***  D70GelNemo  ***
output from eigenvector calculation:
STDOUT:
CUTOFF set to default value (CUTOFF=8)
Build Tirion matrix:
Pdbmat> Computes the Hessian matrix, using an Elastic Network Model.
Pdbmat> Version 3.50, Fevrier 2004.
Pdbmat> Options to be read in pdbmat.dat file.
Pdbmat> Coordinate filename = 2406061052251339624.atom
Pdbmat> Distance cutoff = 8.00
Force constant = 10.00
Origin of mass values = CONS
Pdbmat> Levelshift = 1.0E-09
PRINTing level = 2
Pdbmat> Coordinate file 2406061052251339624.atom to be opened.
Openam> File opened: 2406061052251339624.atom
Pdbmat> Coordinate file in PDB format.
Rdatompdb> Reading pdb file.
Rdatompdb> End of file reached.
Rdatompdb> Number of I/O errors: 0
Rdatompdb> Number of residues found = 1771
First residue number = 1
Last residue number = 1771
Number of atoms found = 27589
Mean number per residue = 15.6
Pdbmat> Coordinate statistics:
= -0.195779 +/- 34.605735 From: -90.345000 To: 77.849000
= 7.712501 +/- 31.664728 From: -85.499000 To: 95.699000
= -13.036961 +/- 30.497226 From: -79.653000 To: 56.944000
Pdbmat> Masses are all set to one.
Openam> File opened: pdbmat.xyzm
Pdbmat> Coordinates and masses considered are saved.
Openam> File opened: pdbmat.sdijb
Pdbmat> Matrix statistics:
Pdbmat> The matrix is -1.7727 % Filled.
Pdbmat> 15417573 non-zero elements.
Pdbmat> 1694941 atom-atom interactions.
Pdbmat> Number per atom= 122.87 +/- 58.50
Maximum number = 268
Minimum number = 17
Pdbmat> Matrix trace = 3.389882E+07
Pdbmat> Larger element = 931.376
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
1771 non-zero elements, NRBL set to 9
Diagonalize Tirion matrix using diagrtb
Diagrtb> Diagonalizes a matrix, using the RTB/BNM approximation.
Diagrtb> Version 2.52, November 2004.
Diagrtb> Options to be read in diagrtb.dat file.
Diagrtb> Options taken into account:
MATRix filename = pdbmat.sdijb
COORdinates filename = 2406061052251339624.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 9
Origin of MASS values = CONS
MATRix FORMat = BINA
Temporary files cleaning = ALL
Output PRINting level = 2
Diagrtb> Memory allocation for Blocpdb.
Blocpdb> Entering in.
Openam> file on opening on unit 10:
diagrtb_work.xyzm
Blocpdb> Coordinate file 2406061052251339624.atom to be opened.
Openam> file on opening on unit 11:
2406061052251339624.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 27589 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 9 residue(s) per block.
Blocpdb> 1771 residues.
