normal Protein in Water using ElNeDyn22

  • ngandhiau
  • ngandhiau's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 years 9 months ago #3900 by ngandhiau
Protein in Water using ElNeDyn22 was created by ngandhiau
Hello,

I used martinize.py script to prepare my CG file using elnedyn22 force field. I went through this forun on issues related to simulating with elnedyn in presence of water and protein.

I tried equilibrating system by first imposing position restraints with time step of 0.010 ps and then gradually releasing position restraints. I also looked at the mailing list asking the users to move BB constraints to the bond section in itp file. I am still not able to increase the timestep to 0.020 ps and run production.

Here is my ITP file and

; MARTINI (elnedyn22) Coarse Grained topology file for "Protein_A"
; Created by py version 2.4
; Using the following options: -f fibril.pdb -o topol.top -x cg_fibril.pdb -n index.ndx -dssp ./dsspcmbi -nt -ff elnedyn22 -ef 1000 -eu 0.9 -p backbone
; Sequence:
; VQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYKVQIVYK
; Secondary Structure:
; CEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEECCEEEEC

[ moleculetype ]
; Name Exclusions
Protein_A 1

[ atoms ]
1 P5 1 VAL BB 1 0.0000 ; C
2 C2 1 VAL SC1 2 0.0000 ; C
3 Nda 2 GLN BB 3 0.0000 ; E
4 P4 2 GLN SC1 4 0.0000 ; E
5 Nda 3 ILE BB 5 0.0000 ; E
6 C1 3 ILE SC1 6 0.0000 ; E
7 Nda 4 VAL BB 7 0.0000 ; E
8 C2 4 VAL SC1 8 0.0000 ; E
9 Nda 5 TYR BB 9 0.0000 ; E
10 SC4 5 TYR SC1 10 0.0000 ; E
11 SC4 5 TYR SC2 11 0.0000 ; E
12 SP1 5 TYR SC3 12 0.0000 ; E
13 P5 6 LYS BB 13 0.0000 ; C
14 C3 6 LYS SC1 14 0.0000 ; C
15 Qd 6 LYS SC2 15 1.0000 ; C
16 P5 7 VAL BB 16 0.0000 ; C
17 C2 7 VAL SC1 17 0.0000 ; C
18 Nda 8 GLN BB 18 0.0000 ; E
19 P4 8 GLN SC1 19 0.0000 ; E
20 Nda 9 ILE BB 20 0.0000 ; E
21 C1 9 ILE SC1 21 0.0000 ; E
22 Nda 10 VAL BB 22 0.0000 ; E
23 C2 10 VAL SC1 23 0.0000 ; E
24 Nda 11 TYR BB 24 0.0000 ; E
25 SC4 11 TYR SC1 25 0.0000 ; E
26 SC4 11 TYR SC2 26 0.0000 ; E
27 SP1 11 TYR SC3 27 0.0000 ; E
28 P5 12 LYS BB 28 0.0000 ; C
29 C3 12 LYS SC1 29 0.0000 ; C
30 Qd 12 LYS SC2 30 1.0000 ; C
31 P5 13 VAL BB 31 0.0000 ; C
32 C2 13 VAL SC1 32 0.0000 ; C
33 Nda 14 GLN BB 33 0.0000 ; E
34 P4 14 GLN SC1 34 0.0000 ; E
35 Nda 15 ILE BB 35 0.0000 ; E
36 C1 15 ILE SC1 36 0.0000 ; E
37 Nda 16 VAL BB 37 0.0000 ; E
38 C2 16 VAL SC1 38 0.0000 ; E
39 Nda 17 TYR BB 39 0.0000 ; E
40 SC4 17 TYR SC1 40 0.0000 ; E
41 SC4 17 TYR SC2 41 0.0000 ; E
42 SP1 17 TYR SC3 42 0.0000 ; E
43 P5 18 LYS BB 43 0.0000 ; C
44 C3 18 LYS SC1 44 0.0000 ; C
45 Qd 18 LYS SC2 45 1.0000 ; C
46 P5 19 VAL BB 46 0.0000 ; C
47 C2 19 VAL SC1 47 0.0000 ; C
48 Nda 20 GLN BB 48 0.0000 ; E
49 P4 20 GLN SC1 49 0.0000 ; E
50 Nda 21 ILE BB 50 0.0000 ; E
51 C1 21 ILE SC1 51 0.0000 ; E
52 Nda 22 VAL BB 52 0.0000 ; E
53 C2 22 VAL SC1 53 0.0000 ; E
54 Nda 23 TYR BB 54 0.0000 ; E
55 SC4 23 TYR SC1 55 0.0000 ; E
56 SC4 23 TYR SC2 56 0.0000 ; E
57 SP1 23 TYR SC3 57 0.0000 ; E
58 P5 24 LYS BB 58 0.0000 ; C
59 C3 24 LYS SC1 59 0.0000 ; C
60 Qd 24 LYS SC2 60 1.0000 ; C
61 P5 25 VAL BB 61 0.0000 ; C
62 C2 25 VAL SC1 62 0.0000 ; C
63 Nda 26 GLN BB 63 0.0000 ; E
64 P4 26 GLN SC1 64 0.0000 ; E
65 Nda 27 ILE BB 65 0.0000 ; E
66 C1 27 ILE SC1 66 0.0000 ; E
67 Nda 28 VAL BB 67 0.0000 ; E
68 C2 28 VAL SC1 68 0.0000 ; E
69 Nda 29 TYR BB 69 0.0000 ; E
70 SC4 29 TYR SC1 70 0.0000 ; E
71 SC4 29 TYR SC2 71 0.0000 ; E
72 SP1 29 TYR SC3 72 0.0000 ; E
73 P5 30 LYS BB 73 0.0000 ; C
74 C3 30 LYS SC1 74 0.0000 ; C
75 Qd 30 LYS SC2 75 1.0000 ; C
76 P5 31 VAL BB 76 0.0000 ; C
77 C2 31 VAL SC1 77 0.0000 ; C
78 Nda 32 GLN BB 78 0.0000 ; E
79 P4 32 GLN SC1 79 0.0000 ; E
80 Nda 33 ILE BB 80 0.0000 ; E
81 C1 33 ILE SC1 81 0.0000 ; E
82 Nda 34 VAL BB 82 0.0000 ; E
83 C2 34 VAL SC1 83 0.0000 ; E
84 Nda 35 TYR BB 84 0.0000 ; E
85 SC4 35 TYR SC1 85 0.0000 ; E
86 SC4 35 TYR SC2 86 0.0000 ; E
87 SP1 35 TYR SC3 87 0.0000 ; E
88 P5 36 LYS BB 88 0.0000 ; C
89 C3 36 LYS SC1 89 0.0000 ; C
90 Qd 36 LYS SC2 90 1.0000 ; C
91 P5 37 VAL BB 91 0.0000 ; C
92 C2 37 VAL SC1 92 0.0000 ; C
93 Nda 38 GLN BB 93 0.0000 ; E
94 P4 38 GLN SC1 94 0.0000 ; E
95 Nda 39 ILE BB 95 0.0000 ; E
96 C1 39 ILE SC1 96 0.0000 ; E
97 Nda 40 VAL BB 97 0.0000 ; E
98 C2 40 VAL SC1 98 0.0000 ; E
99 Nda 41 TYR BB 99 0.0000 ; E
100 SC4 41 TYR SC1 100 0.0000 ; E
101 SC4 41 TYR SC2 101 0.0000 ; E
102 SP1 41 TYR SC3 102 0.0000 ; E
103 P5 42 LYS BB 103 0.0000 ; C
104 C3 42 LYS SC1 104 0.0000 ; C
105 Qd 42 LYS SC2 105 1.0000 ; C
106 P5 43 VAL BB 106 0.0000 ; C
107 C2 43 VAL SC1 107 0.0000 ; C
108 Nda 44 GLN BB 108 0.0000 ; E
109 P4 44 GLN SC1 109 0.0000 ; E
110 Nda 45 ILE BB 110 0.0000 ; E
111 C1 45 ILE SC1 111 0.0000 ; E
112 Nda 46 VAL BB 112 0.0000 ; E
113 C2 46 VAL SC1 113 0.0000 ; E
114 Nda 47 TYR BB 114 0.0000 ; E
115 SC4 47 TYR SC1 115 0.0000 ; E
116 SC4 47 TYR SC2 116 0.0000 ; E
117 SP1 47 TYR SC3 117 0.0000 ; E
118 P5 48 LYS BB 118 0.0000 ; C
119 C3 48 LYS SC1 119 0.0000 ; C
120 Qd 48 LYS SC2 120 1.0000 ; C
121 P5 49 VAL BB 121 0.0000 ; C
122 C2 49 VAL SC1 122 0.0000 ; C
123 Nda 50 GLN BB 123 0.0000 ; E
124 P4 50 GLN SC1 124 0.0000 ; E
125 Nda 51 ILE BB 125 0.0000 ; E
126 C1 51 ILE SC1 126 0.0000 ; E
127 Nda 52 VAL BB 127 0.0000 ; E
128 C2 52 VAL SC1 128 0.0000 ; E
129 Nda 53 TYR BB 129 0.0000 ; E
130 SC4 53 TYR SC1 130 0.0000 ; E
131 SC4 53 TYR SC2 131 0.0000 ; E
132 SP1 53 TYR SC3 132 0.0000 ; E
133 P5 54 LYS BB 133 0.0000 ; C
134 C3 54 LYS SC1 134 0.0000 ; C
135 Qd 54 LYS SC2 135 1.0000 ; C
136 P5 55 VAL BB 136 0.0000 ; C
137 C2 55 VAL SC1 137 0.0000 ; C
138 Nda 56 GLN BB 138 0.0000 ; E
139 P4 56 GLN SC1 139 0.0000 ; E
140 Nda 57 ILE BB 140 0.0000 ; E
141 C1 57 ILE SC1 141 0.0000 ; E
142 Nda 58 VAL BB 142 0.0000 ; E
143 C2 58 VAL SC1 143 0.0000 ; E
144 Nda 59 TYR BB 144 0.0000 ; E
145 SC4 59 TYR SC1 145 0.0000 ; E
146 SC4 59 TYR SC2 146 0.0000 ; E
147 SP1 59 TYR SC3 147 0.0000 ; E
148 P5 60 LYS BB 148 0.0000 ; C
149 C3 60 LYS SC1 149 0.0000 ; C
150 Qd 60 LYS SC2 150 1.0000 ; C
151 P5 61 VAL BB 151 0.0000 ; C
152 C2 61 VAL SC1 152 0.0000 ; C
153 Nda 62 GLN BB 153 0.0000 ; E
154 P4 62 GLN SC1 154 0.0000 ; E
155 Nda 63 ILE BB 155 0.0000 ; E
156 C1 63 ILE SC1 156 0.0000 ; E
157 Nda 64 VAL BB 157 0.0000 ; E
158 C2 64 VAL SC1 158 0.0000 ; E
159 Nda 65 TYR BB 159 0.0000 ; E
160 SC4 65 TYR SC1 160 0.0000 ; E
161 SC4 65 TYR SC2 161 0.0000 ; E
162 SP1 65 TYR SC3 162 0.0000 ; E
163 P5 66 LYS BB 163 0.0000 ; C
164 C3 66 LYS SC1 164 0.0000 ; C
165 Qd 66 LYS SC2 165 1.0000 ; C
166 P5 67 VAL BB 166 0.0000 ; C
167 C2 67 VAL SC1 167 0.0000 ; C
