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Segmentation Fault with mdrun
- AlexC
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11 years 3 months ago #1371
by AlexC
Segmentation Fault with mdrun was created by AlexC
I'm trying to model the self-assembly of a specific architecture of small peptides. however every time I try to run a MD simulation I get hit with a segmentation fault. I can't find the error (if there is one) or a way to get around it.
If anyone can help I'd be grateful, I've put the grompp step and files below.
md.mdp
minsolv1.gro
A6R1S.top
index.ndx
If anyone can help I'd be grateful, I've put the grompp step and files below.
grompp -f ../md.mdp -c minsolv1.gro -p A6R1S.top -n index.ndxmd.mdp
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.1
;
; for use with GROMACS 4
;
; RUN CONTROL PARAMETERS
; MARTINI - Most simulations are stable with dt=40 fs, some (especially rings)
; require 20-30 fs.
; The range of time steps used for parametrization is 20-40 fs, using smaller
; time steps is therefore not recommended.
integrator = md
; Start time and timestep in ps:
tinit = 0.0
dt = 0.025
nsteps = 5000
; Number of steps for center of mass motion removal:
nstcomm = 1
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f):
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log (.log) file and energy (.edr) file:
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for .xtc file:
nstxtcout = 1000
xtc_precision = 100
; NEIGHBORSEARCHING PARAMETERS
; MARTINI - No need for more frequent updates or larger neighborlist cut-off
; due to the use of shifted potential energy functions.
; Neighborlist update frequency:
nstlist = 10
; Neighbor searching algorithm (simple|grid):
ns_type = grid
; Periodic boundary conditions (xyz|none):
pbc = xyz
; Neighborlist cut-off:
rlist = 1.5
; OPTIONS FOR ELECTROSTATICS AND VDW
; MARTINI - VdW and electrostatic interactions are used in their shifted forms.
; Changing to other types of electrostatics will affect the general performance
; of the model.
; Method for doing electrostatics:
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field:
epsilon_r = 15
; Method for doing Van der Waals:
vdw_type = Shift
; Cut-off lengths:
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure?
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; MARTINI -Normal temperature and pressure coupling schemes can be used. It
; is recommended to couple individual groups in your system seperately.
; Temperature coupling:
tcoupl = v-rescale
; Groups to couple separately:
tc-grps = A6R W
; Time constant (ps) and reference temperature (K):
tau_t = 0.3 0.3
ref_t = 300 300
; Pressure coupling:
Pcoupl = no
; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = no
gen_temp = 300
gen_seed = 473529
; OPTIONS FOR BONDS
; MARTINI - For ring systems constraints are defined which are best handled
; using Lincs.
constraints = none
; Type of constraint algorithm:
constraint_algorithm = Lincs
; Do not constrain the start configuration:
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix:
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond rotates over
; more degrees than:
lincs_warnangle = 30
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.1
;
; for use with GROMACS 4
;
; RUN CONTROL PARAMETERS
; MARTINI - Most simulations are stable with dt=40 fs, some (especially rings)
; require 20-30 fs.
; The range of time steps used for parametrization is 20-40 fs, using smaller
; time steps is therefore not recommended.
integrator = md
; Start time and timestep in ps:
tinit = 0.0
dt = 0.025
nsteps = 5000
; Number of steps for center of mass motion removal:
nstcomm = 1
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f):
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log (.log) file and energy (.edr) file:
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for .xtc file:
nstxtcout = 1000
xtc_precision = 100
; NEIGHBORSEARCHING PARAMETERS
; MARTINI - No need for more frequent updates or larger neighborlist cut-off
; due to the use of shifted potential energy functions.
; Neighborlist update frequency:
nstlist = 10
; Neighbor searching algorithm (simple|grid):
ns_type = grid
; Periodic boundary conditions (xyz|none):
pbc = xyz
; Neighborlist cut-off:
rlist = 1.5
; OPTIONS FOR ELECTROSTATICS AND VDW
; MARTINI - VdW and electrostatic interactions are used in their shifted forms.
; Changing to other types of electrostatics will affect the general performance
; of the model.
; Method for doing electrostatics:
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field:
epsilon_r = 15
; Method for doing Van der Waals:
vdw_type = Shift
; Cut-off lengths:
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure?
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; MARTINI -Normal temperature and pressure coupling schemes can be used. It
; is recommended to couple individual groups in your system seperately.
; Temperature coupling:
tcoupl = v-rescale
; Groups to couple separately:
tc-grps = A6R W
; Time constant (ps) and reference temperature (K):
tau_t = 0.3 0.3
ref_t = 300 300
; Pressure coupling:
Pcoupl = no
; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = no
gen_temp = 300
gen_seed = 473529
; OPTIONS FOR BONDS
; MARTINI - For ring systems constraints are defined which are best handled
; using Lincs.
constraints = none
; Type of constraint algorithm:
constraint_algorithm = Lincs
; Do not constrain the start configuration:
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix:
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond rotates over
; more degrees than:
lincs_warnangle = 30
minsolv1.gro
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
A6R
714
1ALA BEP4 1 5.261 4.412 4.261
2ALA BEP4 2 5.065 4.353 4.501
3ALA BEP4 3 5.177 4.313 4.781
4ALA BEP4 4 4.980 4.269 5.018
5ALA BEP4 5 5.072 4.301 5.291