Blocpdb> 139 atoms in block 1
Block first atom: 1
Blocpdb> 148 atoms in block 2
Block first atom: 140
Blocpdb> 150 atoms in block 3
Block first atom: 288
Blocpdb> 141 atoms in block 4
Block first atom: 438
Blocpdb> 128 atoms in block 5
Block first atom: 579
Blocpdb> 132 atoms in block 6
Block first atom: 707
Blocpdb> 142 atoms in block 7
Block first atom: 839
Blocpdb> 135 atoms in block 8
Block first atom: 981
Blocpdb> 131 atoms in block 9
Block first atom: 1116
Blocpdb> 141 atoms in block 10
Block first atom: 1247
Blocpdb> 140 atoms in block 11
Block first atom: 1388
Blocpdb> 134 atoms in block 12
Block first atom: 1528
Blocpdb> 150 atoms in block 13
Block first atom: 1662
Blocpdb> 144 atoms in block 14
Block first atom: 1812
Blocpdb> 112 atoms in block 15
Block first atom: 1956
Blocpdb> 155 atoms in block 16
Block first atom: 2068
Blocpdb> 122 atoms in block 17
Block first atom: 2223
Blocpdb> 144 atoms in block 18
Block first atom: 2345
Blocpdb> 128 atoms in block 19
Block first atom: 2489
Blocpdb> 153 atoms in block 20
Block first atom: 2617
Blocpdb> 143 atoms in block 21
Block first atom: 2770
Blocpdb> 120 atoms in block 22
Block first atom: 2913
Blocpdb> 117 atoms in block 23
Block first atom: 3033
Blocpdb> 132 atoms in block 24
Block first atom: 3150
Blocpdb> 165 atoms in block 25
Block first atom: 3282
Blocpdb> 139 atoms in block 26
Block first atom: 3447
Blocpdb> 122 atoms in block 27
Block first atom: 3586
Blocpdb> 136 atoms in block 28
Block first atom: 3708
Blocpdb> 131 atoms in block 29
Block first atom: 3844
Blocpdb> 129 atoms in block 30
Block first atom: 3975
Blocpdb> 132 atoms in block 31
Block first atom: 4104
Blocpdb> 143 atoms in block 32
Block first atom: 4236
Blocpdb> 151 atoms in block 33
Block first atom: 4379
Blocpdb> 139 atoms in block 34
Block first atom: 4530
Blocpdb> 139 atoms in block 35
Block first atom: 4669
Blocpdb> 149 atoms in block 36
Block first atom: 4808
Blocpdb> 135 atoms in block 37
Block first atom: 4957
Blocpdb> 132 atoms in block 38
Block first atom: 5092
Blocpdb> 157 atoms in block 39
Block first atom: 5224
Blocpdb> 145 atoms in block 40
Block first atom: 5381
Blocpdb> 128 atoms in block 41
Block first atom: 5526
Blocpdb> 143 atoms in block 42
Block first atom: 5654
Blocpdb> 163 atoms in block 43
Block first atom: 5797
Blocpdb> 155 atoms in block 44
Block first atom: 5960
Blocpdb> 146 atoms in block 45
Block first atom: 6115
Blocpdb> 133 atoms in block 46
Block first atom: 6261
Blocpdb> 158 atoms in block 47
Block first atom: 6394
Blocpdb> 131 atoms in block 48
Block first atom: 6552
Blocpdb> 121 atoms in block 49
Block first atom: 6683
Blocpdb> 132 atoms in block 50
Block first atom: 6804
Blocpdb> 135 atoms in block 51
Block first atom: 6936
Blocpdb> 144 atoms in block 52
Block first atom: 7071
Blocpdb> 138 atoms in block 53
Block first atom: 7215
Blocpdb> 156 atoms in block 54
Block first atom: 7353
Blocpdb> 138 atoms in block 55
Block first atom: 7509
Blocpdb> 165 atoms in block 56
Block first atom: 7647
Blocpdb> 122 atoms in block 57
Block first atom: 7812
Blocpdb> 149 atoms in block 58
Block first atom: 7934
Blocpdb> 126 atoms in block 59
Block first atom: 8083
Blocpdb> 167 atoms in block 60
Block first atom: 8209
Blocpdb> 157 atoms in block 61
Block first atom: 8376
Blocpdb> 144 atoms in block 62
Block first atom: 8533
Blocpdb> 154 atoms in block 63
Block first atom: 8677