168 Nda 68 GLN BB 168 0.0000 ; E
169 P4 68 GLN SC1 169 0.0000 ; E
170 Nda 69 ILE BB 170 0.0000 ; E
171 C1 69 ILE SC1 171 0.0000 ; E
172 Nda 70 VAL BB 172 0.0000 ; E
173 C2 70 VAL SC1 173 0.0000 ; E
174 Nda 71 TYR BB 174 0.0000 ; E
175 SC4 71 TYR SC1 175 0.0000 ; E
176 SC4 71 TYR SC2 176 0.0000 ; E
177 SP1 71 TYR SC3 177 0.0000 ; E
178 P5 72 LYS BB 178 0.0000 ; C
179 C3 72 LYS SC1 179 0.0000 ; C
180 Qd 72 LYS SC2 180 1.0000 ; C
181 P5 73 VAL BB 181 0.0000 ; C
182 C2 73 VAL SC1 182 0.0000 ; C
183 Nda 74 GLN BB 183 0.0000 ; E
184 P4 74 GLN SC1 184 0.0000 ; E
185 Nda 75 ILE BB 185 0.0000 ; E
186 C1 75 ILE SC1 186 0.0000 ; E
187 Nda 76 VAL BB 187 0.0000 ; E
188 C2 76 VAL SC1 188 0.0000 ; E
189 Nda 77 TYR BB 189 0.0000 ; E
190 SC4 77 TYR SC1 190 0.0000 ; E
191 SC4 77 TYR SC2 191 0.0000 ; E
192 SP1 77 TYR SC3 192 0.0000 ; E
193 P5 78 LYS BB 193 0.0000 ; C
194 C3 78 LYS SC1 194 0.0000 ; C
195 Qd 78 LYS SC2 195 1.0000 ; C
196 P5 79 VAL BB 196 0.0000 ; C
197 C2 79 VAL SC1 197 0.0000 ; C
198 Nda 80 GLN BB 198 0.0000 ; E
199 P4 80 GLN SC1 199 0.0000 ; E
200 Nda 81 ILE BB 200 0.0000 ; E
201 C1 81 ILE SC1 201 0.0000 ; E
202 Nda 82 VAL BB 202 0.0000 ; E
203 C2 82 VAL SC1 203 0.0000 ; E
204 Nda 83 TYR BB 204 0.0000 ; E
205 SC4 83 TYR SC1 205 0.0000 ; E
206 SC4 83 TYR SC2 206 0.0000 ; E
207 SP1 83 TYR SC3 207 0.0000 ; E
208 P5 84 LYS BB 208 0.0000 ; C
209 C3 84 LYS SC1 209 0.0000 ; C
210 Qd 84 LYS SC2 210 1.0000 ; C
211 P5 85 VAL BB 211 0.0000 ; C
212 C2 85 VAL SC1 212 0.0000 ; C
213 Nda 86 GLN BB 213 0.0000 ; E
214 P4 86 GLN SC1 214 0.0000 ; E
215 Nda 87 ILE BB 215 0.0000 ; E
216 C1 87 ILE SC1 216 0.0000 ; E
217 Nda 88 VAL BB 217 0.0000 ; E
218 C2 88 VAL SC1 218 0.0000 ; E
219 Nda 89 TYR BB 219 0.0000 ; E
220 SC4 89 TYR SC1 220 0.0000 ; E
221 SC4 89 TYR SC2 221 0.0000 ; E
222 SP1 89 TYR SC3 222 0.0000 ; E
223 P5 90 LYS BB 223 0.0000 ; C
224 C3 90 LYS SC1 224 0.0000 ; C
225 Qd 90 LYS SC2 225 1.0000 ; C
226 P5 91 VAL BB 226 0.0000 ; C
227 C2 91 VAL SC1 227 0.0000 ; C
228 Nda 92 GLN BB 228 0.0000 ; E
229 P4 92 GLN SC1 229 0.0000 ; E
230 Nda 93 ILE BB 230 0.0000 ; E
231 C1 93 ILE SC1 231 0.0000 ; E
232 Nda 94 VAL BB 232 0.0000 ; E
233 C2 94 VAL SC1 233 0.0000 ; E
234 Nda 95 TYR BB 234 0.0000 ; E
235 SC4 95 TYR SC1 235 0.0000 ; E
236 SC4 95 TYR SC2 236 0.0000 ; E
237 SP1 95 TYR SC3 237 0.0000 ; E
238 P5 96 LYS BB 238 0.0000 ; C
239 C3 96 LYS SC1 239 0.0000 ; C
240 Qd 96 LYS SC2 240 1.0000 ; C
241 P5 97 VAL BB 241 0.0000 ; C
242 C2 97 VAL SC1 242 0.0000 ; C
243 Nda 98 GLN BB 243 0.0000 ; E
244 P4 98 GLN SC1 244 0.0000 ; E
245 Nda 99 ILE BB 245 0.0000 ; E
246 C1 99 ILE SC1 246 0.0000 ; E
247 Nda 100 VAL BB 247 0.0000 ; E
248 C2 100 VAL SC1 248 0.0000 ; E
249 Nda 101 TYR BB 249 0.0000 ; E
250 SC4 101 TYR SC1 250 0.0000 ; E
251 SC4 101 TYR SC2 251 0.0000 ; E
252 SP1 101 TYR SC3 252 0.0000 ; E
253 P5 102 LYS BB 253 0.0000 ; C
254 C3 102 LYS SC1 254 0.0000 ; C
255 Qd 102 LYS SC2 255 1.0000 ; C
256 P5 103 VAL BB 256 0.0000 ; C
257 C2 103 VAL SC1 257 0.0000 ; C
258 Nda 104 GLN BB 258 0.0000 ; E
259 P4 104 GLN SC1 259 0.0000 ; E
260 Nda 105 ILE BB 260 0.0000 ; E
261 C1 105 ILE SC1 261 0.0000 ; E
262 Nda 106 VAL BB 262 0.0000 ; E
263 C2 106 VAL SC1 263 0.0000 ; E
264 Nda 107 TYR BB 264 0.0000 ; E
265 SC4 107 TYR SC1 265 0.0000 ; E
266 SC4 107 TYR SC2 266 0.0000 ; E
267 SP1 107 TYR SC3 267 0.0000 ; E
268 P5 108 LYS BB 268 0.0000 ; C
269 C3 108 LYS SC1 269 0.0000 ; C
270 Qd 108 LYS SC2 270 1.0000 ; C
271 P5 109 VAL BB 271 0.0000 ; C
272 C2 109 VAL SC1 272 0.0000 ; C
273 Nda 110 GLN BB 273 0.0000 ; E
274 P4 110 GLN SC1 274 0.0000 ; E
275 Nda 111 ILE BB 275 0.0000 ; E
276 C1 111 ILE SC1 276 0.0000 ; E
277 Nda 112 VAL BB 277 0.0000 ; E
278 C2 112 VAL SC1 278 0.0000 ; E
279 Nda 113 TYR BB 279 0.0000 ; E
280 SC4 113 TYR SC1 280 0.0000 ; E
281 SC4 113 TYR SC2 281 0.0000 ; E
282 SP1 113 TYR SC3 282 0.0000 ; E
283 P5 114 LYS BB 283 0.0000 ; C
284 C3 114 LYS SC1 284 0.0000 ; C
285 Qd 114 LYS SC2 285 1.0000 ; C
286 P5 115 VAL BB 286 0.0000 ; C
287 C2 115 VAL SC1 287 0.0000 ; C
288 Nda 116 GLN BB 288 0.0000 ; E
289 P4 116 GLN SC1 289 0.0000 ; E
290 Nda 117 ILE BB 290 0.0000 ; E
291 C1 117 ILE SC1 291 0.0000 ; E
292 Nda 118 VAL BB 292 0.0000 ; E
293 C2 118 VAL SC1 293 0.0000 ; E
294 Nda 119 TYR BB 294 0.0000 ; E
295 SC4 119 TYR SC1 295 0.0000 ; E
296 SC4 119 TYR SC2 296 0.0000 ; E
297 SP1 119 TYR SC3 297 0.0000 ; E
298 P5 120 LYS BB 298 0.0000 ; C
299 C3 120 LYS SC1 299 0.0000 ; C
300 Qd 120 LYS SC2 300 1.0000 ; C
301 P5 121 VAL BB 301 0.0000 ; C
302 C2 121 VAL SC1 302 0.0000 ; C
303 Nda 122 GLN BB 303 0.0000 ; E
304 P4 122 GLN SC1 304 0.0000 ; E
305 Nda 123 ILE BB 305 0.0000 ; E
306 C1 123 ILE SC1 306 0.0000 ; E
307 Nda 124 VAL BB 307 0.0000 ; E
308 C2 124 VAL SC1 308 0.0000 ; E
309 Nda 125 TYR BB 309 0.0000 ; E
310 SC4 125 TYR SC1 310 0.0000 ; E
311 SC4 125 TYR SC2 311 0.0000 ; E
312 SP1 125 TYR SC3 312 0.0000 ; E
313 P5 126 LYS BB 313 0.0000 ; C
314 C3 126 LYS SC1 314 0.0000 ; C
315 Qd 126 LYS SC2 315 1.0000 ; C
316 P5 127 VAL BB 316 0.0000 ; C
317 C2 127 VAL SC1 317 0.0000 ; C
318 Nda 128 GLN BB 318 0.0000 ; E
319 P4 128 GLN SC1 319 0.0000 ; E
320 Nda 129 ILE BB 320 0.0000 ; E
321 C1 129 ILE SC1 321 0.0000 ; E
322 Nda 130 VAL BB 322 0.0000 ; E
323 C2 130 VAL SC1 323 0.0000 ; E
324 Nda 131 TYR BB 324 0.0000 ; E
325 SC4 131 TYR SC1 325 0.0000 ; E
326 SC4 131 TYR SC2 326 0.0000 ; E
327 SP1 131 TYR SC3 327 0.0000 ; E
328 P5 132 LYS BB 328 0.0000 ; C
329 C3 132 LYS SC1 329 0.0000 ; C
330 Qd 132 LYS SC2 330 1.0000 ; C
331 P5 133 VAL BB 331 0.0000 ; C
332 C2 133 VAL SC1 332 0.0000 ; C
333 Nda 134 GLN BB 333 0.0000 ; E
334 P4 134 GLN SC1 334 0.0000 ; E
335 Nda 135 ILE BB 335 0.0000 ; E
336 C1 135 ILE SC1 336 0.0000 ; E
337 Nda 136 VAL BB 337 0.0000 ; E
338 C2 136 VAL SC1 338 0.0000 ; E
339 Nda 137 TYR BB 339 0.0000 ; E
340 SC4 137 TYR SC1 340 0.0000 ; E
341 SC4 137 TYR SC2 341 0.0000 ; E
342 SP1 137 TYR SC3 342 0.0000 ; E
343 P5 138 LYS BB 343 0.0000 ; C
344 C3 138 LYS SC1 344 0.0000 ; C
345 Qd 138 LYS SC2 345 1.0000 ; C
346 P5 139 VAL BB 346 0.0000 ; C
347 C2 139 VAL SC1 347 0.0000 ; C
348 Nda 140 GLN BB 348 0.0000 ; E
349 P4 140 GLN SC1 349 0.0000 ; E
350 Nda 141 ILE BB 350 0.0000 ; E
351 C1 141 ILE SC1 351 0.0000 ; E
352 Nda 142 VAL BB 352 0.0000 ; E
353 C2 142 VAL SC1 353 0.0000 ; E
354 Nda 143 TYR BB 354 0.0000 ; E
355 SC4 143 TYR SC1 355 0.0000 ; E
356 SC4 143 TYR SC2 356 0.0000 ; E
357 SP1 143 TYR SC3 357 0.0000 ; E
358 P5 144 LYS BB 358 0.0000 ; C
359 C3 144 LYS SC1 359 0.0000 ; C
360 Qd 144 LYS SC2 360 1.0000 ; C

