.170 3.250 0.085 3.250
994
+ NONBonded NB 0.170 3.250 0.085 3.250
995
+
996
+ NONBonded O 0.210 2.960 0.105 2.960
997
+ NONBonded O2 0.210 2.960 0.105 2.960
998
+ NONBonded O4 0.200 3.150 0.100 3.150
999
+ NONBonded OH 0.170 3.070 0.085 3.070
1000
+ NONBonded OS 0.170 3.000 0.085 3.000
1001
+ NONBonded OW 0.1521 3.15061 0.1521 3.15061
1002
+
1003
+ NONBonded S 0.250 3.550 0.125 3.550
1004
+ NONBonded SH 0.250 3.550 0.125 3.550
1005
+
1006
+ NONBonded F 0.061 2.940 0.030 2.940
1007
+
1008
+ NONBonded SOD 0.0028 3.33044 0.0014 3.33044
1009
+ NONBonded CAL 0.4496 2.41203 0.2248 2.41203
1010
+ NONBonded CHL 0.1178 4.41724 0.0589 4.41724
1011
+ NONBonded YB 0.050 3.250 0.025 3.250
1012
+
1013
+ !-------water-water and solute-water using geometric means-------
1014
+ NBFIx HW H 0.0000 0.0000 0.0000 0.0000
1015
+ NBFIx HW Ha 0.0000 0.0000 0.0000 0.0000
1016
+ NBFIx HW Hb 0.0000 0.0000 0.0000 0.0000
1017
+ NBFIx HW H3 0.0000 0.0000 0.0000 0.0000
1018
+ NBFIx HW HC 0.0000 0.0000 0.0000 0.0000
1019
+ NBFIx HW HCa 0.0000 0.0000 0.0000 0.0000
1020
+ NBFIx HW HO 0.0000 0.0000 0.0000 0.0000
1021
+ NBFIx HW HS 0.0000 0.0000 0.0000 0.0000
1022
+ NBFIx HW HW 0.0000 0.0000 0.0000 0.0000
1023
+ NBFIx HW C 0.0000 0.0000 0.0000 0.0000
1024
+ NBFIx HW C1 0.0000 0.0000 0.0000 0.0000
1025
+ NBFIx HW CAb 0.0000 0.0000 0.0000 0.0000
1026
+ NBFIx HW C2 0.0000 0.0000 0.0000 0.0000
1027
+ NBFIx HW C2a 0.0000 0.0000 0.0000 0.0000
1028
+ NBFIx HW C2p 0.0000 0.0000 0.0000 0.0000
1029
+ NBFIx HW C3 0.0000 0.0000 0.0000 0.0000
1030
+ NBFIx HW C3a 0.0000 0.0000 0.0000 0.0000
1031
+ NBFIx HW C3b 0.0000 0.0000 0.0000 0.0000
1032
+ NBFIx HW C3c 0.0000 0.0000 0.0000 0.0000
1033
+ NBFIx HW CA 0.0000 0.0000 0.0000 0.0000
1034
+ NBFIx HW CAa 0.0000 0.0000 0.0000 0.0000
1035
+ NBFIx HW CB 0.0000 0.0000 0.0000 0.0000
1036
+ NBFIx HW CC 0.0000 0.0000 0.0000 0.0000
1037
+ NBFIx HW CH 0.0000 0.0000 0.0000 0.0000
1038
+ NBFIx HW CHa 0.0000 0.0000 0.0000 0.0000
1039
+ NBFIx HW CHp 0.0000 0.0000 0.0000 0.0000
1040
+ NBFIx HW C0 0.0000 0.0000 0.0000 0.0000
1041
+ NBFIx HW CT 0.0000 0.0000 0.0000 0.0000
1042
+ NBFIx HW CTf 0.0000 0.0000 0.0000 0.0000
1043
+ NBFIx HW N 0.0000 0.0000 0.0000 0.0000
1044
+ NBFIx HW N2 0.0000 0.0000 0.0000 0.0000
1045
+ NBFIx HW N3 0.0000 0.0000 0.0000 0.0000
1046
+ NBFIx HW NA 0.0000 0.0000 0.0000 0.0000
1047
+ NBFIx HW NB 0.0000 0.0000 0.0000 0.0000
1048
+ NBFIx HW O 0.0000 0.0000 0.0000 0.0000
1049
+ NBFIx HW O2 0.0000 0.0000 0.0000 0.0000
1050
+ NBFIx HW O4 0.0000 0.0000 0.0000 0.0000
1051
+ NBFIx HW OH 0.0000 0.0000 0.0000 0.0000
1052
+ NBFIx HW OS 0.0000 0.0000 0.0000 0.0000
1053
+ NBFIx HW OW 0.0000 0.0000 0.0000 0.0000
1054
+ NBFIx HW S 0.0000 0.0000 0.0000 0.0000
1055
+ NBFIx HW SH 0.0000 0.0000 0.0000 0.0000
1056
+ NBFIx HW F 0.0000 0.0000 0.0000 0.0000
