CHARMM> crystal define Monoclinic 5.3214 11.5689 17.0398 90 97.22 90
Crystal Parameters : Crystal Type = MONO
A = 5.32140 B = 11.56890 C = 17.03980
Alpha = 90.00000 Beta = 97.22000 Gamma = 90.00000
CHARMM> crystal build noper 0 cutoff 30
XBUILD> Building all transformations with a minimum atom-atom
contact distance of less than 30.00 Angstroms.
Range of Grid Search for Transformation 1 :
Lattice Vector A -8 TO 8
Lattice Vector B -4 TO 4
Lattice Vector C -3 TO 3
The number of transformations generated = 328
Number Symop A B C Distance
1 1 -6 -1 -2 29.6412
2 1 -6 0 -2 29.6412
3 1 -5 -1 -2 25.4876
4 1 -5 0 -2 25.4876
5 1 -4 -2 -2 26.9405
6 1 -4 -1 -2 21.8465
7 1 -4 0 -2 21.8465
8 1 -4 1 -2 26.9405
9 1 -3 -2 -2 24.3493
10 1 -3 -1 -2 19.0146
11 1 -3 0 -2 19.0146
12 1 -3 1 -2 24.3493
13 1 -2 -3 -2 28.8510
14 1 -2 -2 -2 22.7294
15 1 -2 -1 -2 17.3918
16 1 -2 0 -2 17.3918
17 1 -2 1 -2 22.7294
18 1 -2 2 -2 28.8510
19 1 -1 -3 -2 27.8205
20 1 -1 -2 -2 21.2888
21 1 -1 -1 -2 17.3214
22 1 -1 0 -2 17.3214
23 1 -1 1 -2 21.2888
24 1 -1 2 -2 27.8205
25 1 0 -3 -2 27.6569
26 1 0 -2 -2 20.9570
27 1 0 -1 -2 18.1661
28 1 0 0 -2 18.1661
29 1 0 1 -2 20.9570
30 1 0 2 -2 27.6569
31 1 -6 -2 -1 29.9740
32 1 -6 -1 -1 26.2629
33 1 -6 0 -1 26.8131
34 1 -6 1 -1 28.2613
35 1 -5 -2 -1 25.4604
36 1 -5 -1 -1 21.4173
37 1 -5 0 -1 21.7779
38 1 -5 1 -1 23.9840
39 1 -5 2 -1 28.3050
40 1 -4 -3 -1 28.2539
41 1 -4 -2 -1 21.2762
42 1 -4 -1 -1 16.7253
43 1 -4 0 -1 16.7253
44 1 -4 1 -1 20.1875
45 1 -4 2 -1 24.7010
46 1 -3 -3 -1 24.5727
47 1 -3 -2 -1 17.5026
48 1 -3 -1 -1 11.6903
49 1 -3 0 -1 11.6903
50 1 -3 1 -1 16.6754
51 1 -3 2 -1 21.8087
52 1 -2 -3 -1 21.5868
53 1 -2 -2 -1 12.9813
54 1 -2 -1 -1 6.8752
55 1 -2 0 -1 6.8752
56 1 -2 1 -1 12.6262
57 1 -2 2 -1 19.9433
58 1 -2 3 -1 28.7933
59 1 -1 -3 -1 19.6163
60 1 -1 -2 -1 9.3446
61 1 -1 -1 -1 2.3977
62 1 -1 0 -1 2.3977
63 1 -1 1 -1 9.3446
64 1 -1 2 -1 19.4032
65 1 -1 3 -1 28.4218
66 1 0 -3 -1 18.9800
67 1 0 -2 -1 7.9223
68 1 0 -1 -1 1.5608
69 1 0 0 -1 1.5608
70 1 0 1 -1 7.9223
71 1 0 2 -1 18.8348
72 1 0 3 -1 28.2227
73 1 -6 -1 0 25.8814
74 1 -6 0 0 25.5000
75 1 -6 1 0 25.7993
76 1 -6 2 0 29.0861
77 1 -5 -2 0 25.4615
78 1 -5 -1 0 20.6754
79 1 -5 0 0 20.5455
80 1 -5 1 0 20.9781
81 1 -5 2 0 24.5955
82 1 -4 -2 0 21.2400
83 1 -4 -1 0 15.5478
84 1 -4 0 0 15.6571
85 1 -4 1 0 15.9549
86 1 -4 2 0 20.5064
87 1 -4 3 0 27.0465
88 1 -3 -3 0 26.8107
89 1 -3 -2 0 17.6209
90 1 -3 -1 0 10.6127
91 1 -3 0 0 10.5683
92 1 -3 1 0 10.8976
93 1 -3 2 0 16.6492
94 1 -3 3 0 23.8719
95 1 -2 -3 0 24.0245
96 1 -2 -2 0 14.7386
97 1 -2 -1 0 5.9059
98 1 -2 0 0 5.9051
99 1 -2 1 0 5.9059
100 1 -2 2 0 13.1219
101 1 -2 3 0 21.5605
102 1 -1 -3 0 22.1274
103 1 -1 -2 0 11.7812
104 1 -1 -1 0 2.4304
105 1 -1 0 0 2.4386
106 1 -1 1 0 2.7631
107 1 -1 2 0 11.1268
108 1 -1 3 0 20.4077
109 1 0 -3 0 20.6090
110 1 0 -2 0 10.5085
111 1 0 -1 0 2.5236
112 1 0 1 0 2.5236
113 1 0 2 0 10.5085
114 1 0 3 0 20.6090
115 1 -6 -1 1 28.8273
116 1 -6 0 1 25.9660
117 1 -6 1 1 25.9660
118 1 -6 2 1 29.2908
119 1 -5 -2 1 28.6564
120 1 -5 -1 1 23.9463
121 1 -5 0 1 20.7577
122 1 -5 1 1 20.7577
123 1 -5 2 1 24.4195
124 1 -4 -2 1 24.9045
125 1 -4 -1 1 19.2994
126 1 -4 0 1 15.6259
127 1 -4 1 1 15.6259
128 1 -4 2 1 19.7814
129 1 -4 3 1 27.2796
130 1 -3 -2 1 21.8154