[ bonds ]
; Backbone bonds
1 3 1 0.37973 150000 ; VAL(C)-GLN(E)
3 5 1 0.37876 150000 ; GLN(E)-ILE(E)
5 7 1 0.37617 150000 ; ILE(E)-VAL(E)
7 9 1 0.38160 150000 ; VAL(E)-TYR(E)
9 13 1 0.37018 150000 ; TYR(E)-LYS(C)
13 16 1 1.51639 150000 ; LYS(C)-VAL(C)
16 18 1 0.38657 150000 ; VAL(C)-GLN(E)
18 20 1 0.38550 150000 ; GLN(E)-ILE(E)
20 22 1 0.37917 150000 ; ILE(E)-VAL(E)
22 24 1 0.37747 150000 ; VAL(E)-TYR(E)
24 28 1 0.37648 150000 ; TYR(E)-LYS(C)
28 31 1 0.99049 150000 ; LYS(C)-VAL(C)
31 33 1 0.37375 150000 ; VAL(C)-GLN(E)
33 35 1 0.38678 150000 ; GLN(E)-ILE(E)
35 37 1 0.37287 150000 ; ILE(E)-VAL(E)
37 39 1 0.38162 150000 ; VAL(E)-TYR(E)
39 43 1 0.38313 150000 ; TYR(E)-LYS(C)
43 46 1 1.42472 150000 ; LYS(C)-VAL(C)
46 48 1 0.38298 150000 ; VAL(C)-GLN(E)
48 50 1 0.38052 150000 ; GLN(E)-ILE(E)
50 52 1 0.37854 150000 ; ILE(E)-VAL(E)
52 54 1 0.38584 150000 ; VAL(E)-TYR(E)
54 58 1 0.38738 150000 ; TYR(E)-LYS(C)
58 61 1 1.07864 150000 ; LYS(C)-VAL(C)
61 63 1 0.37675 150000 ; VAL(C)-GLN(E)
63 65 1 0.38189 150000 ; GLN(E)-ILE(E)
65 67 1 0.38540 150000 ; ILE(E)-VAL(E)
67 69 1 0.38935 150000 ; VAL(E)-TYR(E)
69 73 1 0.37141 150000 ; TYR(E)-LYS(C)
73 76 1 1.43342 150000 ; LYS(C)-VAL(C)
76 78 1 0.38052 150000 ; VAL(C)-GLN(E)
78 80 1 0.38303 150000 ; GLN(E)-ILE(E)
80 82 1 0.38322 150000 ; ILE(E)-VAL(E)
82 84 1 0.38317 150000 ; VAL(E)-TYR(E)
84 88 1 0.37913 150000 ; TYR(E)-LYS(C)
88 91 1 1.09431 150000 ; LYS(C)-VAL(C)
91 93 1 0.37590 150000 ; VAL(C)-GLN(E)
93 95 1 0.38026 150000 ; GLN(E)-ILE(E)
95 97 1 0.38767 150000 ; ILE(E)-VAL(E)
97 99 1 0.37391 150000 ; VAL(E)-TYR(E)
99 103 1 0.38083 150000 ; TYR(E)-LYS(C)
103 106 1 1.40658 150000 ; LYS(C)-VAL(C)
106 108 1 0.37702 150000 ; VAL(C)-GLN(E)
108 110 1 0.38388 150000 ; GLN(E)-ILE(E)
110 112 1 0.38010 150000 ; ILE(E)-VAL(E)
112 114 1 0.38226 150000 ; VAL(E)-TYR(E)
114 118 1 0.38519 150000 ; TYR(E)-LYS(C)
118 121 1 1.13499 150000 ; LYS(C)-VAL(C)
121 123 1 0.37933 150000 ; VAL(C)-GLN(E)
123 125 1 0.38650 150000 ; GLN(E)-ILE(E)
125 127 1 0.38135 150000 ; ILE(E)-VAL(E)
127 129 1 0.37869 150000 ; VAL(E)-TYR(E)
129 133 1 0.37950 150000 ; TYR(E)-LYS(C)
133 136 1 1.45903 150000 ; LYS(C)-VAL(C)
136 138 1 0.37936 150000 ; VAL(C)-GLN(E)
138 140 1 0.37969 150000 ; GLN(E)-ILE(E)
140 142 1 0.37758 150000 ; ILE(E)-VAL(E)
142 144 1 0.38023 150000 ; VAL(E)-TYR(E)
144 148 1 0.37989 150000 ; TYR(E)-LYS(C)
148 151 1 1.07048 150000 ; LYS(C)-VAL(C)
151 153 1 0.37849 150000 ; VAL(C)-GLN(E)
153 155 1 0.37835 150000 ; GLN(E)-ILE(E)
155 157 1 0.38020 150000 ; ILE(E)-VAL(E)
157 159 1 0.38995 150000 ; VAL(E)-TYR(E)
159 163 1 0.37379 150000 ; TYR(E)-LYS(C)
163 166 1 1.38014 150000 ; LYS(C)-VAL(C)
166 168 1 0.37804 150000 ; VAL(C)-GLN(E)
168 170 1 0.38172 150000 ; GLN(E)-ILE(E)
170 172 1 0.38107 150000 ; ILE(E)-VAL(E)
172 174 1 0.37717 150000 ; VAL(E)-TYR(E)
174 178 1 0.38431 150000 ; TYR(E)-LYS(C)
178 181 1 1.07181 150000 ; LYS(C)-VAL(C)
181 183 1 0.37877 150000 ; VAL(C)-GLN(E)
183 185 1 0.38521 150000 ; GLN(E)-ILE(E)
185 187 1 0.37238 150000 ; ILE(E)-VAL(E)
187 189 1 0.37558 150000 ; VAL(E)-TYR(E)
189 193 1 0.38170 150000 ; TYR(E)-LYS(C)
193 196 1 1.28671 150000 ; LYS(C)-VAL(C)
196 198 1 0.38322 150000 ; VAL(C)-GLN(E)
198 200 1 0.38267 150000 ; GLN(E)-ILE(E)
200 202 1 0.38349 150000 ; ILE(E)-VAL(E)
202 204 1 0.38333 150000 ; VAL(E)-TYR(E)
204 208 1 0.38008 150000 ; TYR(E)-LYS(C)
208 211 1 1.10675 150000 ; LYS(C)-VAL(C)
211 213 1 0.38815 150000 ; VAL(C)-GLN(E)
213 215 1 0.38716 150000 ; GLN(E)-ILE(E)
215 217 1 0.38458 150000 ; ILE(E)-VAL(E)
217 219 1 0.37836 150000 ; VAL(E)-TYR(E)
219 223 1 0.37708 150000 ; TYR(E)-LYS(C)
223 226 1 1.35326 150000 ; LYS(C)-VAL(C)
226 228 1 0.38154 150000 ; VAL(C)-GLN(E)
228 230 1 0.37855 150000 ; GLN(E)-ILE(E)
230 232 1 0.37930 150000 ; ILE(E)-VAL(E)
232 234 1 0.37676 150000 ; VAL(E)-TYR(E)
234 238 1 0.38131 150000 ; TYR(E)-LYS(C)
238 241 1 1.11938 150000 ; LYS(C)-VAL(C)
241 243 1 0.38340 150000 ; VAL(C)-GLN(E)
243 245 1 0.37488 150000 ; GLN(E)-ILE(E)
245 247 1 0.37406 150000 ; ILE(E)-VAL(E)
247 249 1 0.37267 150000 ; VAL(E)-TYR(E)
249 253 1 0.37602 150000 ; TYR(E)-LYS(C)
253 256 1 1.35850 150000 ; LYS(C)-VAL(C)
256 258 1 0.38630 150000 ; VAL(C)-GLN(E)
258 260 1 0.38490 150000 ; GLN(E)-ILE(E)
260 262 1 0.38415 150000 ; ILE(E)-VAL(E)
262 264 1 0.37539 150000 ; VAL(E)-TYR(E)
264 268 1 0.37753 150000 ; TYR(E)-LYS(C)
268 271 1 1.12152 150000 ; LYS(C)-VAL(C)
271 273 1 0.38564 150000 ; VAL(C)-GLN(E)
273 275 1 0.38018 150000 ; GLN(E)-ILE(E)
275 277 1 0.38342 150000 ; ILE(E)-VAL(E)
277 279 1 0.37855 150000 ; VAL(E)-TYR(E)
279 283 1 0.37856 150000 ; TYR(E)-LYS(C)
283 286 1 1.35881 150000 ; LYS(C)-VAL(C)
286 288 1 0.38548 150000 ; VAL(C)-GLN(E)
288 290 1 0.37604 150000 ; GLN(E)-ILE(E)
290 292 1 0.38481 150000 ; ILE(E)-VAL(E)
292 294 1 0.37658 150000 ; VAL(E)-TYR(E)
294 298 1 0.36853 150000 ; TYR(E)-LYS(C)
298 301 1 1.06843 150000 ; LYS(C)-VAL(C)
301 303 1 0.38285 150000 ; VAL(C)-GLN(E)
303 305 1 0.38256 150000 ; GLN(E)-ILE(E)
305 307 1 0.37993 150000 ; ILE(E)-VAL(E)
307 309 1 0.38875 150000 ; VAL(E)-TYR(E)
309 313 1 0.38036 150000 ; TYR(E)-LYS(C)
313 316 1 1.40614 150000 ; LYS(C)-VAL(C)
316 318 1 0.39057 150000 ; VAL(C)-GLN(E)
318 320 1 0.37281 150000 ; GLN(E)-ILE(E)
320 322 1 0.38604 150000 ; ILE(E)-VAL(E)
322 324 1 0.37570 150000 ; VAL(E)-TYR(E)
324 328 1 0.38272 150000 ; TYR(E)-LYS(C)
328 331 1 1.11430 150000 ; LYS(C)-VAL(C)
331 333 1 0.37562 150000 ; VAL(C)-GLN(E)
333 335 1 0.37847 150000 ; GLN(E)-ILE(E)
335 337 1 0.38151 150000 ; ILE(E)-VAL(E)
337 339 1 0.37879 150000 ; VAL(E)-TYR(E)
339 343 1 0.37764 150000 ; TYR(E)-LYS(C)
343 346 1 1.44027 150000 ; LYS(C)-VAL(C)
346 348 1 0.38077 150000 ; VAL(C)-GLN(E)
348 350 1 0.38349 150000 ; GLN(E)-ILE(E)
350 352 1 0.38490 150000 ; ILE(E)-VAL(E)
352 354 1 0.37769 150000 ; VAL(E)-TYR(E)
354 358 1 0.37908 150000 ; TYR(E)-LYS(C)
#ifndef NO_RUBBER_BANDS
#ifndef RUBBER_FC
#define RUBBER_FC 1000.000000
#endif
1 31 1 0.48528 RUBBER_FC*1.000000
1 33 1 0.59134 RUBBER_FC*1.000000
1 35 1 0.82909 RUBBER_FC*1.000000
3 31 1 0.62850 RUBBER_FC*1.000000
3 33 1 0.48379 RUBBER_FC*1.000000
3 35 1 0.61765 RUBBER_FC*1.000000
3 37 1 0.70208 RUBBER_FC*1.000000
5 31 1 0.76099 RUBBER_FC*1.000000
5 33 1 0.61540 RUBBER_FC*1.000000
5 35 1 0.49790 RUBBER_FC*1.000000
5 37 1 0.59460 RUBBER_FC*1.000000
5 39 1 0.79526 RUBBER_FC*1.000000
7 33 1 0.82921 RUBBER_FC*1.000000
7 35 1 0.61007 RUBBER_FC*1.000000
7 37 1 0.46647 RUBBER_FC*1.000000
7 39 1 0.59761 RUBBER_FC*1.000000
7 43 1 0.76125 RUBBER_FC*1.000000
9 35 1 0.70215 RUBBER_FC*1.000000
9 37 1 0.60932 RUBBER_FC*1.000000
9 39 1 0.47752 RUBBER_FC*1.000000
9 43 1 0.61601 RUBBER_FC*1.000000
9 46 1 0.89373 RUBBER_FC*1.000000
9 76 1 0.82476 RUBBER_FC*1.000000
13 37 1 0.88368 RUBBER_FC*1.000000
13 39 1 0.62085 RUBBER_FC*1.000000
13 43 1 0.55455 RUBBER_FC*1.000000
16 46 1 0.53722 RUBBER_FC*1.000000
16 48 1 0.55532 RUBBER_FC*1.000000
16 50 1 0.81108 RUBBER_FC*1.000000
18 46 1 0.73061 RUBBER_FC*1.000000
18 48 1 0.52875 RUBBER_FC*1.000000
18 50 1 0.65932 RUBBER_FC*1.000000
18 52 1 0.72146 RUBBER_FC*1.000000
20 46 1 0.78780 RUBBER_FC*1.000000
20 48 1 0.61166 RUBBER_FC*1.000000
20 50 1 0.50629 RUBBER_FC*1.000000
20 52 1 0.60092 RUBBER_FC*1.000000
20 54 1 0.83639 RUBBER_FC*1.000000
22 48 1 0.84109 RUBBER_FC*1.000000
22 50 1 0.63572 RUBBER_FC*1.000000
22 52 1 0.49363 RUBBER_FC*1.000000
22 54 1 0.63556 RUBBER_FC*1.000000
22 58 1 0.71980 RUBBER_FC*1.000000
24 50 1 0.69556 RUBBER_FC*1.000000
24 52 1 0.60290 RUBBER_FC*1.000000
24 54 1 0.50617 RUBBER_FC*1.000000
24 58 1 0.61421 RUBBER_FC*1.000000
28 52 1 0.86007 RUBBER_FC*1.000000
28 54 1 0.64004 RUBBER_FC*1.000000
28 58 1 0.52597 RUBBER_FC*1.000000
31 50 1 0.81733 RUBBER_FC*1.000000
31 54 1 0.80461 RUBBER_FC*1.000000
31 61 1 0.49983 RUBBER_FC*1.000000