6ALA BEP4 6 4.954 4.328 5.554
7ARG BEP5 7 5.146 4.409 5.823
7ARG SEN0 8 4.931 4.607 5.967
7ARG SEQd 9 4.710 4.791 5.804
8ALA BEP4 10 5.340 4.892 5.778
9ALA BEP4 11 5.152 4.835 5.563
10ALA BEP4 12 5.013 4.802 5.380
11ALA BEP4 13 4.821 4.739 5.170
12ALA BEP4 14 4.957 4.755 4.882
13ALA BEP4 15 4.851 4.804 4.635
14ARG BEP5 16 4.964 4.835 4.361
14ARG SEN0 17 4.812 4.645 4.155
14ARG SEQd 18 4.941 4.565 3.863
15ALA BEP4 19 5.286 5.209 4.439
16ALA BEP4 20 5.180 5.221 4.697
17ALA BEP4 21 4.942 5.245 4.878
18ALA BEP4 22 4.907 5.243 5.131
19ALA BEP4 23 4.800 5.247 5.400
20ALA BEP4 24 4.992 5.284 5.636
21ARG BEP5 25 4.955 5.223 5.895
21ARG SEN0 26 5.104 5.378 6.121
21ARG SEQd 27 5.014 5.410 6.432
22ALA BEP4 28 4.775 5.725 5.695
23ALA BEP4 29 4.942 5.745 5.432
24ALA BEP4 30 4.893 5.738 5.161
25ALA BEP4 31 5.102 5.721 4.927
26ALA BEP4 32 4.979 5.697 4.643
27ALA BEP4 33 5.140 5.680 4.399
28ARG BEP5 34 5.041 5.616 4.111
28ARG SEN0 35 5.089 5.325 3.999
28ARG SEQd 36 4.863 5.102 3.936
29W W 37 3.630 9.353 3.462
30W W 38 3.023 0.681 2.124
31W W 39 8.421 1.650 4.588
32W W 40 8.786 5.562 7.498
33W W 41 3.093 3.871 6.040
34W W 42 0.272 5.765 2.772
35W W 43 0.558 7.041 1.079
36W W 44 4.704 3.154 5.747
37W W 45 9.840 6.069 1.277
38W W 46 3.598 9.807 4.983
39W W 47 7.358 4.915 0.538
40W W 48 8.015 1.224 8.107
41W W 49 5.203 4.387 2.301
42W W 50 8.101 5.218 4.406
43W W 51 1.527 1.036 0.220
44W W 52 8.524 4.634 6.996
45W W 53 9.926 5.121 8.992
46W W 54 3.440 6.977 5.961
47W W 55 9.288 5.730 7.469
48W W 56 7.078 6.653 4.355
49W W 57 1.233 6.846 8.418
50W W 58 6.971 5.606 8.682
51W W 59 3.042 1.905 2.016
52W W 60 5.527 7.158 6.682
53W W 61 7.288 2.044 3.081
54W W 62 5.236 6.462 2.769
55W W 63 1.923 3.317 3.120
56W W 64 2.378 9.598 7.839
57W W 65 9.947 2.049 2.636
58W W 66 2.562 5.363 3.264
59W W 67 6.859 9.066 7.300
60W W 68 9.055 4.449 0.442
61W W 69 5.100 6.145 5.713
62W W 70 7.953 0.906 3.104
63W W 71 1.304 2.816 1.505
64W W 72 9.431 8.629 7.508
65W W 73 9.827 1.004 8.258
66W W 74 2.614 8.244 6.530
67W W 75 3.028 2.444 5.032
68W W 76 1.005 8.897 1.843
69W W 77 5.874 6.769 6.730
70W W 78 4.630 5.465 1.976
71W W 79 4.135 7.811 8.247
72W W 80 6.139 3.397 2.473
73W W 81 7.542 3.389 6.444
74W W 82 0.895 7.115 4.316
75W W 83 7.577 6.077 8.881
76W W 84 6.017 8.177 7.971
77W W 85 7.646 3.342 2.511
78W W 86 0.824 6.609 6.349
79W W 87 8.285 2.391 2.049
80W W 88 0.173 9.229 0.773
81W W 89 8.062 0.841 1.223
82W W 90 2.882 2.105 4.135
83W W 91 9.509 9.897 6.859
84W W 92 9.730 3.600 1.081
85W W 93 3.288 7.996 0.072
86W W 94 6.028 3.741 7.212
87W W 95 7.999 4.187 3.755
88W W 96 7.550 0.020 3.286
89W W 97 3.041 4.566 6.201
90W W 98 8.446 2.888 2.053
91W W 99 7.255 6.449 3.904
92W W 100 8.941 4.535 0.948
93W W 101 9.009 4.943 0.617
94W W 102 8.259 9.255 5.892
95W W 103 7.155 9.883 0.560
96W W 104 7.207 1.593 4.186
97W W 105 5.052 2.390 5.865
98W W 106 1.261 4.611 2.069
99W W 107 2.611 7.877 7.823
100W W 108 8.488 5.192 7.896
101W W 109 8.632 9.497 7.133
102W W 110 5.044 6.111 8.345
103W W 111 0.610 6.287 8.749
104W W 112 1.480 9.509 5.612
105W W 113 8.703 9.854 5.159
106W W 114 1.754 7.583 0.811
107W W 115 4.980 1.964 5.561
108W W 116 0.157 5.408 9.371
109W W 117 8.658 1.387 2.740
110W W 118 4.044 5.724 0.359
111W W 119 5.190 2.600 1.169
112W W 120 9.623 2.970 2.943
113W W 121 3.211 5.701 1.782
114W W 122 5.163 9.088 8.991
115W W 123 6.836 0.860 8.932
116W W 124 5.696 9.175 2.461
117W W 125 0.671 2.019 4.618
118W W 126 8.384 8.433 9.911
119W W 127 0.756 5.528 3.634
120W W 128 8.197 1.978 6.055
121W W 129 8.474 9.562 5.524
122W W 130 9.158 8.395 1.639
123W W 131 3.764 2.945 7.865
124W W 132 2.953 1.459 3.717
125W W 133 7.477 4.172 3.484
126W W 134 5.937 3.517 1.511
127W W 135 2.390 0.209 3.504
128W W 136 5.555 6.771 6.316
129W W 137 7.091 5.776 3.139
130W W 138 1.419 9.221 1.796
131W W 139 8.192 9.616 7.406
132W W 140 7.579 2.877 7.403
133W W 141 7.716 5.554 4.270
134W W 142 6.698 5.754 5.117
135W W 143 5.533 8.747 8.831
136W W 144 4.567 4.531 9.490
137W W 145 8.124 0.733 9.455
138W W 146 1.801 2.824 8.749
139W W 147 3.324 6.974 0.042
140W W 148 2.951 1.513 1.667
141W W 149 1.566 2.058 1.394
142W W 150 7.153 5.651 2.630
143W W 151 7.750 0.212 5.130
144W W 152 6.257 1.687 6.385
145W W 153 3.992 3.209 4.064
146W W 154 3.953 4.450 5.180
147W W 155 4.548 6.928 8.663
148W W 156 3.273 1.903 1.549
149W W 157 8.078 9.537 7.913
150W W 158 3.856 2.113 0.804
151W W 159 8.287 3.258 6.753
152W W 160 4.650 0.086 3.232
153W W 161 9.881 5.635 9.757
154W W 162 2.780 2.168 4.648
155W W 163 2.909 3.389 5.904
156W W 164 5.236 0.418 4.586
157W W 165 5.338 5.441 5.293
158W W 166 8.896 1.041 3.703
159W W 167 3.041 2.343 1.388
160W W 168 9.010 4.524 6.815
161W W 169 9.553 1.440 8.166
162W W 170 7.941 7.263 9.404
163W W 171 2.546 2.479 4.293
164W W 172 1.223 9.364 5.177
165W W 173 3.166 9.226 9.822
166W W 174 1.862 5.953 0.832
167W W 175 0.351 3.602 9.750
168W W 176 8.761 9.171 9.485
169W W 177 8.244 1.309 7.640
170W W 178 6.361 3.338 1.770
171W W 179 4.609 1.629 2.306
172W W 180 9.347 4.873 7.027
173W W 181 5.539 6.486 7.008
174W W 182 8.593 9.460 9.892
175W W 183 2.690 1.229 5.238
176W W 184 4.938 5.275 0.611
177W W 185 7.558 3.653 8.616
178W W 186 0.921 2.828 1.143
179W W 187 3.658 8.789 2.046
180W W 188 9.560 0.645 8.528
181W W 189 1.257 2.679 3.608
182W W 190 0.579 2.160 2.049
183W W 191 3.756 7.579 7.476
184W W 192 8.233 0.792 3.529
185W W 193 7.261 3.399 8.971
186W W 194 8.609 1.769 6.310
187W W 195 7.350 0.397 3.591
188W W 196 3.969 7.567 2.097
189W W 197 3.584 8.431 1.665
190W W 198 5.877 0.152 2.385
191W W 199 7.340 5.372 7.794
192W W 200 8.940 4.700 7.304
193W W 201 6.904 5.295 8.077
194W W 202 0.068 1.572 6.434
195W W 203 2.953 1.877 1.140
196W W 204 5.401 4.748 4.624
197W W 205 4.695 9.893 5.878
198W W 206 4.369 1.024 4.083
199W W 207 5.892 8.010 8.451
200W W 208 4.677 5.027 6.277
201W W 209 7.091 9.376 0.432