131 1 -3 -1 1 15.1044
132 1 -3 0 1 10.6813
133 1 -3 1 1 10.6813
134 1 -3 2 1 15.5864
135 1 -3 3 1 24.4091
136 1 -2 -3 1 29.6823
137 1 -2 -2 1 19.7033
138 1 -2 -1 1 11.6937
139 1 -2 0 1 6.3755
140 1 -2 1 1 6.3755
141 1 -2 2 1 12.2963
142 1 -2 3 1 21.9324
143 1 -1 -3 1 28.7100
144 1 -1 -2 1 18.6003
145 1 -1 -1 1 9.5354
146 1 -1 0 1 4.4893
147 1 -1 1 1 4.4893
148 1 -1 2 1 9.5354
149 1 -1 3 1 19.8070
150 1 0 -3 1 28.2227
151 1 0 -2 1 18.8348
152 1 0 -1 1 7.9223
153 1 0 0 1 1.5608
154 1 0 1 1 1.5608
155 1 0 2 1 7.9223
156 1 0 3 1 18.9800
157 1 -4 0 2 26.6130
158 1 -4 1 2 26.6130
159 1 -3 -1 2 26.8944
160 1 -3 0 2 23.5665
161 1 -3 1 2 23.5665
162 1 -3 2 2 26.8944
163 1 -2 -2 2 29.9612
164 1 -2 -1 2 23.9159
165 1 -2 0 2 21.4277
166 1 -2 1 2 21.4277
167 1 -2 2 2 23.9159
168 1 -2 3 2 29.9612
169 1 -1 -2 2 28.3368
170 1 -1 -1 2 21.8464
171 1 -1 0 2 19.4475
172 1 -1 1 2 19.4475
173 1 -1 2 2 21.8464
174 1 -1 3 2 28.3368
175 1 0 -2 2 27.6569
176 1 0 -1 2 20.9570
177 1 0 0 2 18.1661
178 1 0 1 2 18.1661
179 1 0 2 2 20.9570
180 1 0 3 2 27.6569
181 1 6 1 2 29.6412
182 1 6 0 2 29.6412
183 1 5 1 2 25.4876
184 1 5 0 2 25.4876
185 1 4 2 2 26.9405
186 1 4 1 2 21.8465
187 1 4 0 2 21.8465
188 1 4 -1 2 26.9405
189 1 3 2 2 24.3493
190 1 3 1 2 19.0146
191 1 3 0 2 19.0146
192 1 3 -1 2 24.3493
193 1 2 3 2 28.8510
194 1 2 2 2 22.7294
195 1 2 1 2 17.3918
196 1 2 0 2 17.3918
197 1 2 -1 2 22.7294
198 1 2 -2 2 28.8510
199 1 1 3 2 27.8205
200 1 1 2 2 21.2888
201 1 1 1 2 17.3214
202 1 1 0 2 17.3214
203 1 1 -1 2 21.2888
204 1 1 -2 2 27.8205
205 1 6 2 1 29.9740
206 1 6 1 1 26.2629
207 1 6 0 1 26.8131
208 1 6 -1 1 28.2613
209 1 5 2 1 25.4604
210 1 5 1 1 21.4173
211 1 5 0 1 21.7779
212 1 5 -1 1 23.9840
213 1 5 -2 1 28.3050
214 1 4 3 1 28.2539
215 1 4 2 1 21.2762
216 1 4 1 1 16.7253
217 1 4 0 1 16.7253
218 1 4 -1 1 20.1875
219 1 4 -2 1 24.7010
220 1 3 3 1 24.5727
221 1 3 2 1 17.5026
222 1 3 1 1 11.6903
223 1 3 0 1 11.6903
224 1 3 -1 1 16.6754
225 1 3 -2 1 21.8087
226 1 2 3 1 21.5868
227 1 2 2 1 12.9813
228 1 2 1 1 6.8752
229 1 2 0 1 6.8752
230 1 2 -1 1 12.6262
231 1 2 -2 1 19.9433
232 1 2 -3 1 28.7933
233 1 1 3 1 19.6163
234 1 1 2 1 9.3446
235 1 1 1 1 2.3977
236 1 1 0 1 2.3977
237 1 1 -1 1 9.3446
238 1 1 -2 1 19.4032
239 1 1 -3 1 28.4218
240 1 6 1 0 25.8814
241 1 6 0 0 25.5000
242 1 6 -1 0 25.7993
243 1 6 -2 0 29.0861
244 1 5 2 0 25.4615
245 1 5 1 0 20.6754
246 1 5 0 0 20.5455
247 1 5 -1 0 20.9781
248 1 5 -2 0 24.5955
249 1 4 2 0 21.2400
250 1 4 1 0 15.5478
251 1 4 0 0 15.6571
252 1 4 -1 0 15.9549
253 1 4 -2 0 20.5064
254 1 4 -3 0 27.0465
255 1 3 3 0 26.8107
256 1 3 2 0 17.6209
257 1 3 1 0 10.6127
258 1 3 0 0 10.5683
259 1 3 -1 0 10.8976
260 1 3 -2 0 16.6492
261 1 3 -3 0 23.8719
262 1 2 3 0 24.0245
263 1 2 2 0 14.7386
264 1 2 1 0 5.9059
265 1 2 0 0 5.9051
266 1 2 -1 0 5.9059
267 1 2 -2 0 13.1219
268 1 2 -3 0 21.5605
269 1 1 3 0 22.1274
270 1 1 2 0 11.7812
271 1 1 1 0 2.4304
272 1 1 0 0 2.4386
273 1 1 -1 0 2.7631
274 1 1 -2 0 11.1268
275 1 1 -3 0 20.4077
276 1 6 1 -1 28.8273
277 1 6 0 -1 25.9660
278 1 6 -1 -1 25.9660
279 1 6 -2 -1 29.2908
280 1 5 2 -1 28.6564
281 1 5 1 -1 23.9463
282 1 5 0 -1 20.7577
283 1 5 -1 -1 20.7577
284 1 5 -2 -1 24.4195
285 1 4 2 -1 24.9045
286 1 4 1 -1 19.2994
287 1 4 0 -1 15.6259
288 1 4 -1 -1 15.6259