31 63 1 0.63402 RUBBER_FC*1.000000
31 65 1 0.81919 RUBBER_FC*1.000000
33 61 1 0.59841 RUBBER_FC*1.000000
33 63 1 0.48210 RUBBER_FC*1.000000
33 65 1 0.59537 RUBBER_FC*1.000000
33 67 1 0.72223 RUBBER_FC*1.000000
35 61 1 0.78472 RUBBER_FC*1.000000
35 63 1 0.63509 RUBBER_FC*1.000000
35 65 1 0.48066 RUBBER_FC*1.000000
35 67 1 0.58260 RUBBER_FC*1.000000
35 69 1 0.79474 RUBBER_FC*1.000000
35 76 1 0.86649 RUBBER_FC*1.000000
37 63 1 0.83496 RUBBER_FC*1.000000
37 65 1 0.64207 RUBBER_FC*1.000000
37 67 1 0.48519 RUBBER_FC*1.000000
37 69 1 0.63542 RUBBER_FC*1.000000
37 73 1 0.75432 RUBBER_FC*1.000000
39 65 1 0.73624 RUBBER_FC*1.000000
39 67 1 0.60304 RUBBER_FC*1.000000
39 69 1 0.49965 RUBBER_FC*1.000000
39 73 1 0.61134 RUBBER_FC*1.000000
39 76 1 0.89459 RUBBER_FC*1.000000
39 106 1 0.86120 RUBBER_FC*1.000000
43 67 1 0.84667 RUBBER_FC*1.000000
43 69 1 0.62563 RUBBER_FC*1.000000
43 73 1 0.49708 RUBBER_FC*1.000000
46 76 1 0.48849 RUBBER_FC*1.000000
46 78 1 0.60193 RUBBER_FC*1.000000
46 80 1 0.80336 RUBBER_FC*1.000000
48 76 1 0.60937 RUBBER_FC*1.000000
48 78 1 0.46043 RUBBER_FC*1.000000
48 80 1 0.60276 RUBBER_FC*1.000000
48 82 1 0.73235 RUBBER_FC*1.000000
50 76 1 0.76178 RUBBER_FC*1.000000
50 78 1 0.62173 RUBBER_FC*1.000000
50 80 1 0.49966 RUBBER_FC*1.000000
50 82 1 0.60530 RUBBER_FC*1.000000
50 84 1 0.82154 RUBBER_FC*1.000000
52 78 1 0.80401 RUBBER_FC*1.000000
52 80 1 0.62666 RUBBER_FC*1.000000
52 82 1 0.47152 RUBBER_FC*1.000000
52 84 1 0.62051 RUBBER_FC*1.000000
52 88 1 0.69131 RUBBER_FC*1.000000
54 80 1 0.75197 RUBBER_FC*1.000000
54 82 1 0.59624 RUBBER_FC*1.000000
54 84 1 0.48225 RUBBER_FC*1.000000
54 88 1 0.57852 RUBBER_FC*1.000000
58 82 1 0.85481 RUBBER_FC*1.000000
58 84 1 0.66301 RUBBER_FC*1.000000
58 88 1 0.52045 RUBBER_FC*1.000000
61 80 1 0.87070 RUBBER_FC*1.000000
61 84 1 0.81828 RUBBER_FC*1.000000
61 91 1 0.47188 RUBBER_FC*1.000000
61 93 1 0.61858 RUBBER_FC*1.000000
61 95 1 0.81162 RUBBER_FC*1.000000
63 91 1 0.60534 RUBBER_FC*1.000000
63 93 1 0.50026 RUBBER_FC*1.000000
63 95 1 0.61021 RUBBER_FC*1.000000
63 97 1 0.72890 RUBBER_FC*1.000000
65 91 1 0.73339 RUBBER_FC*1.000000
65 93 1 0.60632 RUBBER_FC*1.000000
65 95 1 0.45433 RUBBER_FC*1.000000
65 97 1 0.57585 RUBBER_FC*1.000000
65 99 1 0.81181 RUBBER_FC*1.000000
67 93 1 0.83497 RUBBER_FC*1.000000
67 95 1 0.63078 RUBBER_FC*1.000000
67 97 1 0.47869 RUBBER_FC*1.000000
67 99 1 0.65015 RUBBER_FC*1.000000
67 103 1 0.76065 RUBBER_FC*1.000000
69 95 1 0.74641 RUBBER_FC*1.000000
69 97 1 0.58102 RUBBER_FC*1.000000
69 99 1 0.49441 RUBBER_FC*1.000000
69 103 1 0.55662 RUBBER_FC*1.000000
69 136 1 0.89302 RUBBER_FC*1.000000
73 97 1 0.84217 RUBBER_FC*1.000000
73 99 1 0.67959 RUBBER_FC*1.000000
73 103 1 0.49716 RUBBER_FC*1.000000
76 106 1 0.49022 RUBBER_FC*1.000000
76 108 1 0.59837 RUBBER_FC*1.000000
76 110 1 0.79486 RUBBER_FC*1.000000
78 106 1 0.62910 RUBBER_FC*1.000000
78 108 1 0.48121 RUBBER_FC*1.000000
78 110 1 0.61769 RUBBER_FC*1.000000
78 112 1 0.75887 RUBBER_FC*1.000000
80 106 1 0.72599 RUBBER_FC*1.000000
80 108 1 0.59211 RUBBER_FC*1.000000
80 110 1 0.46182 RUBBER_FC*1.000000
80 112 1 0.60841 RUBBER_FC*1.000000
80 114 1 0.84102 RUBBER_FC*1.000000
82 108 1 0.80223 RUBBER_FC*1.000000
82 110 1 0.60340 RUBBER_FC*1.000000
82 112 1 0.48365 RUBBER_FC*1.000000
82 114 1 0.63803 RUBBER_FC*1.000000
82 118 1 0.73486 RUBBER_FC*1.000000
84 110 1 0.75105 RUBBER_FC*1.000000
84 112 1 0.60375 RUBBER_FC*1.000000
84 114 1 0.50079 RUBBER_FC*1.000000
84 118 1 0.59845 RUBBER_FC*1.000000
88 112 1 0.82023 RUBBER_FC*1.000000
88 114 1 0.66842 RUBBER_FC*1.000000
88 118 1 0.51447 RUBBER_FC*1.000000
91 110 1 0.85288 RUBBER_FC*1.000000
91 114 1 0.81559 RUBBER_FC*1.000000
91 121 1 0.49243 RUBBER_FC*1.000000
91 123 1 0.61665 RUBBER_FC*1.000000
91 125 1 0.84819 RUBBER_FC*1.000000
93 121 1 0.58860 RUBBER_FC*1.000000
93 123 1 0.44893 RUBBER_FC*1.000000
93 125 1 0.61013 RUBBER_FC*1.000000
93 127 1 0.69988 RUBBER_FC*1.000000
95 121 1 0.78568 RUBBER_FC*1.000000
95 123 1 0.59367 RUBBER_FC*1.000000
95 125 1 0.48950 RUBBER_FC*1.000000
95 127 1 0.59233 RUBBER_FC*1.000000
95 129 1 0.81974 RUBBER_FC*1.000000
97 123 1 0.80890 RUBBER_FC*1.000000
97 125 1 0.62054 RUBBER_FC*1.000000
97 127 1 0.46392 RUBBER_FC*1.000000
97 129 1 0.62044 RUBBER_FC*1.000000
97 133 1 0.74987 RUBBER_FC*1.000000
99 125 1 0.71766 RUBBER_FC*1.000000
99 127 1 0.58216 RUBBER_FC*1.000000
99 129 1 0.48127 RUBBER_FC*1.000000
99 133 1 0.57746 RUBBER_FC*1.000000
99 166 1 0.85216 RUBBER_FC*1.000000
103 127 1 0.85047 RUBBER_FC*1.000000
103 129 1 0.66778 RUBBER_FC*1.000000
103 133 1 0.51469 RUBBER_FC*1.000000
106 136 1 0.45695 RUBBER_FC*1.000000
106 138 1 0.60165 RUBBER_FC*1.000000
106 140 1 0.80536 RUBBER_FC*1.000000
108 136 1 0.63580 RUBBER_FC*1.000000
108 138 1 0.52546 RUBBER_FC*1.000000
108 140 1 0.64676 RUBBER_FC*1.000000
108 142 1 0.77160 RUBBER_FC*1.000000
110 136 1 0.77001 RUBBER_FC*1.000000
110 138 1 0.61973 RUBBER_FC*1.000000
110 140 1 0.49638 RUBBER_FC*1.000000
110 142 1 0.61350 RUBBER_FC*1.000000
110 144 1 0.84162 RUBBER_FC*1.000000
112 138 1 0.84007 RUBBER_FC*1.000000
112 140 1 0.63228 RUBBER_FC*1.000000
112 142 1 0.49724 RUBBER_FC*1.000000
112 144 1 0.67479 RUBBER_FC*1.000000
112 148 1 0.75764 RUBBER_FC*1.000000
114 140 1 0.76725 RUBBER_FC*1.000000
114 142 1 0.59971 RUBBER_FC*1.000000
114 144 1 0.52724 RUBBER_FC*1.000000
114 148 1 0.58399 RUBBER_FC*1.000000
118 142 1 0.84639 RUBBER_FC*1.000000
118 144 1 0.74981 RUBBER_FC*1.000000
118 148 1 0.58039 RUBBER_FC*1.000000
121 144 1 0.81148 RUBBER_FC*1.000000
121 151 1 0.52253 RUBBER_FC*1.000000
121 153 1 0.61535 RUBBER_FC*1.000000
121 155 1 0.86674 RUBBER_FC*1.000000
123 151 1 0.59413 RUBBER_FC*1.000000
123 153 1 0.46573 RUBBER_FC*1.000000
123 155 1 0.60179 RUBBER_FC*1.000000
123 157 1 0.77740 RUBBER_FC*1.000000
125 151 1 0.72314 RUBBER_FC*1.000000
125 153 1 0.59521 RUBBER_FC*1.000000
125 155 1 0.46387 RUBBER_FC*1.000000
125 157 1 0.62978 RUBBER_FC*1.000000
125 159 1 0.81129 RUBBER_FC*1.000000
125 166 1 0.88828 RUBBER_FC*1.000000
125 196 1 0.89122 RUBBER_FC*1.000000
127 153 1 0.80255 RUBBER_FC*1.000000
127 155 1 0.61062 RUBBER_FC*1.000000
127 157 1 0.51700 RUBBER_FC*1.000000
127 159 1 0.68203 RUBBER_FC*1.000000
127 163 1 0.78879 RUBBER_FC*1.000000
129 155 1 0.71346 RUBBER_FC*1.000000
129 157 1 0.58259 RUBBER_FC*1.000000
129 159 1 0.49264 RUBBER_FC*1.000000
129 163 1 0.56641 RUBBER_FC*1.000000
129 196 1 0.82256 RUBBER_FC*1.000000
133 157 1 0.83277 RUBBER_FC*1.000000
133 159 1 0.68140 RUBBER_FC*1.000000
133 163 1 0.51426 RUBBER_FC*1.000000
136 166 1 0.55286 RUBBER_FC*1.000000
136 168 1 0.62710 RUBBER_FC*1.000000
136 170 1 0.86493 RUBBER_FC*1.000000
138 166 1 0.64384 RUBBER_FC*1.000000
138 168 1 0.48060 RUBBER_FC*1.000000
138 170 1 0.61915 RUBBER_FC*1.000000
138 172 1 0.74403 RUBBER_FC*1.000000
140 166 1 0.78693 RUBBER_FC*1.000000
140 168 1 0.60460 RUBBER_FC*1.000000
140 170 1 0.48564 RUBBER_FC*1.000000
140 172 1 0.59510 RUBBER_FC*1.000000
140 174 1 0.83462 RUBBER_FC*1.000000
142 168 1 0.84250 RUBBER_FC*1.000000
142 170 1 0.63320 RUBBER_FC*1.000000
142 172 1 0.49138 RUBBER_FC*1.000000
142 174 1 0.66717 RUBBER_FC*1.000000
142 178 1 0.75966 RUBBER_FC*1.000000
144 170 1 0.71841 RUBBER_FC*1.000000
144 172 1 0.59315 RUBBER_FC*1.000000
144 174 1 0.52766 RUBBER_FC*1.000000
144 178 1 0.59461 RUBBER_FC*1.000000
148 172 1 0.80234 RUBBER_FC*1.000000
148 174 1 0.67783 RUBBER_FC*1.000000
148 178 1 0.49376 RUBBER_FC*1.000000
151 170 1 0.85206 RUBBER_FC*1.000000
151 174 1 0.84173 RUBBER_FC*1.000000
151 181 1 0.47854 RUBBER_FC*1.000000
151 183 1 0.58575 RUBBER_FC*1.000000
151 185 1 0.80799 RUBBER_FC*1.000000
153 181 1 0.64429 RUBBER_FC*1.000000
153 183 1 0.49764 RUBBER_FC*1.000000
153 185 1 0.61989 RUBBER_FC*1.000000
153 187 1 0.78283 RUBBER_FC*1.000000
155 181 1 0.76646 RUBBER_FC*1.000000