1057
+ NBFIx HW SOD 0.0000 0.0000 0.0000 0.0000
1058
+ NBFIx HW CAL 0.0000 0.0000 0.0000 0.0000
1059
+ NBFIx HW CHL 0.0000 0.0000 0.0000 0.0000
1060
+ NBFIx HW YB 0.0000 0.0000 0.0000 0.0000
1061
+ NBFIx OW H 0.0000 0.0000 0.0000 0.0000
1062
+ NBFIx OW Ha 0.0000 0.0000 0.0000 0.0000
1063
+ NBFIx OW Hb 0.0000 0.0000 0.0000 0.0000
1064
+ NBFIx OW H3 0.0000 0.0000 0.0000 0.0000
1065
+ NBFIx OW HC 53081.7588 119.7610 0.0000 0.0000
1066
+ NBFIx OW HCa 64519.8220 132.0350 0.0000 0.0000
1067
+ NBFIx OW HO 0.0000 0.0000 0.0000 0.0000
1068
+ NBFIx OW HS 0.0000 0.0000 0.0000 0.0000
1069
+ NBFIx OW HW 0.0000 0.0000 0.0000 0.0000
1070
+ NBFIx OW C 1374911.4762 833.6754 0.0000 0.0000
1071
+ NBFIx OW C1 1374911.4762 833.6754 0.0000 0.0000
1072
+ NBFIx OW CAb 808000.4812 577.4875 0.0000 0.0000
1073
+ NBFIx OW C2 1578101.9789 919.6029 0.0000 0.0000
1074
+ NBFIx OW C2a 1858487.7977 997.9589 0.0000 0.0000
1075
+ NBFIx OW C2p 1578101.9789 919.6029 0.0000 0.0000
1076
+ NBFIx OW C3 2180785.8308 1166.5378 0.0000 0.0000
1077
+ NBFIx OW C3a 2263277.1285 1215.3201 0.0000 0.0000
1078
+ NBFIx OW C3b 1894168.1137 1103.7832 0.0000 0.0000
1079
+ NBFIx OW C3c 2240513.6686 1153.6607 0.0000 0.0000
1080
+ NBFIx OW CA 808000.4812 577.4875 0.0000 0.0000
1081
+ NBFIx OW CAa 44266.2357 124.2628 0.0000 0.0000
1082
+ NBFIx OW CB 1615712.5135 979.6847 0.0000 0.0000
1083
+ NBFIx OW CC 1615712.5135 979.6847 0.0000 0.0000
1084
+ NBFIx OW CH 1299388.6061 757.1890 0.0000 0.0000
1085
+ NBFIx OW CHa 1405406.1563 787.4731 0.0000 0.0000
1086
+ NBFIx OW CHp 1405406.1563 787.4731 0.0000 0.0000
1087
+ NBFIx OW C0 1027256.8902 598.6105 0.0000 0.0000
1088
+ NBFIx OW CT 720564.2561 537.3839 0.0000 0.0000
1089
+ NBFIx OW CTf 447701.4404 417.0177 0.0000 0.0000
1090
+ NBFIx OW N 741339.4434 690.5308 0.0000 0.0000
1091
+ NBFIx OW N2 741339.4434 690.5308 0.0000 0.0000
1092
+ NBFIx OW N3 741339.4434 690.5308 0.0000 0.0000
1093
+ NBFIx OW NA 741339.4434 690.5308 0.0000 0.0000
1094
+ NBFIx OW NB 741339.4434 690.5308 0.0000 0.0000
1095
+ NBFIx OW O 470275.5443 579.8202 0.0000 0.0000
1096
+ NBFIx OW O2 470275.5443 579.8202 0.0000 0.0000
1097
+ NBFIx OW O4 666608.4302 681.9542 0.0000 0.0000
1098
+ NBFIx OW OH 526680.4460 582.0337 0.0000 0.0000
1099
+ NBFIx OW OS 458611.0030 543.1212 0.0000 0.0000
1100
+ NBFIx OW OW 582002.6617 595.0550 0.0000 0.0000
1101
+ NBFIx OW S 1526977.3803 1091.3489 0.0000 0.0000
1102
+ NBFIx OW SH 1526977.3803 1091.3489 0.0000 0.0000
1103
+ NBFIx OW F 243355.6205 306.2072 0.0000 0.0000
1104
+ NBFIx OW SOD 110174.5234 95.3657 0.0000 0.0000
1105
+ NBFIx OW CAL 201466.0460 459.0604 0.0000 0.0000
1106
+ NBFIx OW CHL 3890192.6027 1443.2254 0.0000 0.0000
1107
+ NBFIx OW YB 402047.7621 374.4929 0.0000 0.0000
1108
+ !------------------------------L-J----------------------