289 1 4 -2 -1 19.7814
290 1 4 -3 -1 27.2796
291 1 3 2 -1 21.8154
292 1 3 1 -1 15.1044
293 1 3 0 -1 10.6813
294 1 3 -1 -1 10.6813
295 1 3 -2 -1 15.5864
296 1 3 -3 -1 24.4091
297 1 2 3 -1 29.6823
298 1 2 2 -1 19.7033
299 1 2 1 -1 11.6937
300 1 2 0 -1 6.3755
301 1 2 -1 -1 6.3755
302 1 2 -2 -1 12.2963
303 1 2 -3 -1 21.9324
304 1 1 3 -1 28.7100
305 1 1 2 -1 18.6003
306 1 1 1 -1 9.5354
307 1 1 0 -1 4.4893
308 1 1 -1 -1 4.4893
309 1 1 -2 -1 9.5354
310 1 1 -3 -1 19.8070
311 1 4 0 -2 26.6130
312 1 4 -1 -2 26.6130
313 1 3 1 -2 26.8944
314 1 3 0 -2 23.5665
315 1 3 -1 -2 23.5665
316 1 3 -2 -2 26.8944
317 1 2 2 -2 29.9612
318 1 2 1 -2 23.9159
319 1 2 0 -2 21.4277
320 1 2 -1 -2 21.4277
321 1 2 -2 -2 23.9159
322 1 2 -3 -2 29.9612
323 1 1 2 -2 28.3368
324 1 1 1 -2 21.8464
325 1 1 0 -2 19.4475
326 1 1 -1 -2 19.4475
327 1 1 -2 -2 21.8464
328 1 1 -3 -2 28.3368
THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET
328 Transformations have been processed.
CHARMM> !(-X, Y+1/2,-Z)
CHARMM>
CHARMM> image BYSEgments xcen 0.0 ycen 0.0 zcen 0.0 select all end
SELRPN> 194 atoms have been selected out of 194
IMAGE CENTERING ON FOR SOME ATOMS
CHARMM> !update inbfrq -1 imgfrq -1 ihbfrq 0 -
CHARMM> !ewald pmewald kappa 0.34 fftx 64 ffty 64 fftz 64 order 6 lrc -
CHARMM> !@eatom @etrun @vatom @vtrun cutnb @cutnb ctonnb @ctonnb ctofnb @ctofnb -
CHARMM> !cutim @cutim
CHARMM>
CHARMM> nbonds atom vatom switch vswitch bycb -
CHARMM> ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 LRC -
CHARMM> inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 -
CHARMM> ewald pmew fftx 64 ffty 64 fftz 64 kappa .34 spline order 6
SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
: updating the image atom lists and remapping
Transformation Atoms Groups Residues Min-Distance
1 C001 has 0 0 0 28.06
2 C002 has 0 0 0 28.06
3 C003 has 0 0 0 23.89
4 C004 has 0 0 0 23.89
5 C005 has 0 0 0 21.39
6 C006 has 0 0 0 20.26
7 C007 has 0 0 0 20.26
8 C008 has 0 0 0 21.54
9 C009 has 0 0 0 18.82
10 C010 has 0 0 0 17.52
11 C011 has 0 0 0 17.52
12 C012 has 0 0 0 18.99
13 C013 has 0 0 0 24.49
14 C014 has 0 0 0 17.53
15 C015 has 0 0 0 16.13
16 C016 has 0 0 0 16.13
17 C017 has 0 0 0 17.72
18 C018 has 0 0 0 21.88
19 C019 has 0 0 0 24.61
20 C020 has 0 0 0 17.69
21 C021 has 0 0 0 16.30
22 C022 has 0 0 0 16.30
23 C023 has 0 0 0 17.66
24 C024 has 0 0 0 21.69
25 C025 has 0 0 0 24.95
26 C026 has 0 0 0 18.16
27 C027 has 0 0 0 16.81
28 C028 has 0 0 0 16.81
29 C029 has 0 0 0 18.17
30 C030 has 0 0 0 22.11
31 C031 has 0 0 0 25.89
32 C032 has 0 0 0 24.35
33 C033 has 0 0 0 24.35
34 C034 has 0 0 0 24.91
35 C035 has 0 0 0 20.83
36 C036 has 0 0 0 19.29
37 C037 has 0 0 0 19.29
38 C038 has 0 0 0 19.99
39 C039 has 0 0 0 22.15
40 C040 has 0 0 0 23.37
41 C041 has 0 0 0 15.93
42 C042 has 30 1 1 14.37
43 C043 has 55 2 2 14.37
44 C044 has 0 0 0 15.34
45 C045 has 0 0 0 18.25
46 C046 has 0 0 0 20.55
47 C047 has 30 1 1 11.38
48 C048 has 122 6 4 9.08
49 C049 has 194 10 6 9.08
50 C050 has 118 6 4 10.92
51 C051 has 0 0 0 15.24
52 C052 has 0 0 0 18.82
53 C053 has 97 5 3 7.84
54 C054 has 194 10 6 3.78
55 C055 has 194 10 6 3.78
56 C056 has 194 10 6 5.67
57 C057 has 0 0 0 13.16
58 C058 has 0 0 0 21.92
59 C059 has 0 0 0 18.43
60 C060 has 97 5 3 6.86
61 C061 has 194 10 6 0.00
62 C062 has 194 10 6 0.00