155 183 1 0.60900 RUBBER_FC*1.000000
155 185 1 0.47797 RUBBER_FC*1.000000
155 187 1 0.60483 RUBBER_FC*1.000000
155 189 1 0.80383 RUBBER_FC*1.000000
155 196 1 0.86175 RUBBER_FC*1.000000
157 183 1 0.84710 RUBBER_FC*1.000000
157 185 1 0.61503 RUBBER_FC*1.000000
157 187 1 0.48409 RUBBER_FC*1.000000
157 189 1 0.65342 RUBBER_FC*1.000000
157 193 1 0.82152 RUBBER_FC*1.000000
159 185 1 0.71979 RUBBER_FC*1.000000
159 187 1 0.58926 RUBBER_FC*1.000000
159 189 1 0.49896 RUBBER_FC*1.000000
159 193 1 0.59573 RUBBER_FC*1.000000
159 196 1 0.82936 RUBBER_FC*1.000000
159 226 1 0.84673 RUBBER_FC*1.000000
163 187 1 0.82111 RUBBER_FC*1.000000
163 189 1 0.68828 RUBBER_FC*1.000000
163 193 1 0.54974 RUBBER_FC*1.000000
166 196 1 0.46716 RUBBER_FC*1.000000
166 198 1 0.56467 RUBBER_FC*1.000000
166 200 1 0.82225 RUBBER_FC*1.000000
168 196 1 0.64365 RUBBER_FC*1.000000
168 198 1 0.49052 RUBBER_FC*1.000000
168 200 1 0.62664 RUBBER_FC*1.000000
168 202 1 0.76508 RUBBER_FC*1.000000
170 196 1 0.76020 RUBBER_FC*1.000000
170 198 1 0.59163 RUBBER_FC*1.000000
170 200 1 0.47314 RUBBER_FC*1.000000
170 202 1 0.61096 RUBBER_FC*1.000000
170 204 1 0.82164 RUBBER_FC*1.000000
172 198 1 0.85272 RUBBER_FC*1.000000
172 200 1 0.64045 RUBBER_FC*1.000000
172 202 1 0.52913 RUBBER_FC*1.000000
172 204 1 0.67123 RUBBER_FC*1.000000
172 208 1 0.76777 RUBBER_FC*1.000000
174 200 1 0.70425 RUBBER_FC*1.000000
174 202 1 0.59032 RUBBER_FC*1.000000
174 204 1 0.48689 RUBBER_FC*1.000000
174 208 1 0.58425 RUBBER_FC*1.000000
178 202 1 0.88007 RUBBER_FC*1.000000
178 204 1 0.70156 RUBBER_FC*1.000000
178 208 1 0.57040 RUBBER_FC*1.000000
181 200 1 0.83645 RUBBER_FC*1.000000
181 204 1 0.84379 RUBBER_FC*1.000000
181 211 1 0.48328 RUBBER_FC*1.000000
181 213 1 0.61913 RUBBER_FC*1.000000
181 215 1 0.84051 RUBBER_FC*1.000000
183 211 1 0.63670 RUBBER_FC*1.000000
183 213 1 0.51204 RUBBER_FC*1.000000
183 215 1 0.65877 RUBBER_FC*1.000000
183 217 1 0.77704 RUBBER_FC*1.000000
185 211 1 0.79496 RUBBER_FC*1.000000
185 213 1 0.60324 RUBBER_FC*1.000000
185 215 1 0.48879 RUBBER_FC*1.000000
185 217 1 0.57778 RUBBER_FC*1.000000
185 219 1 0.79978 RUBBER_FC*1.000000
185 226 1 0.89779 RUBBER_FC*1.000000
187 213 1 0.85788 RUBBER_FC*1.000000
187 215 1 0.64960 RUBBER_FC*1.000000
187 217 1 0.49999 RUBBER_FC*1.000000
187 219 1 0.65311 RUBBER_FC*1.000000
187 223 1 0.71873 RUBBER_FC*1.000000
189 215 1 0.68551 RUBBER_FC*1.000000
189 217 1 0.58204 RUBBER_FC*1.000000
189 219 1 0.49162 RUBBER_FC*1.000000
189 223 1 0.56803 RUBBER_FC*1.000000
189 226 1 0.86190 RUBBER_FC*1.000000
189 256 1 0.87831 RUBBER_FC*1.000000
193 217 1 0.86382 RUBBER_FC*1.000000
193 219 1 0.65638 RUBBER_FC*1.000000
193 223 1 0.51834 RUBBER_FC*1.000000
196 226 1 0.49465 RUBBER_FC*1.000000
196 228 1 0.63323 RUBBER_FC*1.000000
196 230 1 0.83628 RUBBER_FC*1.000000
198 226 1 0.58512 RUBBER_FC*1.000000
198 228 1 0.47018 RUBBER_FC*1.000000
198 230 1 0.59094 RUBBER_FC*1.000000
198 232 1 0.78092 RUBBER_FC*1.000000
200 226 1 0.73696 RUBBER_FC*1.000000
200 228 1 0.60938 RUBBER_FC*1.000000
200 230 1 0.46127 RUBBER_FC*1.000000
200 232 1 0.60878 RUBBER_FC*1.000000
200 234 1 0.82980 RUBBER_FC*1.000000
202 228 1 0.81829 RUBBER_FC*1.000000
202 230 1 0.58906 RUBBER_FC*1.000000
202 232 1 0.46397 RUBBER_FC*1.000000
202 234 1 0.64371 RUBBER_FC*1.000000
202 238 1 0.75349 RUBBER_FC*1.000000
204 230 1 0.71764 RUBBER_FC*1.000000
204 232 1 0.58421 RUBBER_FC*1.000000
204 234 1 0.50805 RUBBER_FC*1.000000
204 238 1 0.58364 RUBBER_FC*1.000000
208 232 1 0.82185 RUBBER_FC*1.000000
208 234 1 0.67979 RUBBER_FC*1.000000
208 238 1 0.50588 RUBBER_FC*1.000000
211 230 1 0.87957 RUBBER_FC*1.000000
211 234 1 0.87427 RUBBER_FC*1.000000
211 241 1 0.47950 RUBBER_FC*1.000000
211 243 1 0.60651 RUBBER_FC*1.000000
211 245 1 0.83461 RUBBER_FC*1.000000
213 241 1 0.61275 RUBBER_FC*1.000000
213 243 1 0.46901 RUBBER_FC*1.000000
213 245 1 0.58579 RUBBER_FC*1.000000
213 247 1 0.76661 RUBBER_FC*1.000000
215 241 1 0.79378 RUBBER_FC*1.000000
215 243 1 0.61239 RUBBER_FC*1.000000
215 245 1 0.46803 RUBBER_FC*1.000000
215 247 1 0.60936 RUBBER_FC*1.000000
215 249 1 0.82311 RUBBER_FC*1.000000
215 256 1 0.88162 RUBBER_FC*1.000000
217 243 1 0.83779 RUBBER_FC*1.000000
217 245 1 0.61478 RUBBER_FC*1.000000
217 247 1 0.49313 RUBBER_FC*1.000000
217 249 1 0.67525 RUBBER_FC*1.000000
217 253 1 0.85791 RUBBER_FC*1.000000
219 245 1 0.70398 RUBBER_FC*1.000000
219 247 1 0.57055 RUBBER_FC*1.000000
219 249 1 0.51240 RUBBER_FC*1.000000
219 253 1 0.62842 RUBBER_FC*1.000000
219 286 1 0.89261 RUBBER_FC*1.000000
223 247 1 0.82259 RUBBER_FC*1.000000
223 249 1 0.69781 RUBBER_FC*1.000000
223 253 1 0.58931 RUBBER_FC*1.000000
226 256 1 0.50669 RUBBER_FC*1.000000
226 258 1 0.59926 RUBBER_FC*1.000000
226 260 1 0.77795 RUBBER_FC*1.000000
228 256 1 0.65174 RUBBER_FC*1.000000
228 258 1 0.48306 RUBBER_FC*1.000000
228 260 1 0.59520 RUBBER_FC*1.000000
228 262 1 0.75418 RUBBER_FC*1.000000
230 256 1 0.80752 RUBBER_FC*1.000000
230 258 1 0.62199 RUBBER_FC*1.000000
230 260 1 0.46800 RUBBER_FC*1.000000
230 262 1 0.60397 RUBBER_FC*1.000000
230 264 1 0.80295 RUBBER_FC*1.000000
232 258 1 0.85537 RUBBER_FC*1.000000
232 260 1 0.62459 RUBBER_FC*1.000000
232 262 1 0.50533 RUBBER_FC*1.000000
232 264 1 0.63206 RUBBER_FC*1.000000
232 268 1 0.72267 RUBBER_FC*1.000000
234 260 1 0.72543 RUBBER_FC*1.000000
234 262 1 0.60217 RUBBER_FC*1.000000
234 264 1 0.47782 RUBBER_FC*1.000000
234 268 1 0.53836 RUBBER_FC*1.000000
238 262 1 0.87785 RUBBER_FC*1.000000
238 264 1 0.69559 RUBBER_FC*1.000000
238 268 1 0.51310 RUBBER_FC*1.000000
241 260 1 0.88686 RUBBER_FC*1.000000
241 264 1 0.88439 RUBBER_FC*1.000000
241 271 1 0.49242 RUBBER_FC*1.000000
241 273 1 0.60201 RUBBER_FC*1.000000
241 275 1 0.83228 RUBBER_FC*1.000000
243 271 1 0.63157 RUBBER_FC*1.000000
243 273 1 0.48195 RUBBER_FC*1.000000
243 275 1 0.59687 RUBBER_FC*1.000000
243 277 1 0.75315 RUBBER_FC*1.000000
245 271 1 0.80295 RUBBER_FC*1.000000
245 273 1 0.61154 RUBBER_FC*1.000000
245 275 1 0.46612 RUBBER_FC*1.000000
245 277 1 0.58496 RUBBER_FC*1.000000
245 279 1 0.79022 RUBBER_FC*1.000000
247 273 1 0.85813 RUBBER_FC*1.000000
247 275 1 0.61686 RUBBER_FC*1.000000
247 277 1 0.48086 RUBBER_FC*1.000000
247 279 1 0.63172 RUBBER_FC*1.000000
247 283 1 0.82942 RUBBER_FC*1.000000
249 275 1 0.71283 RUBBER_FC*1.000000
249 277 1 0.58702 RUBBER_FC*1.000000
249 279 1 0.48093 RUBBER_FC*1.000000
249 283 1 0.60866 RUBBER_FC*1.000000
249 316 1 0.89466 RUBBER_FC*1.000000
253 277 1 0.87582 RUBBER_FC*1.000000
253 279 1 0.66907 RUBBER_FC*1.000000
253 283 1 0.56047 RUBBER_FC*1.000000
256 286 1 0.48775 RUBBER_FC*1.000000
256 288 1 0.59423 RUBBER_FC*1.000000
256 290 1 0.79961 RUBBER_FC*1.000000
258 286 1 0.65822 RUBBER_FC*1.000000
258 288 1 0.50486 RUBBER_FC*1.000000
258 290 1 0.60837 RUBBER_FC*1.000000
258 292 1 0.73499 RUBBER_FC*1.000000
260 286 1 0.79562 RUBBER_FC*1.000000
260 288 1 0.62186 RUBBER_FC*1.000000
260 290 1 0.47101 RUBBER_FC*1.000000
260 292 1 0.59303 RUBBER_FC*1.000000
260 294 1 0.79134 RUBBER_FC*1.000000
262 288 1 0.83098 RUBBER_FC*1.000000
262 290 1 0.59964 RUBBER_FC*1.000000
262 292 1 0.45014 RUBBER_FC*1.000000
262 294 1 0.61162 RUBBER_FC*1.000000
262 298 1 0.78538 RUBBER_FC*1.000000
264 290 1 0.69855 RUBBER_FC*1.000000
264 292 1 0.57292 RUBBER_FC*1.000000
264 294 1 0.46790 RUBBER_FC*1.000000
264 298 1 0.58104 RUBBER_FC*1.000000
268 292 1 0.83677 RUBBER_FC*1.000000
268 294 1 0.67880 RUBBER_FC*1.000000
268 298 1 0.55598 RUBBER_FC*1.000000
271 290 1 0.84482 RUBBER_FC*1.000000
271 294 1 0.85164 RUBBER_FC*1.000000
271 301 1 0.47323 RUBBER_FC*1.000000
271 303 1 0.60805 RUBBER_FC*1.000000
271 305 1 0.86490 RUBBER_FC*1.000000
273 301 1 0.61380 RUBBER_FC*1.000000
273 303 1 0.47764 RUBBER_FC*1.000000
273 305 1 0.64947 RUBBER_FC*1.000000
273 307 1 0.76824 RUBBER_FC*1.000000
275 301 1 0.78759 RUBBER_FC*1.000000