202W W 210 1.398 8.722 9.788
203W W 211 7.068 3.504 8.491
204W W 212 7.794 4.139 5.347
205W W 213 4.567 5.263 7.683
206W W 214 6.963 5.506 9.206
207W W 215 4.584 2.154 5.852
208W W 216 3.472 8.022 7.471
209W W 217 9.543 3.489 1.914
210W W 218 4.375 5.889 2.169
211W W 219 5.926 9.052 2.010
212W W 220 5.987 8.737 2.426
213W W 221 1.241 0.100 4.001
214W W 222 3.959 8.037 2.328
215W W 223 4.595 8.715 4.358
216W W 224 2.962 2.392 5.551
217W W 225 8.428 4.447 2.961
218W W 226 4.253 0.899 0.840
219W W 227 0.178 7.359 7.452
220W W 228 3.340 3.188 7.687
221W W 229 6.869 7.196 8.568
222W W 230 0.447 5.093 9.061
223W W 231 5.570 1.632 7.854
224W W 232 7.685 9.660 7.275
225W W 233 2.263 2.294 4.704
226W W 234 8.477 2.594 1.610
227W W 235 5.937 9.627 2.344
228W W 236 2.144 0.839 8.344
229W W 237 4.955 4.740 9.775
230W W 238 2.357 4.771 6.398
231W W 239 8.399 7.626 9.014
232W W 240 3.418 2.122 1.095
233W W 241 8.478 4.900 7.458
234W W 242 4.693 0.620 4.199
235W W 243 9.103 9.500 5.094
236W W 244 2.691 9.469 7.433
237W W 245 5.287 2.767 6.622
238W W 246 8.013 3.011 7.134
239W W 247 3.862 5.899 2.007
240W W 248 1.944 9.769 8.758
241W W 249 3.080 4.229 0.592
242W W 250 6.156 3.803 1.897
243W W 251 1.793 5.421 9.515
244W W 252 9.883 0.270 6.852
245W W 253 8.586 6.643 4.948
246W W 254 7.793 6.774 1.516
247W W 255 8.419 6.129 6.557
248W W 256 7.829 0.472 3.378
249W W 257 9.705 1.094 8.762
250W W 258 4.065 9.458 7.714
251W W 259 4.498 9.716 0.382
252W W 260 2.815 7.556 8.187
253W W 261 2.332 3.724 6.680
254W W 262 6.493 3.831 7.444
255W W 263 1.922 4.910 9.491
256W W 264 8.244 3.871 5.291
257W W 265 8.362 4.133 3.374
258W W 266 9.432 9.088 5.129
259W W 267 2.580 1.928 9.931
260W W 268 3.759 7.968 1.833
261W W 269 2.145 7.969 2.086
262W W 270 1.359 0.505 5.233
263W W 271 1.831 8.313 1.840
264W W 272 7.567 6.963 1.081
265W W 273 9.423 2.059 2.566
266W W 274 7.017 8.273 5.970
267W W 275 6.842 8.770 5.967
268W W 276 9.024 8.345 3.554
269W W 277 5.522 8.382 8.452
270W W 278 7.650 9.704 5.182
271W W 279 0.905 5.909 3.299
272W W 280 3.320 3.555 9.531
273W W 281 8.208 5.729 4.339
274W W 282 4.479 5.424 0.403
275W W 283 3.023 1.003 1.583
276W W 284 2.531 8.260 6.009
277W W 285 4.001 8.046 7.466
278W W 286 0.634 1.232 3.465
279W W 287 9.377 5.779 9.740
280W W 288 8.158 2.031 0.291
281W W 289 3.528 5.245 4.154
282W W 290 9.141 8.995 3.097
283W W 291 4.567 8.015 4.695
284W W 292 0.467 8.890 0.486
285W W 293 1.084 6.897 4.759
286W W 294 9.422 4.650 0.764
287W W 295 5.979 2.035 3.984
288W W 296 1.841 0.901 7.917
289W W 297 9.182 9.092 7.564
290W W 298 4.711 2.127 3.224
291W W 299 2.548 7.578 3.900
292W W 300 8.125 9.911 5.349
293W W 301 7.099 7.074 9.026
294W W 302 3.274 0.557 1.682
295W W 303 1.007 8.381 9.881
296W W 304 0.023 6.400 0.909
297W W 305 2.962 5.018 6.932
298W W 306 1.606 5.385 6.028
299W W 307 8.515 8.940 9.889
300W W 308 2.565 1.782 3.864
301W W 309 4.281 8.819 3.945
302W W 310 5.525 8.026 8.066
303W W 311 3.196 2.015 5.280
304W W 312 2.475 5.171 2.123
305W W 313 7.200 9.899 3.667
306W W 314 8.927 7.873 3.773
307W W 315 9.957 0.801 0.177
308W W 316 8.233 9.906 8.258
309W W 317 9.616 0.397 0.176
310W W 318 8.388 2.780 9.049
311W W 319 4.319 0.587 9.270
312W W 320 5.676 4.488 2.517
313W W 321 2.575 6.636 0.800
314W W 322 5.344 8.549 6.853
315W W 323 0.573 1.582 6.280
316W W 324 3.080 3.532 2.491
317W W 325 8.835 9.392 3.251
318W W 326 6.994 1.520 4.664
319W W 327 3.622 5.903 1.524
320W W 328 5.058 2.816 5.559
321W W 329 2.789 5.772 7.850
322W W 330 4.876 1.115 4.189
323W W 331 6.886 0.481 1.862
324W W 332 6.610 2.607 5.204
325W W 333 2.570 6.260 4.799
326W W 334 4.181 7.674 4.578
327W W 335 8.227 2.678 2.482
328W W 336 4.036 6.912 8.784
329W W 337 5.842 2.947 9.381
330W W 338 6.569 9.266 0.437
331W W 339 2.680 3.662 6.291
332W W 340 0.497 6.598 0.800
333W W 341 7.866 2.666 0.545
334W W 342 0.254 1.052 2.718
335W W 343 7.339 8.874 7.193
336W W 344 3.721 5.485 5.068
337W W 345 8.315 6.807 1.462
338W W 346 5.136 9.327 6.930
339W W 347 0.024 3.991 0.881
340W W 348 2.775 8.063 3.152
341W W 349 7.429 7.127 9.435
342W W 350 4.728 0.031 0.735
343W W 351 5.468 4.709 9.887
344W W 352 2.261 7.208 1.309
345W W 353 6.901 9.513 3.871
346W W 354 2.300 8.490 6.877
347W W 355 3.510 7.777 2.252
348W W 356 5.375 4.972 5.091
349W W 357 9.136 1.623 2.672
350W W 358 9.349 0.777 8.990
351W W 359 3.491 5.584 9.193
352W W 360 5.414 4.529 8.187
353W W 361 6.343 7.869 7.692
354W W 362 7.097 1.130 8.563
355W W 363 2.602 3.476 2.277
356W W 364 1.494 8.711 1.907
357W W 365 0.713 4.247 6.478
358W W 366 0.119 1.552 2.624
359W W 367 0.885 8.584 0.347
360W W 368 6.829 7.580 4.862
361W W 369 3.749 7.891 7.900
362W W 370 6.672 7.117 3.534
363W W 371 0.235 1.248 6.051
364W W 372 6.483 0.470 8.966
365W W 373 8.262 3.078 4.134
366W W 374 0.450 4.699 6.429
367W W 375 4.789 4.967 1.906
368W W 376 9.247 9.247 3.541
369W W 377 2.997 1.977 3.637
370W W 378 9.436 8.750 1.362
371W W 379 8.892 8.862 3.539
372W W 380 8.099 7.164 3.249
373W W 381 6.041 5.834 8.182
374W W 382 1.685 9.146 5.291
375W W 383 4.230 9.286 0.237
376W W 384 8.918 8.815 1.432
377W W 385 8.918 5.480 7.996
378W W 386 4.501 4.041 9.305
379W W 387 4.478 7.593 5.007
380W W 388 7.702 3.163 0.452
381W W 389 2.253 8.058 4.048
382W W 390 2.225 5.246 9.764
383W W 391 7.060 5.110 8.539
384W W 392 4.994 4.958 7.638
385W W 393 8.644 5.655 6.507
386W W 394 7.648 6.989 2.626
387W W 395 6.248 3.369 7.515
388W W 396 9.559 6.880 7.980
389W W 397 9.163 0.281 6.770
390W W 398 3.603 8.758 8.905
391W W 399 5.284 3.416 4.334
392W W 400 7.084 5.987 9.035
393W W 401 5.181 4.911 6.274
394W W 402 7.911 3.748 5.682
395W W 403 9.263 7.006 9.838
396W W 404 6.314 3.259 1.250
397W W 405 9.317 1.994 5.434
398W W 406 4.692 8.407 3.267
399W W 407 2.403 1.588 0.294
400W W 408 2.801 2.463 6.731
401W W 409 6.738 6.443 4.011
402W W 410 5.088 0.235 5.801
403W W 411 2.459 0.104 0.381