63 C063 has 194 10 6 1.26
64 C064 has 0 0 0 12.11
65 C065 has 0 0 0 22.04
66 C066 has 0 0 0 18.43
67 C067 has 97 5 3 6.86
68 C068 has 194 10 6 0.00
69 C069 has 194 10 6 0.00
70 C070 has 194 10 6 1.54
71 C071 has 0 0 0 12.33
72 C072 has 0 0 0 22.33
73 C073 has 0 0 0 24.47
74 C074 has 0 0 0 24.32
75 C075 has 0 0 0 24.32
76 C076 has 0 0 0 25.27
77 C077 has 0 0 0 21.32
78 C078 has 0 0 0 19.17
79 C079 has 0 0 0 19.02
80 C080 has 0 0 0 19.02
81 C081 has 0 0 0 20.22
82 C082 has 0 0 0 16.39
83 C083 has 55 2 2 13.87
84 C084 has 139 7 5 13.73
85 C085 has 22 1 1 13.73
86 C086 has 0 0 0 15.35
87 C087 has 0 0 0 22.98
88 C088 has 0 0 0 20.78
89 C089 has 55 2 2 11.79
90 C090 has 194 10 6 8.58
91 C091 has 194 10 6 8.43
92 C092 has 194 10 6 8.43
93 C093 has 34 2 1 10.87
94 C094 has 0 0 0 20.27
95 C095 has 0 0 0 18.93
96 C096 has 105 5 4 8.09
97 C097 has 194 10 6 3.28
98 C098 has 194 10 6 3.13
99 C099 has 194 10 6 3.13
100 C100 has 119 6 4 7.55
101 C101 has 0 0 0 18.70
102 C102 has 0 0 0 18.43
103 C103 has 135 7 4 6.86
104 C104 has 194 10 6 0.00
105 C105 has 194 10 6 0.00
106 C106 has 194 10 6 0.00
107 C107 has 119 6 4 6.86
108 C108 has 0 0 0 18.43
109 C109 has 0 0 0 18.43
110 C110 has 160 8 5 6.86
111 C111 has 194 10 6 0.00
115 C115 has 0 0 0 26.12
116 C116 has 0 0 0 25.18
117 C117 has 0 0 0 25.18
118 C118 has 0 0 0 26.10
119 C119 has 0 0 0 23.27
120 C120 has 0 0 0 21.05
121 C121 has 0 0 0 19.87
122 C122 has 0 0 0 19.87
123 C123 has 0 0 0 21.03
124 C124 has 0 0 0 18.79
125 C125 has 0 0 0 16.03
126 C126 has 22 1 1 14.58
127 C127 has 22 1 1 14.58
128 C128 has 0 0 0 16.12
129 C129 has 0 0 0 23.50
130 C130 has 0 0 0 14.88
131 C131 has 63 3 2 10.72
132 C132 has 122 6 4 9.32
133 C133 has 97 5 3 9.32
134 C134 has 22 1 1 11.58
135 C135 has 0 0 0 20.66
136 C136 has 0 0 0 22.36
137 C137 has 0 0 0 12.10
138 C138 has 172 9 6 5.46
139 C139 has 194 10 6 4.22
140 C140 has 186 9 6 4.22
141 C141 has 64 3 2 8.06
142 C142 has 0 0 0 18.91
143 C143 has 0 0 0 21.80
144 C144 has 0 0 0 11.21
145 C145 has 172 9 6 1.12
146 C146 has 194 10 6 0.29
147 C147 has 194 10 6 1.57
148 C148 has 97 5 3 7.05
149 C149 has 0 0 0 18.50
157 C157 has 0 0 0 24.99
158 C158 has 0 0 0 24.99
159 C159 has 0 0 0 21.47
160 C160 has 0 0 0 21.44
161 C161 has 0 0 0 21.50
162 C162 has 0 0 0 22.87
163 C163 has 0 0 0 22.62
164 C164 has 0 0 0 18.79
165 C165 has 0 0 0 18.75
166 C166 has 0 0 0 18.82
167 C167 has 0 0 0 20.77
168 C168 has 0 0 0 26.91
169 C169 has 0 0 0 21.46
170 C170 has 0 0 0 17.37
171 C171 has 0 0 0 17.33
172 C172 has 0 0 0 17.40
173 C173 has 0 0 0 19.87
174 C174 has 0 0 0 26.22
Total of 7284 atoms and 369 groups and 232 residues were included
Total heap storage needed = 291775
Fill Ewald table: Number of points= 10000 EWXmax= 4.250000
fill erfc table: linear inter has rms error = 0.979220D-08 maximum error = 0.218740D-07
fill erfc table: cubic spline has rms error = 0.360331D-11 maximum error = 0.108438D-10
NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYCB NOEXtnd EWALd
CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.000 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
PME EWALD OPTIONS: KAPPA = 0.340 QCOR = 0.000 Bspline order = 6
FFTX= 64 FFTY= 64 FFTZ= 64
Using Pub FFT
Real-to-Complex FFT
There are 0 atom pairs and 0 atom exclusions.