275 303 1 0.58468 RUBBER_FC*1.000000
275 305 1 0.49796 RUBBER_FC*1.000000
275 307 1 0.59742 RUBBER_FC*1.000000
275 309 1 0.84252 RUBBER_FC*1.000000
275 316 1 0.88783 RUBBER_FC*1.000000
277 303 1 0.82740 RUBBER_FC*1.000000
277 305 1 0.65098 RUBBER_FC*1.000000
277 307 1 0.50200 RUBBER_FC*1.000000
277 309 1 0.67321 RUBBER_FC*1.000000
277 313 1 0.72901 RUBBER_FC*1.000000
279 305 1 0.67354 RUBBER_FC*1.000000
279 307 1 0.56228 RUBBER_FC*1.000000
279 309 1 0.49618 RUBBER_FC*1.000000
279 313 1 0.58755 RUBBER_FC*1.000000
279 316 1 0.88901 RUBBER_FC*1.000000
283 307 1 0.81429 RUBBER_FC*1.000000
283 309 1 0.58248 RUBBER_FC*1.000000
283 313 1 0.47296 RUBBER_FC*1.000000
286 316 1 0.49362 RUBBER_FC*1.000000
286 318 1 0.60667 RUBBER_FC*1.000000
286 320 1 0.81231 RUBBER_FC*1.000000
288 316 1 0.65321 RUBBER_FC*1.000000
288 318 1 0.50593 RUBBER_FC*1.000000
288 320 1 0.61393 RUBBER_FC*1.000000
288 322 1 0.71818 RUBBER_FC*1.000000
290 316 1 0.82750 RUBBER_FC*1.000000
290 318 1 0.65975 RUBBER_FC*1.000000
290 320 1 0.52947 RUBBER_FC*1.000000
290 322 1 0.59763 RUBBER_FC*1.000000
290 324 1 0.78812 RUBBER_FC*1.000000
292 318 1 0.88588 RUBBER_FC*1.000000
292 320 1 0.69439 RUBBER_FC*1.000000
292 322 1 0.51641 RUBBER_FC*1.000000
292 324 1 0.64465 RUBBER_FC*1.000000
292 328 1 0.79084 RUBBER_FC*1.000000
294 320 1 0.74768 RUBBER_FC*1.000000
294 322 1 0.60101 RUBBER_FC*1.000000
294 324 1 0.48929 RUBBER_FC*1.000000
294 328 1 0.59801 RUBBER_FC*1.000000
298 322 1 0.85166 RUBBER_FC*1.000000
298 324 1 0.62725 RUBBER_FC*1.000000
298 328 1 0.48766 RUBBER_FC*1.000000
301 320 1 0.83079 RUBBER_FC*1.000000
301 324 1 0.87404 RUBBER_FC*1.000000
301 331 1 0.49628 RUBBER_FC*1.000000
301 333 1 0.59863 RUBBER_FC*1.000000
301 335 1 0.84048 RUBBER_FC*1.000000
303 331 1 0.62925 RUBBER_FC*1.000000
303 333 1 0.48071 RUBBER_FC*1.000000
303 335 1 0.60906 RUBBER_FC*1.000000
303 337 1 0.75193 RUBBER_FC*1.000000
305 331 1 0.77711 RUBBER_FC*1.000000
305 333 1 0.58799 RUBBER_FC*1.000000
305 335 1 0.45005 RUBBER_FC*1.000000
305 337 1 0.58628 RUBBER_FC*1.000000
305 339 1 0.82639 RUBBER_FC*1.000000
305 346 1 0.80522 RUBBER_FC*1.000000
307 333 1 0.82047 RUBBER_FC*1.000000
307 335 1 0.61702 RUBBER_FC*1.000000
307 337 1 0.48665 RUBBER_FC*1.000000
307 339 1 0.63187 RUBBER_FC*1.000000
307 343 1 0.69980 RUBBER_FC*1.000000
309 335 1 0.72686 RUBBER_FC*1.000000
309 337 1 0.58469 RUBBER_FC*1.000000
309 339 1 0.48093 RUBBER_FC*1.000000
309 343 1 0.56439 RUBBER_FC*1.000000
313 337 1 0.86057 RUBBER_FC*1.000000
313 339 1 0.67188 RUBBER_FC*1.000000
313 343 1 0.51514 RUBBER_FC*1.000000
316 346 1 0.50570 RUBBER_FC*1.000000
316 348 1 0.58180 RUBBER_FC*1.000000
316 350 1 0.81706 RUBBER_FC*1.000000
318 346 1 0.64361 RUBBER_FC*1.000000
318 348 1 0.46220 RUBBER_FC*1.000000
318 350 1 0.60235 RUBBER_FC*1.000000
318 352 1 0.68859 RUBBER_FC*1.000000
320 331 1 0.88075 RUBBER_FC*1.000000
320 346 1 0.78095 RUBBER_FC*1.000000
320 348 1 0.60673 RUBBER_FC*1.000000
320 350 1 0.48771 RUBBER_FC*1.000000
320 352 1 0.54814 RUBBER_FC*1.000000
320 354 1 0.79606 RUBBER_FC*1.000000
322 348 1 0.85682 RUBBER_FC*1.000000
322 350 1 0.67172 RUBBER_FC*1.000000
322 352 1 0.47192 RUBBER_FC*1.000000
322 354 1 0.60819 RUBBER_FC*1.000000
322 358 1 0.67480 RUBBER_FC*1.000000
324 350 1 0.77831 RUBBER_FC*1.000000
324 352 1 0.60744 RUBBER_FC*1.000000
324 354 1 0.51436 RUBBER_FC*1.000000
324 358 1 0.60300 RUBBER_FC*1.000000
328 352 1 0.88891 RUBBER_FC*1.000000
328 354 1 0.66148 RUBBER_FC*1.000000
328 358 1 0.55663 RUBBER_FC*1.000000
331 350 1 0.78317 RUBBER_FC*1.000000
335 346 1 0.87540 RUBBER_FC*1.000000
#endif
; Sidechain bonds
3 4 1 0.30000 2400 ; GLN
5 6 1 0.22500 13250 ; ILE
9 10 1 0.33500 6000 ; TYR
9 11 1 0.33500 6000 ; TYR
13 14 1 0.25000 12500 ; LYS
14 15 1 0.30000 9700 ; LYS
18 19 1 0.30000 2400 ; GLN
20 21 1 0.22500 13250 ; ILE
24 25 1 0.33500 6000 ; TYR
24 26 1 0.33500 6000 ; TYR
28 29 1 0.25000 12500 ; LYS
29 30 1 0.30000 9700 ; LYS
33 34 1 0.30000 2400 ; GLN
35 36 1 0.22500 13250 ; ILE
39 40 1 0.33500 6000 ; TYR
39 41 1 0.33500 6000 ; TYR
43 44 1 0.25000 12500 ; LYS
44 45 1 0.30000 9700 ; LYS
48 49 1 0.30000 2400 ; GLN
50 51 1 0.22500 13250 ; ILE
54 55 1 0.33500 6000 ; TYR
54 56 1 0.33500 6000 ; TYR
58 59 1 0.25000 12500 ; LYS
59 60 1 0.30000 9700 ; LYS
63 64 1 0.30000 2400 ; GLN
65 66 1 0.22500 13250 ; ILE
69 70 1 0.33500 6000 ; TYR
69 71 1 0.33500 6000 ; TYR
73 74 1 0.25000 12500 ; LYS
74 75 1 0.30000 9700 ; LYS
78 79 1 0.30000 2400 ; GLN
80 81 1 0.22500 13250 ; ILE
84 85 1 0.33500 6000 ; TYR
84 86 1 0.33500 6000 ; TYR
88 89 1 0.25000 12500 ; LYS
89 90 1 0.30000 9700 ; LYS
93 94 1 0.30000 2400 ; GLN
95 96 1 0.22500 13250 ; ILE
99 100 1 0.33500 6000 ; TYR
99 101 1 0.33500 6000 ; TYR
103 104 1 0.25000 12500 ; LYS
104 105 1 0.30000 9700 ; LYS
108 109 1 0.30000 2400 ; GLN
110 111 1 0.22500 13250 ; ILE
114 115 1 0.33500 6000 ; TYR
114 116 1 0.33500 6000 ; TYR
118 119 1 0.25000 12500 ; LYS
119 120 1 0.30000 9700 ; LYS
123 124 1 0.30000 2400 ; GLN
125 126 1 0.22500 13250 ; ILE
129 130 1 0.33500 6000 ; TYR
129 131 1 0.33500 6000 ; TYR
133 134 1 0.25000 12500 ; LYS
134 135 1 0.30000 9700 ; LYS
138 139 1 0.30000 2400 ; GLN
140 141 1 0.22500 13250 ; ILE
144 145 1 0.33500 6000 ; TYR
144 146 1 0.33500 6000 ; TYR
148 149 1 0.25000 12500 ; LYS
149 150 1 0.30000 9700 ; LYS
153 154 1 0.30000 2400 ; GLN
155 156 1 0.22500 13250 ; ILE
159 160 1 0.33500 6000 ; TYR
159 161 1 0.33500 6000 ; TYR
163 164 1 0.25000 12500 ; LYS
164 165 1 0.30000 9700 ; LYS
168 169 1 0.30000 2400 ; GLN
170 171 1 0.22500 13250 ; ILE
174 175 1 0.33500 6000 ; TYR
174 176 1 0.33500 6000 ; TYR
178 179 1 0.25000 12500 ; LYS
179 180 1 0.30000 9700 ; LYS
183 184 1 0.30000 2400 ; GLN
185 186 1 0.22500 13250 ; ILE
189 190 1 0.33500 6000 ; TYR
189 191 1 0.33500 6000 ; TYR
193 194 1 0.25000 12500 ; LYS
194 195 1 0.30000 9700 ; LYS
198 199 1 0.30000 2400 ; GLN
200 201 1 0.22500 13250 ; ILE
204 205 1 0.33500 6000 ; TYR
204 206 1 0.33500 6000 ; TYR
208 209 1 0.25000 12500 ; LYS
209 210 1 0.30000 9700 ; LYS
213 214 1 0.30000 2400 ; GLN
215 216 1 0.22500 13250 ; ILE
219 220 1 0.33500 6000 ; TYR
219 221 1 0.33500 6000 ; TYR
223 224 1 0.25000 12500 ; LYS
224 225 1 0.30000 9700 ; LYS
228 229 1 0.30000 2400 ; GLN
230 231 1 0.22500 13250 ; ILE
234 235 1 0.33500 6000 ; TYR
234 236 1 0.33500 6000 ; TYR
238 239 1 0.25000 12500 ; LYS
239 240 1 0.30000 9700 ; LYS
243 244 1 0.30000 2400 ; GLN
245 246 1 0.22500 13250 ; ILE
249 250 1 0.33500 6000 ; TYR
249 251 1 0.33500 6000 ; TYR
253 254 1 0.25000 12500 ; LYS
254 255 1 0.30000 9700 ; LYS
258 259 1 0.30000 2400 ; GLN
260 261 1 0.22500 13250 ; ILE
264 265 1 0.33500 6000 ; TYR
264 266 1 0.33500 6000 ; TYR
268 269 1 0.25000 12500 ; LYS
269 270 1 0.30000 9700 ; LYS
273 274 1 0.30000 2400 ; GLN
275 276 1 0.22500 13250 ; ILE
279 280 1 0.33500 6000 ; TYR
279 281 1 0.33500 6000 ; TYR
283 284 1 0.25000 12500 ; LYS
284 285 1 0.30000 9700 ; LYS
288 289 1 0.30000 2400 ; GLN
290 291 1 0.22500 13250 ; ILE
294 295 1 0.33500 6000 ; TYR
294 296 1 0.33500 6000 ; TYR
298 299 1 0.25000 12500 ; LYS
299 300 1 0.30000 9700 ; LYS
303 304 1 0.30000 2400 ; GLN
305 306 1 0.22500 13250 ; ILE
309 310 1 0.33500 6000 ; TYR
309 311 1 0.33500 6000 ; TYR
313 314 1 0.25000 12500 ; LYS
314 315 1 0.30000 9700 ; LYS
318 319 1 0.30000 2400 ; GLN
320 321 1 0.22500 13250 ; ILE
324 325 1 0.33500 6000 ; TYR
324 326 1 0.33500 6000 ; TYR
328 329 1 0.25000 12500 ; LYS
329 330 1 0.30000 9700 ; LYS
333 334 1 0.30000 2400 ; GLN
335 336 1 0.22500 13250 ; ILE
339 340 1 0.33500 6000 ; TYR
339 341 1 0.33500 6000 ; TYR
343 344 1 0.25000 12500 ; LYS
344 345 1 0.30000 9700 ; LYS
348 349 1 0.30000 2400 ; GLN
350 351 1 0.22500 13250 ; ILE
354 355 1 0.33500 6000 ; TYR
354 356 1 0.33500 6000 ; TYR
358 359 1 0.25000 12500 ; LYS
359 360 1 0.30000 9700 ; LYS