404W W 412 4.207 0.045 0.674
405W W 413 8.898 4.976 8.153
406W W 414 7.966 9.431 5.492
407W W 415 1.192 0.823 1.858
408W W 416 2.205 7.192 3.789
409W W 417 0.438 1.437 3.024
410W W 418 9.422 8.026 3.686
411W W 419 5.371 3.934 4.468
412W W 420 9.841 9.599 1.515
413W W 421 7.930 3.649 6.200
414W W 422 5.713 1.260 0.515
415W W 423 8.093 5.429 3.921
416W W 424 2.876 7.886 3.637
417W W 425 2.997 0.186 1.927
418W W 426 0.802 9.976 0.145
419W W 427 1.672 5.274 8.075
420W W 428 6.910 6.654 3.564
421W W 429 6.888 9.209 4.307
422W W 430 7.647 7.410 3.362
423W W 431 4.613 5.765 7.519
424W W 432 2.734 1.980 1.601
425W W 433 9.141 8.263 4.060
426W W 434 9.482 5.817 3.417
427W W 435 3.715 5.992 5.216
428W W 436 6.977 7.742 5.345
429W W 437 2.398 7.583 9.286
430W W 438 6.176 7.138 3.705
431W W 439 1.259 3.096 4.722
432W W 440 9.352 7.828 5.524
433W W 441 1.964 0.363 3.233
434W W 442 3.273 4.709 0.487
435W W 443 1.397 6.960 4.342
436W W 444 0.527 7.677 7.684
437W W 445 8.127 2.048 4.773
438W W 446 4.111 9.531 0.688
439W W 447 5.867 1.849 6.054
440W W 448 5.176 5.193 1.634
441W W 449 3.879 1.205 4.162
442W W 450 5.400 9.118 2.037
443W W 451 0.326 9.764 1.642
444W W 452 7.807 2.540 2.195
445W W 453 6.907 1.240 1.369
446W W 454 5.252 6.595 1.460
447W W 455 1.773 2.596 3.559
448W W 456 5.086 7.742 8.957
449W W 457 5.454 2.058 5.776
450W W 458 6.115 4.496 2.814
451W W 459 3.701 3.331 6.792
452W W 460 6.371 2.863 6.410
453W W 461 7.006 5.377 6.341
454W W 462 9.932 1.295 3.049
455W W 463 7.106 5.746 2.113
456W W 464 7.637 6.929 3.149
457W W 465 4.678 5.276 1.489
458W W 466 9.331 9.305 4.659
459W W 467 6.692 1.495 4.233
460W W 468 1.586 3.250 1.420
461W W 469 5.106 8.083 6.799
462W W 470 8.239 7.563 6.793
463W W 471 9.216 9.471 2.892
464W W 472 2.087 7.571 4.139
465W W 473 6.236 6.819 9.764
466W W 474 5.208 0.709 4.151
467W W 475 5.313 5.664 5.769
468W W 476 5.131 1.708 8.135
469W W 477 3.357 9.999 4.554
470W W 478 9.303 6.978 2.738
471W W 479 3.702 5.221 3.053
472W W 480 1.911 5.053 6.308
473W W 481 4.746 2.417 5.429
474W W 482 1.421 8.226 9.601
475W W 483 8.269 2.627 8.556
476W W 484 9.145 0.379 8.711
477W W 485 6.599 9.968 9.077
478W W 486 3.994 0.515 0.591
479W W 487 3.637 3.105 7.267
480W W 488 4.752 5.296 4.408
481W W 489 7.350 2.781 0.534
482W W 490 1.087 3.118 1.876
483W W 491 4.684 7.527 4.530
484W W 492 7.144 3.896 8.835
485W W 493 2.647 1.229 5.764
486W W 494 2.384 1.103 6.788
487W W 495 0.197 9.399 6.918
488W W 496 8.622 0.613 3.833
489W W 497 7.733 5.071 4.060
490W W 498 7.303 5.000 1.055
491W W 499 4.907 7.101 4.736
492W W 500 5.266 5.154 9.693
493W W 501 4.156 8.486 9.713
494W W 502 3.665 2.427 7.928
495W W 503 1.577 5.734 5.631
496W W 504 8.748 2.531 8.753
497W W 505 7.878 2.277 1.740
498W W 506 0.814 4.108 6.974
499W W 507 1.554 3.039 3.369
500W W 508 1.665 7.961 0.449
501W W 509 5.269 2.366 5.386
502W W 510 1.469 8.324 0.121
503W W 511 5.597 4.389 0.284
504W W 512 6.543 1.257 6.510
505W W 513 2.423 8.085 7.370
506W W 514 2.575 2.211 5.124
507W W 515 0.070 1.805 3.084
508W W 516 6.196 1.661 4.285
509W W 517 0.525 3.998 0.054
510W W 518 8.962 3.056 6.352
511W W 519 7.049 2.310 3.470
512W W 520 5.422 7.074 1.319
513W W 521 9.722 4.936 8.540
514W W 522 9.677 8.437 1.710
515W W 523 5.528 9.028 6.749
516W W 524 2.738 0.581 1.698
517W W 525 2.469 4.645 2.098
518W W 526 4.993 0.295 8.192
519W W 527 8.660 7.375 7.049
520W W 528 4.181 8.834 5.277
521W W 529 4.368 2.071 2.149
522W W 530 8.689 2.359 7.888
523W W 531 9.717 3.054 9.731
524W W 532 4.526 4.739 7.741
525W W 533 2.069 7.176 9.343
526W W 534 2.219 7.137 5.227
527W W 535 5.525 3.156 9.019
528W W 536 2.585 5.218 0.580
529W W 537 4.597 5.521 6.130
530W W 538 2.735 0.204 3.903
531W W 539 8.020 2.773 1.778
532W W 540 6.026 2.466 9.484
533W W 541 9.389 8.712 3.463
534W W 542 9.753 6.079 9.512
535W W 543 6.444 9.425 4.128
536W W 544 3.942 0.399 6.650
537W W 545 3.157 1.161 8.980
538W W 546 1.115 1.115 1.425
539W W 547 7.647 0.844 9.652
540W W 548 9.765 3.547 3.906
541W W 549 8.160 1.213 2.730
542W W 550 3.823 4.423 8.777
543W W 551 7.378 9.792 7.680
544W W 552 1.855 8.456 9.783
545W W 553 6.740 9.734 0.275
546W W 554 2.074 2.376 8.808
547W W 555 7.131 6.191 3.464
548W W 556 9.490 9.021 5.647
549W W 557 0.195 1.766 5.960
550W W 558 2.588 8.382 8.232
551W W 559 0.996 3.515 4.907
552W W 560 1.149 8.426 4.164
553W W 561 9.961 9.823 7.118
554W W 562 3.393 7.491 9.967
555W W 563 2.267 8.591 4.053
556W W 564 2.512 6.744 1.311
557W W 565 7.965 3.043 2.218
558W W 566 6.011 2.996 8.886
559W W 567 8.844 7.892 4.291
560W W 568 3.162 5.020 6.446
561W W 569 5.611 9.345 7.161
562W W 570 5.503 4.544 5.375
563W W 571 7.397 2.475 3.836
564W W 572 4.145 4.411 9.193
565W W 573 3.986 8.970 3.535
566W W 574 0.465 2.423 8.466
567W W 575 2.086 9.747 8.251
568W W 576 2.481 6.720 5.039
569W W 577 4.166 6.040 7.453
570W W 578 3.282 2.776 8.010
571W W 579 9.677 2.491 2.726
572W W 580 4.185 4.226 9.685
573W W 581 0.311 2.855 6.604
574W W 582 7.553 1.290 8.351
575W W 583 6.405 3.744 1.432
576W W 584 9.064 9.908 4.770
577W W 585 8.800 9.910 0.067
578W W 586 1.160 9.106 5.690
579W W 587 0.268 5.902 9.525
580W W 588 8.095 7.935 1.941
581W W 589 1.938 7.984 7.546
582W W 590 3.812 1.760 9.514
583W W 591 5.409 6.439 8.156
584W W 592 5.043 5.184 1.122
585W W 593 0.419 5.707 3.273
586W W 594 1.216 6.619 2.670
587W W 595 1.941 2.793 3.102
588W W 596 1.405 2.979 6.306
589W W 597 9.642 1.659 2.817
590W W 598 9.570 2.849 0.195
591W W 599 0.652 2.645 0.720
592W W 600 6.189 7.823 2.480
593W W 601 0.169 1.474 3.478
594W W 602 3.459 2.691 7.524
595W W 603 3.326 3.117 2.280
596W W 604 7.916 4.391 3.279
597W W 605 3.925 4.814 2.803
598W W 606 8.462 1.079 3.143
599W W 607 3.759 3.611 7.236
600W W 608 0.212 0.260 7.267
601W W 609 2.796 3.612 9.550
602W W 610 0.376 1.646 4.387
603W W 611 8.351 2.085 1.626
604W W 612 4.011 8.409 1.967
605W W 613 5.153 0.666 6.096
606W W 614 8.017 6.693 1.044