Blocpdb> 160 atoms in block 64
Block first atom: 8831
Blocpdb> 148 atoms in block 65
Block first atom: 8991
Blocpdb> 139 atoms in block 66
Block first atom: 9139
Blocpdb> 160 atoms in block 67
Block first atom: 9278
Blocpdb> 124 atoms in block 68
Block first atom: 9438
Blocpdb> 134 atoms in block 69
Block first atom: 9562
Blocpdb> 125 atoms in block 70
Block first atom: 9696
Blocpdb> 166 atoms in block 71
Block first atom: 9821
Blocpdb> 143 atoms in block 72
Block first atom: 9987
Blocpdb> 167 atoms in block 73
Block first atom: 10130
Blocpdb> 158 atoms in block 74
Block first atom: 10297
Blocpdb> 126 atoms in block 75
Block first atom: 10455
Blocpdb> 153 atoms in block 76
Block first atom: 10581
Blocpdb> 147 atoms in block 77
Block first atom: 10734
Blocpdb> 128 atoms in block 78
Block first atom: 10881
Blocpdb> 152 atoms in block 79
Block first atom: 11009
Blocpdb> 151 atoms in block 80
Block first atom: 11161
Blocpdb> 158 atoms in block 81
Block first atom: 11312
Blocpdb> 153 atoms in block 82
Block first atom: 11470
Blocpdb> 149 atoms in block 83
Block first atom: 11623
Blocpdb> 143 atoms in block 84
Block first atom: 11772
Blocpdb> 143 atoms in block 85
Block first atom: 11915
Blocpdb> 156 atoms in block 86
Block first atom: 12058
Blocpdb> 125 atoms in block 87
Block first atom: 12214
Blocpdb> 154 atoms in block 88
Block first atom: 12339
Blocpdb> 148 atoms in block 89
Block first atom: 12493
Blocpdb> 132 atoms in block 90
Block first atom: 12641
Blocpdb> 153 atoms in block 91
Block first atom: 12773
Blocpdb> 140 atoms in block 92
Block first atom: 12926
Blocpdb> 145 atoms in block 93
Block first atom: 13066
Blocpdb> 146 atoms in block 94
Block first atom: 13211
Blocpdb> 151 atoms in block 95
Block first atom: 13357
Blocpdb> 117 atoms in block 96
Block first atom: 13508
Blocpdb> 118 atoms in block 97
Block first atom: 13625
Blocpdb> 141 atoms in block 98
Block first atom: 13743
Blocpdb> 136 atoms in block 99
Block first atom: 13884
Blocpdb> 140 atoms in block 100
Block first atom: 14020
Blocpdb> 177 atoms in block 101
Block first atom: 14160
Blocpdb> 157 atoms in block 102
Block first atom: 14337
Blocpdb> 155 atoms in block 103
Block first atom: 14494
Blocpdb> 138 atoms in block 104
Block first atom: 14649
Blocpdb> 167 atoms in block 105
Block first atom: 14787
Blocpdb> 150 atoms in block 106
Block first atom: 14954
Blocpdb> 141 atoms in block 107
Block first atom: 15104
Blocpdb> 154 atoms in block 108
Block first atom: 15245
Blocpdb> 164 atoms in block 109
Block first atom: 15399
Blocpdb> 156 atoms in block 110
Block first atom: 15563
Blocpdb> 141 atoms in block 111
Block first atom: 15719
Blocpdb> 159 atoms in block 112
Block first atom: 15860
Blocpdb> 140 atoms in block 113
Block first atom: 16019
Blocpdb> 146 atoms in block 114
Block first atom: 16159
Blocpdb> 150 atoms in block 115
Block first atom: 16305
Blocpdb> 141 atoms in block 116
Block first atom: 16455
Blocpdb> 146 atoms in block 117
Block first atom: 16596
Blocpdb> 163 atoms in block 118
Block first atom: 16742
Blocpdb> 138 atoms in block 119
Block first atom: 16905
Blocpdb> 127 atoms in block 120
Block first atom: 17043
Blocpdb> 133 atoms in block 121
Block first atom: 17170
Blocpdb> 129 atoms in block 122
Block first atom: 17303
Blocpdb> 119 atoms in block 123
Block first atom: 17432
Blocpdb> 111 atoms in block 124
Block first atom: 17551
Blocpdb> 137 atoms in block 125