[ constraints ]
1 2 1 0.20000 ; VAL
7 8 1 0.20000 ; VAL
10 11 1 0.24000 ; TYR
10 12 1 0.31000 ; TYR
11 12 1 0.31000 ; TYR
16 17 1 0.20000 ; VAL
22 23 1 0.20000 ; VAL
25 26 1 0.24000 ; TYR
25 27 1 0.31000 ; TYR
26 27 1 0.31000 ; TYR
31 32 1 0.20000 ; VAL
37 38 1 0.20000 ; VAL
40 41 1 0.24000 ; TYR
40 42 1 0.31000 ; TYR
41 42 1 0.31000 ; TYR
46 47 1 0.20000 ; VAL
52 53 1 0.20000 ; VAL
55 56 1 0.24000 ; TYR
55 57 1 0.31000 ; TYR
56 57 1 0.31000 ; TYR
61 62 1 0.20000 ; VAL
67 68 1 0.20000 ; VAL
70 71 1 0.24000 ; TYR
70 72 1 0.31000 ; TYR
71 72 1 0.31000 ; TYR
76 77 1 0.20000 ; VAL
82 83 1 0.20000 ; VAL
85 86 1 0.24000 ; TYR
85 87 1 0.31000 ; TYR
86 87 1 0.31000 ; TYR
91 92 1 0.20000 ; VAL
97 98 1 0.20000 ; VAL
100 101 1 0.24000 ; TYR
100 102 1 0.31000 ; TYR
101 102 1 0.31000 ; TYR
106 107 1 0.20000 ; VAL
112 113 1 0.20000 ; VAL
115 116 1 0.24000 ; TYR
115 117 1 0.31000 ; TYR
116 117 1 0.31000 ; TYR
121 122 1 0.20000 ; VAL
127 128 1 0.20000 ; VAL
130 131 1 0.24000 ; TYR
130 132 1 0.31000 ; TYR
131 132 1 0.31000 ; TYR
136 137 1 0.20000 ; VAL
142 143 1 0.20000 ; VAL
145 146 1 0.24000 ; TYR
145 147 1 0.31000 ; TYR
146 147 1 0.31000 ; TYR
151 152 1 0.20000 ; VAL
157 158 1 0.20000 ; VAL
160 161 1 0.24000 ; TYR
160 162 1 0.31000 ; TYR
161 162 1 0.31000 ; TYR
166 167 1 0.20000 ; VAL
172 173 1 0.20000 ; VAL
175 176 1 0.24000 ; TYR
175 177 1 0.31000 ; TYR
176 177 1 0.31000 ; TYR
181 182 1 0.20000 ; VAL
187 188 1 0.20000 ; VAL
190 191 1 0.24000 ; TYR
190 192 1 0.31000 ; TYR
191 192 1 0.31000 ; TYR
196 197 1 0.20000 ; VAL
202 203 1 0.20000 ; VAL
205 206 1 0.24000 ; TYR
205 207 1 0.31000 ; TYR
206 207 1 0.31000 ; TYR
211 212 1 0.20000 ; VAL
217 218 1 0.20000 ; VAL
220 221 1 0.24000 ; TYR
220 222 1 0.31000 ; TYR
221 222 1 0.31000 ; TYR
226 227 1 0.20000 ; VAL
232 233 1 0.20000 ; VAL
235 236 1 0.24000 ; TYR
235 237 1 0.31000 ; TYR
236 237 1 0.31000 ; TYR
241 242 1 0.20000 ; VAL
247 248 1 0.20000 ; VAL
250 251 1 0.24000 ; TYR
250 252 1 0.31000 ; TYR
251 252 1 0.31000 ; TYR
256 257 1 0.20000 ; VAL
262 263 1 0.20000 ; VAL
265 266 1 0.24000 ; TYR
265 267 1 0.31000 ; TYR
266 267 1 0.31000 ; TYR
271 272 1 0.20000 ; VAL
277 278 1 0.20000 ; VAL
280 281 1 0.24000 ; TYR
280 282 1 0.31000 ; TYR
281 282 1 0.31000 ; TYR
286 287 1 0.20000 ; VAL
292 293 1 0.20000 ; VAL
295 296 1 0.24000 ; TYR
295 297 1 0.31000 ; TYR
296 297 1 0.31000 ; TYR
301 302 1 0.20000 ; VAL
307 308 1 0.20000 ; VAL
310 311 1 0.24000 ; TYR
310 312 1 0.31000 ; TYR
311 312 1 0.31000 ; TYR
316 317 1 0.20000 ; VAL
322 323 1 0.20000 ; VAL
325 326 1 0.24000 ; TYR
325 327 1 0.31000 ; TYR
326 327 1 0.31000 ; TYR
331 332 1 0.20000 ; VAL
337 338 1 0.20000 ; VAL
340 341 1 0.24000 ; TYR
340 342 1 0.31000 ; TYR
341 342 1 0.31000 ; TYR
346 347 1 0.20000 ; VAL
352 353 1 0.20000 ; VAL
355 356 1 0.24000 ; TYR
355 357 1 0.31000 ; TYR
356 357 1 0.31000 ; TYR