607W W 615 4.944 3.008 4.119
608W W 616 5.937 7.132 6.354
609W W 617 3.533 8.296 2.171
610W W 618 2.267 8.264 7.840
611W W 619 0.737 0.788 1.593
612W W 620 1.655 6.871 9.461
613W W 621 7.957 4.463 9.697
614W W 622 9.592 0.103 3.456
615W W 623 6.911 8.948 0.672
616W W 624 2.934 8.245 0.373
617W W 625 9.352 0.260 8.241
618W W 626 8.902 7.942 5.777
619W W 627 2.761 8.296 7.033
620W W 628 7.479 1.878 5.372
621W W 629 6.745 7.948 6.282
622W W 630 5.344 4.874 4.034
623W W 631 4.800 5.093 0.133
624W W 632 6.975 4.305 3.328
625W W 633 7.216 9.609 3.234
626W W 634 6.980 3.685 0.287
627W W 635 8.244 9.248 9.558
628W W 636 6.484 4.354 3.528
629W W 637 5.304 8.922 7.219
630W W 638 4.969 4.506 7.906
631W W 639 4.456 8.124 9.469
632W W 640 6.522 2.143 0.744
633W W 641 4.944 3.020 0.029
634W W 642 5.954 9.427 2.834
635W W 643 0.014 8.478 8.807
636W W 644 2.799 5.584 2.093
637W W 645 4.274 0.067 2.681
638W W 646 1.065 3.276 1.378
639W W 647 9.229 9.735 3.342
640W W 648 6.928 5.697 7.738
641W W 649 0.294 4.989 7.392
642W W 650 5.235 2.403 0.681
643W W 651 0.605 0.880 5.243
644W W 652 8.936 5.089 7.643
645W W 653 9.949 2.754 6.974
646W W 654 1.879 7.097 4.192
647W W 655 8.578 4.913 0.916
648W W 656 6.223 9.202 2.433
649W W 657 9.805 4.824 7.284
650W W 658 1.086 9.610 8.506
651W W 659 0.425 2.932 7.113
652W W 660 6.210 1.774 0.523
653W W 661 2.046 3.044 3.554
654W W 662 8.024 9.850 4.845
655W W 663 6.078 8.265 2.213
656W W 664 5.207 6.746 6.704
657W W 665 3.945 6.791 3.513
658W W 666 7.522 4.524 5.113
659W W 667 2.626 2.651 4.782
660W W 668 7.739 0.223 4.606
661W W 669 2.630 2.699 5.298
662W W 670 7.547 2.423 3.336
663W W 671 1.582 0.765 9.771
664W W 672 7.401 0.479 3.073
665W W 673 1.136 5.564 5.864
666W W 674 0.401 4.422 6.874
667W W 675 0.235 8.960 2.459
668W W 676 6.849 8.705 8.427
669W W 677 4.215 9.627 8.191
670W W 678 1.462 2.579 3.133
671W W 679 6.532 5.661 8.086
672W W 680 0.620 4.572 1.484
673W W 681 8.802 6.308 5.294
674W W 682 1.207 6.278 3.073
675W W 683 6.525 1.698 2.779
676W W 684 9.666 0.700 0.605
677W W 685 6.264 2.851 4.889
678W W 686 8.987 9.786 6.854
679W W 687 2.368 4.944 0.975
680W W 688 2.131 1.304 8.095
681W W 689 9.876 7.838 3.497
682W W 690 5.760 3.355 8.592
683W W 691 1.576 9.755 8.382
684W W 692 4.993 5.868 6.144
685W W 693 4.700 6.430 8.585
686W W 694 6.775 9.596 0.787
687W W 695 4.274 2.265 2.962
688W W 696 0.039 7.068 7.867
689W W 697 9.841 1.788 1.124
690W W 698 4.153 2.611 7.980
691W W 699 4.466 3.152 4.291
692W W 700 4.275 7.957 1.916
693W W 701 4.198 7.651 7.751
694W W 702 2.524 5.494 2.538
695W W 703 4.362 6.544 8.974
696W W 704 2.412 1.972 4.325
697W W 705 2.944 8.068 7.468
698W W 706 1.643 5.798 8.017
699W W 707 5.393 7.880 8.553
700W W 708 7.289 9.347 7.416
701W W 709 1.970 5.590 8.375
702W W 710 1.574 0.045 6.781
703W W 711 4.154 5.514 7.473
704W W 712 6.766 2.024 3.121
705W W 713 8.769 6.044 6.171
706W W 714 5.551 5.963 8.331
10.00000 10.00000 10.00000
714
1ALA BEP4 1 5.261 4.412 4.261
2ALA BEP4 2 5.065 4.353 4.501
3ALA BEP4 3 5.177 4.313 4.781
4ALA BEP4 4 4.980 4.269 5.018
5ALA BEP4 5 5.072 4.301 5.291
6ALA BEP4 6 4.954 4.328 5.554
7ARG BEP5 7 5.146 4.409 5.823
7ARG SEN0 8 4.931 4.607 5.967
7ARG SEQd 9 4.710 4.791 5.804
8ALA BEP4 10 5.340 4.892 5.778
9ALA BEP4 11 5.152 4.835 5.563
10ALA BEP4 12 5.013 4.802 5.380
11ALA BEP4 13 4.821 4.739 5.170
12ALA BEP4 14 4.957 4.755 4.882
13ALA BEP4 15 4.851 4.804 4.635
14ARG BEP5 16 4.964 4.835 4.361
14ARG SEN0 17 4.812 4.645 4.155
14ARG SEQd 18 4.941 4.565 3.863
15ALA BEP4 19 5.286 5.209 4.439
16ALA BEP4 20 5.180 5.221 4.697
17ALA BEP4 21 4.942 5.245 4.878
18ALA BEP4 22 4.907 5.243 5.131
19ALA BEP4 23 4.800 5.247 5.400
20ALA BEP4 24 4.992 5.284 5.636
21ARG BEP5 25 4.955 5.223 5.895
21ARG SEN0 26 5.104 5.378 6.121
21ARG SEQd 27 5.014 5.410 6.432
22ALA BEP4 28 4.775 5.725 5.695
23ALA BEP4 29 4.942 5.745 5.432
24ALA BEP4 30 4.893 5.738 5.161
25ALA BEP4 31 5.102 5.721 4.927
26ALA BEP4 32 4.979 5.697 4.643
27ALA BEP4 33 5.140 5.680 4.399
28ARG BEP5 34 5.041 5.616 4.111
28ARG SEN0 35 5.089 5.325 3.999
28ARG SEQd 36 4.863 5.102 3.936
29W W 37 3.630 9.353 3.462
30W W 38 3.023 0.681 2.124
31W W 39 8.421 1.650 4.588
32W W 40 8.786 5.562 7.498
33W W 41 3.093 3.871 6.040
34W W 42 0.272 5.765 2.772
35W W 43 0.558 7.041 1.079
36W W 44 4.704 3.154 5.747
37W W 45 9.840 6.069 1.277
38W W 46 3.598 9.807 4.983
39W W 47 7.358 4.915 0.538
40W W 48 8.015 1.224 8.107
41W W 49 5.203 4.387 2.301
42W W 50 8.101 5.218 4.406
43W W 51 1.527 1.036 0.220
44W W 52 8.524 4.634 6.996
45W W 53 9.926 5.121 8.992
46W W 54 3.440 6.977 5.961
47W W 55 9.288 5.730 7.469
48W W 56 7.078 6.653 4.355
49W W 57 1.233 6.846 8.418
50W W 58 6.971 5.606 8.682
51W W 59 3.042 1.905 2.016
52W W 60 5.527 7.158 6.682
53W W 61 7.288 2.044 3.081
54W W 62 5.236 6.462 2.769
55W W 63 1.923 3.317 3.120
56W W 64 2.378 9.598 7.839
57W W 65 9.947 2.049 2.636
58W W 66 2.562 5.363 3.264
59W W 67 6.859 9.066 7.300
60W W 68 9.055 4.449 0.442
61W W 69 5.100 6.145 5.713
62W W 70 7.953 0.906 3.104
63W W 71 1.304 2.816 1.505
64W W 72 9.431 8.629 7.508
65W W 73 9.827 1.004 8.258
66W W 74 2.614 8.244 6.530
67W W 75 3.028 2.444 5.032
68W W 76 1.005 8.897 1.843
69W W 77 5.874 6.769 6.730
70W W 78 4.630 5.465 1.976
71W W 79 4.135 7.811 8.247
72W W 80 6.139 3.397 2.473
73W W 81 7.542 3.389 6.444
74W W 82 0.895 7.115 4.316
75W W 83 7.577 6.077 8.881
76W W 84 6.017 8.177 7.971
77W W 85 7.646 3.342 2.511
78W W 86 0.824 6.609 6.349
79W W 87 8.285 2.391 2.049
80W W 88 0.173 9.229 0.773
81W W 89 8.062 0.841 1.223
82W W 90 2.882 2.105 4.135
83W W 91 9.509 9.897 6.859
84W W 92 9.730 3.600 1.081
85W W 93 3.288 7.996 0.072
86W W 94 6.028 3.741 7.212
87W W 95 7.999 4.187 3.755
88W W 96 7.550 0.020 3.286
89W W 97 3.041 4.566 6.201
90W W 98 8.446 2.888 2.053
91W W 99 7.255 6.449 3.904
92W W 100 8.941 4.535 0.948
93W W 101 9.009 4.943 0.617
94W W 102 8.259 9.255 5.892