There are 0 group pairs and 0 group exclusions.
1753 1753 1746
: Ran out of space. RESIZING
with mode 5 found 1144 exclusions and 802 interactions(1-4)
found 14 group exclusions.
found 0 image group exclusions.
Generating nonbond list with Exclusion mode = 5
Allocate space for 5000 Thole shielding pairs
== PRIMARY == SPACE FOR 0 ATOM PAIRS AND 0 GROUP PAIRS
== IMAGES === SPACE FOR 0 ATOM PAIRS AND 0 GROUP PAIRS
=========================================
TRIAL run of list...........
=========================================
Using Image CUBE search
Using Image CUBE search
NBNDGCM found:
16918 atom pairs
292162 image atom pairs
0 self atom pairs
16918 total atom pairs
292162 total image pairs
CHARMM>
CHARMM> ener
SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
: updating the image atom lists and remapping
Transformation Atoms Groups Residues Min-Distance
1 C001 has 0 0 0 28.06
2 C002 has 0 0 0 28.06
3 C003 has 0 0 0 23.89
4 C004 has 0 0 0 23.89
5 C005 has 0 0 0 21.39
6 C006 has 0 0 0 20.26
7 C007 has 0 0 0 20.26
8 C008 has 0 0 0 21.54
9 C009 has 0 0 0 18.82
10 C010 has 0 0 0 17.52
11 C011 has 0 0 0 17.52
12 C012 has 0 0 0 18.99
13 C013 has 0 0 0 24.49
14 C014 has 0 0 0 17.53
15 C015 has 0 0 0 16.13
16 C016 has 0 0 0 16.13
17 C017 has 0 0 0 17.72
18 C018 has 0 0 0 21.88
19 C019 has 0 0 0 24.61
20 C020 has 0 0 0 17.69
21 C021 has 0 0 0 16.30
22 C022 has 0 0 0 16.30
23 C023 has 0 0 0 17.66
24 C024 has 0 0 0 21.69
25 C025 has 0 0 0 24.95
26 C026 has 0 0 0 18.16
27 C027 has 0 0 0 16.81
28 C028 has 0 0 0 16.81
29 C029 has 0 0 0 18.17
30 C030 has 0 0 0 22.11
31 C031 has 0 0 0 25.89
32 C032 has 0 0 0 24.35
33 C033 has 0 0 0 24.35
34 C034 has 0 0 0 24.91
35 C035 has 0 0 0 20.83
36 C036 has 0 0 0 19.29
37 C037 has 0 0 0 19.29
38 C038 has 0 0 0 19.99
39 C039 has 0 0 0 22.15
40 C040 has 0 0 0 23.37
41 C041 has 0 0 0 15.93
42 C042 has 30 1 1 14.37
43 C043 has 55 2 2 14.37
44 C044 has 0 0 0 15.34
45 C045 has 0 0 0 18.25
46 C046 has 0 0 0 20.55
47 C047 has 30 1 1 11.38
48 C048 has 122 6 4 9.08
49 C049 has 194 10 6 9.08
50 C050 has 118 6 4 10.92
51 C051 has 0 0 0 15.24
52 C052 has 0 0 0 18.82
53 C053 has 97 5 3 7.84
54 C054 has 194 10 6 3.78
55 C055 has 194 10 6 3.78
56 C056 has 194 10 6 5.67
57 C057 has 0 0 0 13.16
58 C058 has 0 0 0 21.92
59 C059 has 0 0 0 18.43
60 C060 has 97 5 3 6.86
61 C061 has 194 10 6 0.00
62 C062 has 194 10 6 0.00
63 C063 has 194 10 6 1.26
64 C064 has 0 0 0 12.11
65 C065 has 0 0 0 22.04
66 C066 has 0 0 0 18.43
67 C067 has 97 5 3 6.86
68 C068 has 194 10 6 0.00
69 C069 has 194 10 6 0.00
70 C070 has 194 10 6 1.54
71 C071 has 0 0 0 12.33
72 C072 has 0 0 0 22.33
73 C073 has 0 0 0 24.47
74 C074 has 0 0 0 24.32
75 C075 has 0 0 0 24.32