[ angles ]
; Backbone angles
1 3 5 2 112.17172 40 ; VAL(C)-GLN(E)-ILE(E)
3 5 7 2 111.45585 40 ; GLN(E)-ILE(E)-VAL(E)
5 7 9 2 105.19977 40 ; ILE(E)-VAL(E)-TYR(E)
7 9 13 2 139.96459 40 ; VAL(E)-TYR(E)-LYS(C)
9 13 16 2 57.50881 40 ; TYR(E)-LYS(C)-VAL(C)
13 16 18 2 127.80150 40 ; LYS(C)-VAL(C)-GLN(E)
16 18 20 2 109.96416 40 ; VAL(C)-GLN(E)-ILE(E)
18 20 22 2 108.49944 40 ; G

Please Log in or Create an account to join the conversation.

  • ngandhiau
  • ngandhiau's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 years 9 months ago #3901 by ngandhiau
Replied by ngandhiau on topic Protein in Water using ElNeDyn22
The warnings I receive

WARNING 1 : The bond in molecule-type Protein_A between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option. WARNING 2 [file equil.mdp]: For proper integration of the Berendsen thermostat, tau-t (0.5) should be at least 5 times larger than nsttcouple*dt (0.2) Number of degrees of freedom in T-Coupling group Protein is 11517.00 Number of degrees of freedom in T-Coupling group Other is 198744.00 Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 53134.398 Using frame at t = 53134.4 ps Starting time for run is 0 ps NOTE 4 [file equil.mdp]: This run will generate roughly 3918 Mb of data There were 4 notes There were 2 warnings ------------------------------------------------------- Program grompp, VERSION 4.6.5 Source code file: /ivec/cle50/build/gromacs-4.6.5/src/kernel/grompp.c, line: 1910 Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "You Look Better Upside Down" (Throwing Muses)[file topol.top, line 16]:
The bond in molecule-type Protein_A between atoms 1 BB and 3 BB has an
estimated oscillational period of 9.7e-02 ps, which is less than 5 times
the time step of 2.0e-02 ps.
Maybe you forgot to change the constraints mdp option.


WARNING 2 : For proper integration of the Berendsen thermostat, tau-t (0.5) should be at least 5 times larger than nsttcouple*dt (0.2) Number of degrees of freedom in T-Coupling group Protein is 11517.00 Number of degrees of freedom in T-Coupling group Other is 198744.00 Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 53134.398 Using frame at t = 53134.4 ps Starting time for run is 0 ps NOTE 4 [file equil.mdp]: This run will generate roughly 3918 Mb of data There were 4 notes There were 2 warnings ------------------------------------------------------- Program grompp, VERSION 4.6.5 Source code file: /ivec/cle50/build/gromacs-4.6.5/src/kernel/grompp.c, line: 1910 Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "You Look Better Upside Down" (Throwing Muses)[file equil.mdp]:
For proper integration of the Berendsen thermostat, tau-t (0.5) should be
at least 5 times larger than nsttcouple*dt (0.2)

Number of degrees of freedom in T-Coupling group Protein is 11517.00
Number of degrees of freedom in T-Coupling group Other is 198744.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
Last frame -1 time 53134.398
Using frame at t = 53134.4 ps
Starting time for run is 0 ps

NOTE 4 : This run will generate roughly 3918 Mb of data There were 4 notes There were 2 warnings ------------------------------------------------------- Program grompp, VERSION 4.6.5 Source code file: /ivec/cle50/build/gromacs-4.6.5/src/kernel/grompp.c, line: 1910 Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "You Look Better Upside Down" (Throwing Muses)[file equil.mdp]:
This run will generate roughly 3918 Mb of data


There were 4 notes

There were 2 warnings

Program grompp, VERSION 4.6.5
Source code file: /ivec/cle50/build/gromacs-4.6.5/src/kernel/grompp.c, line: 1910

Fatal error:
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors

"You Look Better Upside Down" (Throwing Muses)

Please Log in or Create an account to join the conversation.

More
9 years 9 months ago #3902 by Clement
Replied by Clement on topic Protein in Water using ElNeDyn22

ngandhiau wrote: WARNING 1 (file topol.top, line 16):
The bond in molecule-type Protein_A between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps.
Maybe you forgot to change the constraints mdp option.


You can ignore that. It does not matter with Martini.

ngandhiau wrote: WARNING 2 (file equil.mdp):
For proper integration of the Berendsen thermostat, tau-t (0.5) should be at least 5 times larger than nsttcouple*dt (0.2)


Mmmmh... This is as well not really important in this case (even though I'd use a value of 1.0 for tau-t with the Berendsen thermostat).

You can "safely" ignore both of these warnings by adding the "-maxwarn 2 " flag to your grompp command line.

Please Log in or Create an account to join the conversation.

  • ngandhiau
  • ngandhiau's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 years 9 months ago #3903 by ngandhiau
Replied by ngandhiau on topic Protein in Water using ElNeDyn22
Thanks Clement.

I ignored the warnings and the job runs. However, I don't see that my protein is moving at all (~ 200ns). Is it a visualisation artifact? I haven't imposed any position restraints.

Any feedback on this is appreciated.

Please Log in or Create an account to join the conversation.

More
9 years 9 months ago #3904 by Clement
Replied by Clement on topic Protein in Water using ElNeDyn22
It depends what do you mean by "moving"... Rotational/lateral diffusion? Backbone deformation? What do you expect?

Please Log in or Create an account to join the conversation.

Time to create page: 0.124 seconds