95W W 103 7.155 9.883 0.560
96W W 104 7.207 1.593 4.186
97W W 105 5.052 2.390 5.865
98W W 106 1.261 4.611 2.069
99W W 107 2.611 7.877 7.823
100W W 108 8.488 5.192 7.896
101W W 109 8.632 9.497 7.133
102W W 110 5.044 6.111 8.345
103W W 111 0.610 6.287 8.749
104W W 112 1.480 9.509 5.612
105W W 113 8.703 9.854 5.159
106W W 114 1.754 7.583 0.811
107W W 115 4.980 1.964 5.561
108W W 116 0.157 5.408 9.371
109W W 117 8.658 1.387 2.740
110W W 118 4.044 5.724 0.359
111W W 119 5.190 2.600 1.169
112W W 120 9.623 2.970 2.943
113W W 121 3.211 5.701 1.782
114W W 122 5.163 9.088 8.991
115W W 123 6.836 0.860 8.932
116W W 124 5.696 9.175 2.461
117W W 125 0.671 2.019 4.618
118W W 126 8.384 8.433 9.911
119W W 127 0.756 5.528 3.634
120W W 128 8.197 1.978 6.055
121W W 129 8.474 9.562 5.524
122W W 130 9.158 8.395 1.639
123W W 131 3.764 2.945 7.865
124W W 132 2.953 1.459 3.717
125W W 133 7.477 4.172 3.484
126W W 134 5.937 3.517 1.511
127W W 135 2.390 0.209 3.504
128W W 136 5.555 6.771 6.316
129W W 137 7.091 5.776 3.139
130W W 138 1.419 9.221 1.796
131W W 139 8.192 9.616 7.406
132W W 140 7.579 2.877 7.403
133W W 141 7.716 5.554 4.270
134W W 142 6.698 5.754 5.117
135W W 143 5.533 8.747 8.831
136W W 144 4.567 4.531 9.490
137W W 145 8.124 0.733 9.455
138W W 146 1.801 2.824 8.749
139W W 147 3.324 6.974 0.042
140W W 148 2.951 1.513 1.667
141W W 149 1.566 2.058 1.394
142W W 150 7.153 5.651 2.630
143W W 151 7.750 0.212 5.130
144W W 152 6.257 1.687 6.385
145W W 153 3.992 3.209 4.064
146W W 154 3.953 4.450 5.180
147W W 155 4.548 6.928 8.663
148W W 156 3.273 1.903 1.549
149W W 157 8.078 9.537 7.913
150W W 158 3.856 2.113 0.804
151W W 159 8.287 3.258 6.753
152W W 160 4.650 0.086 3.232
153W W 161 9.881 5.635 9.757
154W W 162 2.780 2.168 4.648
155W W 163 2.909 3.389 5.904
156W W 164 5.236 0.418 4.586
157W W 165 5.338 5.441 5.293
158W W 166 8.896 1.041 3.703
159W W 167 3.041 2.343 1.388
160W W 168 9.010 4.524 6.815
161W W 169 9.553 1.440 8.166
162W W 170 7.941 7.263 9.404
163W W 171 2.546 2.479 4.293
164W W 172 1.223 9.364 5.177
165W W 173 3.166 9.226 9.822
166W W 174 1.862 5.953 0.832
167W W 175 0.351 3.602 9.750
168W W 176 8.761 9.171 9.485
169W W 177 8.244 1.309 7.640
170W W 178 6.361 3.338 1.770
171W W 179 4.609 1.629 2.306
172W W 180 9.347 4.873 7.027
173W W 181 5.539 6.486 7.008
174W W 182 8.593 9.460 9.892
175W W 183 2.690 1.229 5.238
176W W 184 4.938 5.275 0.611
177W W 185 7.558 3.653 8.616
178W W 186 0.921 2.828 1.143
179W W 187 3.658 8.789 2.046
180W W 188 9.560 0.645 8.528
181W W 189 1.257 2.679 3.608
182W W 190 0.579 2.160 2.049
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187W W 195 7.350 0.397 3.591
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190W W 198 5.877 0.152 2.385
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193W W 201 6.904 5.295 8.077
194W W 202 0.068 1.572 6.434
195W W 203 2.953 1.877 1.140
196W W 204 5.401 4.748 4.624
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198W W 206 4.369 1.024 4.083
199W W 207 5.892 8.010 8.451
200W W 208 4.677 5.027 6.277
201W W 209 7.091 9.376 0.432
202W W 210 1.398 8.722 9.788
203W W 211 7.068 3.504 8.491
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205W W 213 4.567 5.263 7.683
206W W 214 6.963 5.506 9.206
207W W 215 4.584 2.154 5.852
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213W W 221 1.241 0.100 4.001
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215W W 223 4.595 8.715 4.358
216W W 224 2.962 2.392 5.551
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219W W 227 0.178 7.359 7.452
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221W W 229 6.869 7.196 8.568
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223W W 231 5.570 1.632 7.854
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225W W 233 2.263 2.294 4.704
226W W 234 8.477 2.594 1.610
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250W W 258 4.065 9.458 7.714
251W W 259 4.498 9.716 0.382
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283W W 291 4.567 8.015 4.695
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288W W 296 1.841 0.901 7.917
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290W W 298 4.711 2.127 3.224
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292W W 300 8.125 9.911 5.349
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294W W 302 3.274 0.557 1.682
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296W W 304 0.023 6.400 0.909
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301W W 309 4.281 8.819 3.945
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304W W 312 2.475 5.171 2.123
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316W W 324 3.080 3.532 2.491
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325W W 333 2.570 6.260 4.799
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331W W 339 2.680 3.662 6.291
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334W W 342 0.254 1.052 2.718
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336W W 344 3.721 5.485 5.068
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339W W 347 0.024 3.991 0.881
340W W 348 2.775 8.063 3.152
341W W 349 7.429 7.127 9.435
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344W W 352 2.261 7.208 1.309
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500W W 508 1.665 7.961 0.449
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539W W 547 7.647 0.844 9.652
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705W W 713 8.769 6.044 6.171
706W W 714 5.551 5.963 8.331
10.00000 10.00000 10.00000
A6R1S.top
Warning: Spoiler!
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;
; Example topology file for MARTINI 2.0
;
; First include the file containing all particle definitions,
; the interaction matrix, plus the topology for water.
#include "martini_v2.1.itp"
; Then include the file(s) containing the topologies of other
; molecules present in your system.