76 C076 has 0 0 0 25.27
77 C077 has 0 0 0 21.32
78 C078 has 0 0 0 19.17
79 C079 has 0 0 0 19.02
80 C080 has 0 0 0 19.02
81 C081 has 0 0 0 20.22
82 C082 has 0 0 0 16.39
83 C083 has 55 2 2 13.87
84 C084 has 139 7 5 13.73
85 C085 has 22 1 1 13.73
86 C086 has 0 0 0 15.35
87 C087 has 0 0 0 22.98
88 C088 has 0 0 0 20.78
89 C089 has 55 2 2 11.79
90 C090 has 194 10 6 8.58
91 C091 has 194 10 6 8.43
92 C092 has 194 10 6 8.43
93 C093 has 34 2 1 10.87
94 C094 has 0 0 0 20.27
95 C095 has 0 0 0 18.93
96 C096 has 105 5 4 8.09
97 C097 has 194 10 6 3.28
98 C098 has 194 10 6 3.13
99 C099 has 194 10 6 3.13
100 C100 has 119 6 4 7.55
101 C101 has 0 0 0 18.70
102 C102 has 0 0 0 18.43
103 C103 has 135 7 4 6.86
104 C104 has 194 10 6 0.00
105 C105 has 194 10 6 0.00
106 C106 has 194 10 6 0.00
107 C107 has 119 6 4 6.86
108 C108 has 0 0 0 18.43
109 C109 has 0 0 0 18.43
110 C110 has 160 8 5 6.86
111 C111 has 194 10 6 0.00
115 C115 has 0 0 0 26.12
116 C116 has 0 0 0 25.18
117 C117 has 0 0 0 25.18
118 C118 has 0 0 0 26.10
119 C119 has 0 0 0 23.27
120 C120 has 0 0 0 21.05
121 C121 has 0 0 0 19.87
122 C122 has 0 0 0 19.87
123 C123 has 0 0 0 21.03
124 C124 has 0 0 0 18.79
125 C125 has 0 0 0 16.03
126 C126 has 22 1 1 14.58
127 C127 has 22 1 1 14.58
128 C128 has 0 0 0 16.12
129 C129 has 0 0 0 23.50
130 C130 has 0 0 0 14.88
131 C131 has 63 3 2 10.72
132 C132 has 122 6 4 9.32
133 C133 has 97 5 3 9.32
134 C134 has 22 1 1 11.58
135 C135 has 0 0 0 20.66
136 C136 has 0 0 0 22.36
137 C137 has 0 0 0 12.10
138 C138 has 172 9 6 5.46
139 C139 has 194 10 6 4.22
140 C140 has 186 9 6 4.22
141 C141 has 64 3 2 8.06
142 C142 has 0 0 0 18.91
143 C143 has 0 0 0 21.80
144 C144 has 0 0 0 11.21
145 C145 has 172 9 6 1.12
146 C146 has 194 10 6 0.29
147 C147 has 194 10 6 1.57
148 C148 has 97 5 3 7.05
149 C149 has 0 0 0 18.50
157 C157 has 0 0 0 24.99
158 C158 has 0 0 0 24.99
159 C159 has 0 0 0 21.47
160 C160 has 0 0 0 21.44
161 C161 has 0 0 0 21.50
162 C162 has 0 0 0 22.87
163 C163 has 0 0 0 22.62
164 C164 has 0 0 0 18.79
165 C165 has 0 0 0 18.75
166 C166 has 0 0 0 18.82
167 C167 has 0 0 0 20.77
168 C168 has 0 0 0 26.91
169 C169 has 0 0 0 21.46
170 C170 has 0 0 0 17.37
171 C171 has 0 0 0 17.33
172 C172 has 0 0 0 17.40
173 C173 has 0 0 0 19.87
174 C174 has 0 0 0 26.22
Total of 7284 atoms and 369 groups and 232 residues were included
found 0 image group exclusions.
NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYCB NOEXtnd EWALd
CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.000 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
PME EWALD OPTIONS: KAPPA = 0.340 QCOR = 0.000 Bspline order = 6
FFTX= 64 FFTY= 64 FFTZ= 64
Using Pub FFT
Real-to-Complex FFT
There are 16918 atom pairs and 1946 atom exclusions.