#include "martini_v2.1_aminoacids.itp"
#include "A6R.itp"
; Define a name for your system
[ system ]
A6R
; Define the composition of your system
; The molecule names should correspond to those defined in the itp file(s).
[ molecules ]
A6R 4
W 678
; Example topology file for MARTINI 2.0
;
; First include the file containing all particle definitions,
; the interaction matrix, plus the topology for water.
#include "martini_v2.1.itp"
; Then include the file(s) containing the topologies of other
; molecules present in your system.
#include "martini_v2.1_aminoacids.itp"
#include "A6R.itp"
; Define a name for your system
[ system ]
A6R
; Define the composition of your system
; The molecule names should correspond to those defined in the itp file(s).
[ molecules ]
A6R 4
W 678
index.ndx
Warning: Spoiler!
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[ Click to hide ]
[ System ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
211 212 213 214 215 216 217 218 219 220 221 222 223 224 225
226 227 228 229 230 231 232 233 234 235 236 237 238 239 240
241 242 243 244 245 246 247 248 249 250 251 252 253 254 255
256 257 258 259 260 261 262 263 264 265 266 267 268 269 270
271 272 273 274 275 276 277 278 279 280 281 282 283 284 285
286 287 288 289 290 291 292 293 294 295 296 297 298 299 300
301 302 303 304 305 306 307 308 309 310 311 312 313 314 315
316 317 318 319 320 321 322 323 324 325 326 327 328 329 330
331 332 333 334 335 336 337 338 339 340 341 342 343 344 345
346 347 348 349 350 351 352 353 354 355 356 357 358 359 360
361 362 363 364 365 366 367 368 369 370 371 372 373 374 375
376 377 378 379 380 381 382 383 384 385 386 387 388 389 390
391 392 393 394 395 396 397 398 399 400 401 402 403 404 405
406 407 408 409 410 411 412 413 414 415 416 417 418 419 420
421 422 423 424 425 426 427 428 429 430 431 432 433 434 435
436 437 438 439 440 441 442 443 444 445 446 447 448 449 450
451 452 453 454 455 456 457 458 459 460 461 462 463 464 465
466 467 468 469 470 471 472 473 474 475 476 477 478 479 480
481 482 483 484 485 486 487 488 489 490 491 492 493 494 495
496 497 498 499 500 501 502 503 504 505 506 507 508 509 510
511 512 513 514 515 516 517 518 519 520 521 522 523 524 525
526 527 528 529 530 531 532 533 534 535 536 537 538 539 540
541 542 543 544 545 546 547 548 549 550 551 552 553 554 555
556 557 558 559 560 561 562 563 564 565 566 567 568 569 570
571 572 573 574 575 576 577 578 579 580 581 582 583 584 585
586 587 588 589 590 591 592 593 594 595 596 597 598 599 600
601 602 603 604 605 606 607 608 609 610 611 612 613 614 615
616 617 618 619 620 621 622 623 624 625 626 627 628 629 630
631 632 633 634 635 636 637 638 639 640 641 642 643 644 645
646 647 648 649 650 651 652 653 654 655 656 657 658 659 660
661 662 663 664 665 666 667 668 669 670 671 672 673 674 675
676 677 678 679 680 681 682 683 684 685 686 687 688 689 690
691 692 693 694 695 696 697 698 699 700 701 702 703 704 705
706 707 708 709 710 711 712 713 714
[ A6R ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36
[ W ]
37 38 39 40 41 42 43 44 45 46 47 48 49 50 51
52 53 54 55 56 57 58 59 60 61 62 63 64 65 66
67 68 69 70 71 72 73 74 75 76 77 78 79 80 81
82 83 84 85 86 87 88 89 90 91 92 93 94 95 96
97 98 99 100 101 102 103 104 105 106 107 108 109 110 111
112 113 114 115 116 117 118 119 120 121 122 123 124 125 126
127 128 129 130 131 132 133 134 135 136 137 138 139 140 141
142 143 144 145 146 147 148 149 150 151 152 153 154 155 156
157 158 159 160 161 162 163 164 165 166 167 168 169 170 171
172 173 174 175 176 177 178 179 180 181 182 183 184 185 186
187 188 189 190 191 192 193 194 195 196 197 198 199 200 201
202 203 204 205 206 207 208 209 210 211 212 213 214 215 216
217 218 219 220 221 222 223 224 225 226 227 228 229 230 231
232 233 234 235 236 237 238 239 240 241 242 243 244 245 246
247 248 249 250 251 252 253 254 255 256 257 258 259 260 261
262 263 264 265 266 267 268 269 270 271 272 273 274 275 276
277 278 279 280 281 282 283 284 285 286 287 288 289 290 291
292 293 294 295 296 297 298 299 300 301 302 303 304 305 306
307 308 309 310 311 312 313 314 315 316 317 318 319 320 321
322 323 324 325 326 327 328 329 330 331 332 333 334 335 336
337 338 339 340 341 342 343 344 345 346 347 348 349 350 351
352 353 354 355 356 357 358 359 360 361 362 363 364 365 366
367 368 369 370 371 372 373 374 375 376 377 378 379 380 381
382 383 384 385 386 387 388 389 390 391 392 393 394 395 396
397 398 399 400 401 402 403 404 405 406 407 408 409 410 411
412 413 414 415 416 417 418 419 420 421 422 423 424 425 426
427 428 429 430 431 432 433 434 435 436 437 438 439 440 441
442 443 444 445 446 447 448 449 450 451 452 453 454 455 456
457 458 459 460 461 462 463 464 465 466 467 468 469 470 471
472 473 474 475 476 477 478 479 480 481 482 483 484 485 486
487 488 489 490 491 492 493 494 495 496 497 498 499 500 501
502 503 504 505 506 507 508 509 510 511 512 513 514 515 516
517 518 519 520 521 522 523 524 525 526 527 528 529 530 531
532 533 534 535 536 537 538 539 540 541 542 543 544 545 546
547 548 549 550 551 552 553 554 555 556 557 558 559 560 561
562 563 564 565 566 567 568 569 570 571 572 573 574 575 576
577 578 579 580 581 582 583 584 585 586 587 588 589 590 591
592 593 594 595 596 597 598 599 600 601 602 603 604 605 606
607 608 609 610 611 612 613 614 615 616 617 618 619 620 621
622 623 624 625 626 627 628 629 630 631 632 633 634 635 636
637 638 639 640 641 642 643 644 645 646 647 648 649 650 651
652 653 654 655 656 657 658 659 660 661 662 663 664 665 666
667 668 669 670 671 672 673 674 675 676 677 678 679 680 681
682 683 684 685 686 687 688 689 690 691 692 693 694 695 696
697 698 699 700 701 702 703 704 705 706 707 708 709 710 711
712 713 714
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
211 212 213 214 215 216 217 218 219 220 221 222 223 224 225
226 227 228 229 230 231 232 233 234 235 236 237 238 239 240
241 242 243 244 245 246 247 248 249 250 251 252 253 254 255
256 257 258 259 260 261 262 263 264 265 266 267 268 269 270
271 272 273 274 275 276 277 278 279 280 281 282 283 284 285
286 287 288 289 290 291 292 293 294 295 296 297 298 299 300
301 302 303 304 305 306 307 308 309 310 311 312 313 314 315
316 317 318 319 320 321 322 323 324 325 326 327 328 329 330
331 332 333 334 335 336 337 338 339 340 341 342 343 344 345
346 347 348 349 350 351 352 353 354 355 356 357 358 359 360
361 362 363 364 365 366 367 368 369 370 371 372 373 374 375
376 377 378 379 380 381 382 383 384 385 386 387 388 389 390
391 392 393 394 395 396 397 398 399 400 401 402 403 404 405