There are 0 group pairs and 14 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 21993 ATOM PAIRS AND 0 GROUP PAIRS
== IMAGES === SPACE FOR 379810 ATOM PAIRS AND 0 GROUP PAIRS
Using Image CUBE search
NBNDGCM found:
16918 atom pairs
292162 image atom pairs
0 self atom pairs
16918 total atom pairs
292162 total image pairs
ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ENER CROSS: CMAPs PMF1D PMF2D PRIMO
ENER EXTERN: VDWaals ELEC HBONds ASP USER
ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
ENER EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
ENER LRCor: EVDW VIRI
---------- --------- --------- --------- --------- ---------
ENER> 0 NaN 0.00000 NaN
ENER INTERN> 291.17021 68.74474 60.35920 83.68291 0.03064
ENER CROSS> -10.14152 0.00000 0.00000 0.00000
ENER EXTERN> 200.16780 NaN 0.00000 0.00000 0.00000
ENER IMAGES> 324.20643 -62.58982 0.00000 0.00000 0.00000
ENER EWALD> 23.24862 -31944.61258 31862.78470 0.00000 0.00000
ENER LRCor> -2.16473 -4.32864
---------- --------- --------- --------- --------- ---------
CHARMM>
CHARMM> ! minimization
CHARMM>
CHARMM> cons harm force 100000. sele .not. type D* end
SELRPN> 134 atoms have been selected out of 194
CSTRAN: Harmonic Restraints
ABSOlute type as set number 1. Number of selected atoms: 134
Reference coordinates set to main coordinates.
Mass weighting will NOT be used for new restraints.
The force constant of 100000.00000 will be used.
An exponent of 2 will be used.
The XYZ scale factors are: 1.00000 1.00000 1.00000
A total of 134 atoms are restrained.
CHARMM> mini ABNR nstep 1000 nprint 20
SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
: updating the image atom lists and remapping
Transformation Atoms Groups Residues Min-Distance
1 C001 has 0 0 0 28.06
2 C002 has 0 0 0 28.06
3 C003 has 0 0 0 23.89
4 C004 has 0 0 0 23.89
5 C005 has 0 0 0 21.39
6 C006 has 0 0 0 20.26
7 C007 has 0 0 0 20.26
8 C008 has 0 0 0 21.54
9 C009 has 0 0 0 18.82
10 C010 has 0 0 0 17.52
11 C011 has 0 0 0 17.52
12 C012 has 0 0 0 18.99
13 C013 has 0 0 0 24.49
14 C014 has 0 0 0 17.53
15 C015 has 0 0 0 16.13
16 C016 has 0 0 0 16.13
17 C017 has 0 0 0 17.72
18 C018 has 0 0 0 21.88
19 C019 has 0 0 0 24.61
20 C020 has 0 0 0 17.69
21 C021 has 0 0 0 16.30
22 C022 has 0 0 0 16.30
23 C023 has 0 0 0 17.66
24 C024 has 0 0 0 21.69
25 C025 has 0 0 0 24.95
26 C026 has 0 0 0 18.16
27 C027 has 0 0 0 16.81
28 C028 has 0 0 0 16.81
29 C029 has 0 0 0 18.17
30 C030 has 0 0 0 22.11
31 C031 has 0 0 0 25.89
32 C032 has 0 0 0 24.35
33 C033 has 0 0 0 24.35
34 C034 has 0 0 0 24.91
35 C035 has 0 0 0 20.83
36 C036 has 0 0 0 19.29
37 C037 has 0 0 0 19.29
38 C038 has 0 0 0 19.99
39 C039 has 0 0 0 22.15
40 C040 has 0 0 0 23.37
41 C041 has 0 0 0 15.93
42 C042 has 30 1 1 14.37
43 C043 has 55 2 2 14.37
44 C044 has 0 0 0 15.34
45 C045 has 0 0 0 18.25
46 C046 has 0 0 0 20.55
47 C047 has 30 1 1 11.38
48 C048 has 122 6 4 9.08
49 C049 has 194 10 6 9.08
50 C050 has 118 6 4 10.92
51 C051 has 0 0 0 15.24
52 C052 has 0 0 0 18.82
53 C053 has 97 5 3 7.84
54 C054 has 194 10 6 3.78
55 C055 has 194 10 6 3.78
56 C056 has 194 10 6 5.67
57 C057 has 0 0 0 13.16
58 C058 has 0 0 0 21.92
59 C059 has 0 0 0 18.43
60 C060 has 97 5 3 6.86
61 C061 has 194 10 6 0.00
62 C062 has 194 10 6 0.00
63 C063 has 194 10 6 1.26
64 C064 has 0 0 0 12.11
65 C065 has 0 0 0 22.04
66 C066 has 0 0 0 18.43
67 C067 has 97 5 3 6.86
68 C068 has 194 10 6 0.00
69 C069 has 194 10 6 0.00
70 C070 has 194 10 6 1.54
71 C071 has 0 0 0 12.33
72 C072 has 0 0 0 22.33
73 C073 has 0 0 0 24.47
74 C074 has 0 0 0 24.32
75 C075 has 0 0 0 24.32
76 C076 has 0 0 0 25.27
77 C077 has 0 0 0 21.32
78 C078 has 0 0 0 19.17
79 C079 has 0 0 0 19.02
80 C080 has 0 0 0 19.02
81 C081 has 0 0 0 20.22
82 C082 has 0 0 0 16.39
83 C083 has 55 2 2 13.87
84 C084 has 139 7 5 13.73
85 C085 has 22 1 1 13.73
86 C086 has 0 0 0 15.35
87 C087 has 0 0 0 22.98
88 C088 has 0 0 0 20.78
89 C089 has 55 2 2 11.79
90 C090 has 194 10 6 8.58
91 C091 has 194 10 6 8.43