406 407 408 409 410 411 412 413 414 415 416 417 418 419 420
421 422 423 424 425 426 427 428 429 430 431 432 433 434 435
436 437 438 439 440 441 442 443 444 445 446 447 448 449 450
451 452 453 454 455 456 457 458 459 460 461 462 463 464 465
466 467 468 469 470 471 472 473 474 475 476 477 478 479 480
481 482 483 484 485 486 487 488 489 490 491 492 493 494 495
496 497 498 499 500 501 502 503 504 505 506 507 508 509 510
511 512 513 514 515 516 517 518 519 520 521 522 523 524 525
526 527 528 529 530 531 532 533 534 535 536 537 538 539 540
541 542 543 544 545 546 547 548 549 550 551 552 553 554 555
556 557 558 559 560 561 562 563 564 565 566 567 568 569 570
571 572 573 574 575 576 577 578 579 580 581 582 583 584 585
586 587 588 589 590 591 592 593 594 595 596 597 598 599 600
601 602 603 604 605 606 607 608 609 610 611 612 613 614 615
616 617 618 619 620 621 622 623 624 625 626 627 628 629 630
631 632 633 634 635 636 637 638 639 640 641 642 643 644 645
646 647 648 649 650 651 652 653 654 655 656 657 658 659 660
661 662 663 664 665 666 667 668 669 670 671 672 673 674 675
676 677 678 679 680 681 682 683 684 685 686 687 688 689 690
691 692 693 694 695 696 697 698 699 700 701 702 703 704 705
706 707 708 709 710 711 712 713 714
[ A6R ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36
[ W ]
37 38 39 40 41 42 43 44 45 46 47 48 49 50 51
52 53 54 55 56 57 58 59 60 61 62 63 64 65 66
67 68 69 70 71 72 73 74 75 76 77 78 79 80 81
82 83 84 85 86 87 88 89 90 91 92 93 94 95 96
97 98 99 100 101 102 103 104 105 106 107 108 109 110 111
112 113 114 115 116 117 118 119 120 121 122 123 124 125 126
127 128 129 130 131 132 133 134 135 136 137 138 139 140 141
142 143 144 145 146 147 148 149 150 151 152 153 154 155 156
157 158 159 160 161 162 163 164 165 166 167 168 169 170 171
172 173 174 175 176 177 178 179 180 181 182 183 184 185 186
187 188 189 190 191 192 193 194 195 196 197 198 199 200 201
202 203 204 205 206 207 208 209 210 211 212 213 214 215 216
217 218 219 220 221 222 223 224 225 226 227 228 229 230 231
232 233 234 235 236 237 238 239 240 241 242 243 244 245 246
247 248 249 250 251 252 253 254 255 256 257 258 259 260 261
262 263 264 265 266 267 268 269 270 271 272 273 274 275 276
277 278 279 280 281 282 283 284 285 286 287 288 289 290 291
292 293 294 295 296 297 298 299 300 301 302 303 304 305 306
307 308 309 310 311 312 313 314 315 316 317 318 319 320 321
322 323 324 325 326 327 328 329 330 331 332 333 334 335 336
337 338 339 340 341 342 343 344 345 346 347 348 349 350 351
352 353 354 355 356 357 358 359 360 361 362 363 364 365 366
367 368 369 370 371 372 373 374 375 376 377 378 379 380 381
382 383 384 385 386 387 388 389 390 391 392 393 394 395 396
397 398 399 400 401 402 403 404 405 406 407 408 409 410 411
412 413 414 415 416 417 418 419 420 421 422 423 424 425 426
427 428 429 430 431 432 433 434 435 436 437 438 439 440 441
442 443 444 445 446 447 448 449 450 451 452 453 454 455 456
457 458 459 460 461 462 463 464 465 466 467 468 469 470 471
472 473 474 475 476 477 478 479 480 481 482 483 484 485 486
487 488 489 490 491 492 493 494 495 496 497 498 499 500 501
502 503 504 505 506 507 508 509 510 511 512 513 514 515 516
517 518 519 520 521 522 523 524 525 526 527 528 529 530 531
532 533 534 535 536 537 538 539 540 541 542 543 544 545 546
547 548 549 550 551 552 553 554 555 556 557 558 559 560 561
562 563 564 565 566 567 568 569 570 571 572 573 574 575 576
577 578 579 580 581 582 583 584 585 586 587 588 589 590 591
592 593 594 595 596 597 598 599 600 601 602 603 604 605 606
607 608 609 610 611 612 613 614 615 616 617 618 619 620 621
622 623 624 625 626 627 628 629 630 631 632 633 634 635 636
637 638 639 640 641 642 643 644 645 646 647 648 649 650 651
652 653 654 655 656 657 658 659 660 661 662 663 664 665 666
667 668 669 670 671 672 673 674 675 676 677 678 679 680 681
682 683 684 685 686 687 688 689 690 691 692 693 694 695 696
697 698 699 700 701 702 703 704 705 706 707 708 709 710 711
712 713 714
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- djurre
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11 years 3 months ago #1373
by djurre
Replied by djurre on topic Segmentation Fault with mdrun
You didn't include the itp file, so I couldn't really test anything. The water in gro file looks strangly spread out (very low density). And since you are not using pressure coupling, strange things might be happening there?
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- AlexC
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- Posts: 6
11 years 3 months ago #1374
by AlexC
Replied by AlexC on topic Segmentation Fault with mdrun
We now think that the error is due to multiple small errors in files, commands and scripts that we created and are in the process of fixing, however feel free to have a go with the attatched .itp file.
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;;; SJM topology ffsjm
;;; Generated by seq2cgtop_0.9.pl written by Senthil K. Kandasamy
;;; SEQ: AAAAAAR
;;; SSD: EEEEEEE
;;; Total Number of Amino Acid Residues: 7
[moleculetype]
;molname exclusions
A6R 1
[atoms]
1 P4 1 ALA BEP4 1 1.000
2 P4 2 ALA BEP4 2 0.000
3 P4 3 ALA BEP4 3 0.000
4 P4 4 ALA BEP4 4 0.000
5 P4 5 ALA BEP4 5 0.000
6 P4 6 ALA BEP4 6 0.000
7 P5 7 ARG BEP5 7 -1.00
8 N0 7 ARG SEN0 8 0.000
9 Qd 7 ARG SEQd 9 1.000
[ bonds ]
1 2 1 0.350 1250
2 3 1 0.350 1250
3 4 1 0.350 1250
4 5 1 0.350 1250
5 6 1 0.350 1250
6 7 1 0.350 1250
7 8 1 0.330 5000
8 9 1 0.340 5000
[angles]
1 2 3 2 134.00 25
2 3 4 2 134.00 25
3 4 5 2 134.00 25
4 5 6 2 134.00 25
5 6 7 2 134.00 25
6 7 8 2 100.00 25
7 8 9 2 180.00 25
[dihedrals]
1 2 3 4 2 180.00 10
2 3 4 5 2 180.00 10
3 4 5 6 2 180.00 10
4 5 6 7 2 180.00 10
;;; Generated by seq2cgtop_0.9.pl written by Senthil K. Kandasamy
;;; SEQ: AAAAAAR
;;; SSD: EEEEEEE
;;; Total Number of Amino Acid Residues: 7
[moleculetype]
;molname exclusions
A6R 1
[atoms]
1 P4 1 ALA BEP4 1 1.000
2 P4 2 ALA BEP4 2 0.000
3 P4 3 ALA BEP4 3 0.000
4 P4 4 ALA BEP4 4 0.000
5 P4 5 ALA BEP4 5 0.000
6 P4 6 ALA BEP4 6 0.000
7 P5 7 ARG BEP5 7 -1.00
8 N0 7 ARG SEN0 8 0.000
9 Qd 7 ARG SEQd 9 1.000
[ bonds ]
1 2 1 0.350 1250
2 3 1 0.350 1250
3 4 1 0.350 1250
4 5 1 0.350 1250
5 6 1 0.350 1250
6 7 1 0.350 1250
7 8 1 0.330 5000
8 9 1 0.340 5000
[angles]
1 2 3 2 134.00 25
2 3 4 2 134.00 25
3 4 5 2 134.00 25
4 5 6 2 134.00 25
5 6 7 2 134.00 25
6 7 8 2 100.00 25
7 8 9 2 180.00 25
[dihedrals]
1 2 3 4 2 180.00 10
2 3 4 5 2 180.00 10
3 4 5 6 2 180.00 10
4 5 6 7 2 180.00 10
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