92 C092 has 194 10 6 8.43
93 C093 has 34 2 1 10.87
94 C094 has 0 0 0 20.27
95 C095 has 0 0 0 18.93
96 C096 has 105 5 4 8.09
97 C097 has 194 10 6 3.28
98 C098 has 194 10 6 3.13
99 C099 has 194 10 6 3.13
100 C100 has 119 6 4 7.55
101 C101 has 0 0 0 18.70
102 C102 has 0 0 0 18.43
103 C103 has 135 7 4 6.86
104 C104 has 194 10 6 0.00
105 C105 has 194 10 6 0.00
106 C106 has 194 10 6 0.00
107 C107 has 119 6 4 6.86
108 C108 has 0 0 0 18.43
109 C109 has 0 0 0 18.43
110 C110 has 160 8 5 6.86
111 C111 has 194 10 6 0.00
115 C115 has 0 0 0 26.12
116 C116 has 0 0 0 25.18
117 C117 has 0 0 0 25.18
118 C118 has 0 0 0 26.10
119 C119 has 0 0 0 23.27
120 C120 has 0 0 0 21.05
121 C121 has 0 0 0 19.87
122 C122 has 0 0 0 19.87
123 C123 has 0 0 0 21.03
124 C124 has 0 0 0 18.79
125 C125 has 0 0 0 16.03
126 C126 has 22 1 1 14.58
127 C127 has 22 1 1 14.58
128 C128 has 0 0 0 16.12
129 C129 has 0 0 0 23.50
130 C130 has 0 0 0 14.88
131 C131 has 63 3 2 10.72
132 C132 has 122 6 4 9.32
133 C133 has 97 5 3 9.32
134 C134 has 22 1 1 11.58
135 C135 has 0 0 0 20.66
136 C136 has 0 0 0 22.36
137 C137 has 0 0 0 12.10
138 C138 has 172 9 6 5.46
139 C139 has 194 10 6 4.22
140 C140 has 186 9 6 4.22
141 C141 has 64 3 2 8.06
142 C142 has 0 0 0 18.91
143 C143 has 0 0 0 21.80
144 C144 has 0 0 0 11.21
145 C145 has 172 9 6 1.12
146 C146 has 194 10 6 0.29
147 C147 has 194 10 6 1.57
148 C148 has 97 5 3 7.05
149 C149 has 0 0 0 18.50
157 C157 has 0 0 0 24.99
158 C158 has 0 0 0 24.99
159 C159 has 0 0 0 21.47
160 C160 has 0 0 0 21.44
161 C161 has 0 0 0 21.50
162 C162 has 0 0 0 22.87
163 C163 has 0 0 0 22.62
164 C164 has 0 0 0 18.79
165 C165 has 0 0 0 18.75
166 C166 has 0 0 0 18.82
167 C167 has 0 0 0 20.77
168 C168 has 0 0 0 26.91
169 C169 has 0 0 0 21.46
170 C170 has 0 0 0 17.37
171 C171 has 0 0 0 17.33
172 C172 has 0 0 0 17.40
173 C173 has 0 0 0 19.87
174 C174 has 0 0 0 26.22
Total of 7284 atoms and 369 groups and 232 residues were included
found 0 image group exclusions.
NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYCB NOEXtnd EWALd
CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.000 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
PME EWALD OPTIONS: KAPPA = 0.340 QCOR = 0.000 Bspline order = 6
FFTX= 64 FFTY= 64 FFTZ= 64
Using Pub FFT
Real-to-Complex FFT
There are 16918 atom pairs and 1946 atom exclusions.
There are 0 group pairs and 14 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 21993 ATOM PAIRS AND 0 GROUP PAIRS
== IMAGES === SPACE FOR 379810 ATOM PAIRS AND 0 GROUP PAIRS
Using Image CUBE search
NBNDGCM found:
16918 atom pairs
292162 image atom pairs
0 self atom pairs
16918 total atom pairs
292162 total image pairs
ABNER> An energy minimization has been requested.
EIGRNG = 0.0005000 MINDIM = 5
NPRINT = 20 NSTEP = 1000
PSTRCT = 0.0000000 SDSTP = 0.0200000
STPLIM = 1.0000000 STRICT = 0.1000000
TOLFUN = 0.0000000 TOLGRD = 0.0000000
TOLITR = 100 TOLSTP = 0.0000000
FMEM = 0.0000000
MINI MIN: Cycle ENERgy Delta-E GRMS Step-size
MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
MINI CROSS: CMAPs PMF1D PMF2D PRIMO
MINI EXTERN: VDWaals ELEC HBONds ASP USER
MINI IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
MINI EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
MINI LRCor: EVDW VIRI
---------- --------- --------- --------- --------- ---------
MINI> 0 NaN NaN NaN 0.00000
MINI INTERN> 291.17021 68.74474 60.35920 83.68291 0.03064
MINI CROSS> -10.14152 0.00000 0.00000 0.00000
MINI EXTERN> 200.16780 NaN 0.00000 0.00000 0.00000
MINI IMAGES> 324.20643 -62.58982 0.00000 0.00000 0.00000
MINI EWALD> 23.24862 -31944.61258 31862.78470 0.00000 0.00000
MINI LRCor> -2.16473 -4.32864
---------- --------- --------- --------- --------- ---------
UPDECI: Image update at step 1
: updating the image atom lists and remapping
Transformation Atoms Groups Residues Min-Distance
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[4774,1],0]
Exit code: 174
--------------------------------------------------------------------------