Block first atom: 17662
Blocpdb> 118 atoms in block 126
Block first atom: 17799
Blocpdb> 157 atoms in block 127
Block first atom: 17917
Blocpdb> 169 atoms in block 128
Block first atom: 18074
Blocpdb> 132 atoms in block 129
Block first atom: 18243
Blocpdb> 145 atoms in block 130
Block first atom: 18375
Blocpdb> 133 atoms in block 131
Block first atom: 18520
Blocpdb> 121 atoms in block 132
Block first atom: 18653
Blocpdb> 115 atoms in block 133
Block first atom: 18774
Blocpdb> 117 atoms in block 134
Block first atom: 18889
Blocpdb> 131 atoms in block 135
Block first atom: 19006
Blocpdb> 147 atoms in block 136
Block first atom: 19137
Blocpdb> 147 atoms in block 137
Block first atom: 19284
Blocpdb> 145 atoms in block 138
Block first atom: 19431
Blocpdb> 132 atoms in block 139
Block first atom: 19576
Blocpdb> 155 atoms in block 140
Block first atom: 19708
Blocpdb> 150 atoms in block 141
Block first atom: 19863
Blocpdb> 154 atoms in block 142
Block first atom: 20013
Blocpdb> 126 atoms in block 143
Block first atom: 20167
Blocpdb> 136 atoms in block 144
Block first atom: 20293
Blocpdb> 108 atoms in block 145
Block first atom: 20429
Blocpdb> 148 atoms in block 146
Block first atom: 20537
Blocpdb> 132 atoms in block 147
Block first atom: 20685
Blocpdb> 149 atoms in block 148
Block first atom: 20817
Blocpdb> 126 atoms in block 149
Block first atom: 20966
Blocpdb> 144 atoms in block 150
Block first atom: 21092
Blocpdb> 146 atoms in block 151
Block first atom: 21236
Blocpdb> 125 atoms in block 152
Block first atom: 21382
Blocpdb> 142 atoms in block 153
Block first atom: 21507
Blocpdb> 147 atoms in block 154
Block first atom: 21649
Blocpdb> 155 atoms in block 155
Block first atom: 21796
Blocpdb> 111 atoms in block 156
Block first atom: 21951
Blocpdb> 128 atoms in block 157
Block first atom: 22062
Blocpdb> 130 atoms in block 158
Block first atom: 22190
Blocpdb> 116 atoms in block 159
Block first atom: 22320
Blocpdb> 136 atoms in block 160
Block first atom: 22436
Blocpdb> 138 atoms in block 161
Block first atom: 22572
Blocpdb> 156 atoms in block 162
Block first atom: 22710
Blocpdb> 114 atoms in block 163
Block first atom: 22866
Blocpdb> 125 atoms in block 164
Block first atom: 22980
Blocpdb> 133 atoms in block 165
Block first atom: 23105
Blocpdb> 132 atoms in block 166
Block first atom: 23238
Blocpdb> 144 atoms in block 167
Block first atom: 23370
Blocpdb> 143 atoms in block 168
Block first atom: 23514
Blocpdb> 154 atoms in block 169
Block first atom: 23657
Blocpdb> 116 atoms in block 170
Block first atom: 23811
Blocpdb> 137 atoms in block 171
Block first atom: 23927
Blocpdb> 146 atoms in block 172
Block first atom: 24064
Blocpdb> 147 atoms in block 173
Block first atom: 24210
Blocpdb> 144 atoms in block 174
Block first atom: 24357
Blocpdb> 151 atoms in block 175
Block first atom: 24501
Blocpdb> 138 atoms in block 176
Block first atom: 24652
Blocpdb> 118 atoms in block 177
Block first atom: 24790
Blocpdb> 132 atoms in block 178
Block first atom: 24908
Blocpdb> 134 atoms in block 179
Block first atom: 25040
Blocpdb> 135 atoms in block 180
Block first atom: 25174
Blocpdb> 132 atoms in block 181
Block first atom: 25309
Blocpdb> 127 atoms in block 182
Block first atom: 25441
Blocpdb> 141 atoms in block 183
Block first atom: 25568
Blocpdb> 133 atoms in block 184
Block first atom: 25709
Blocpdb> 125 atoms in block 185
Block first atom: 25842
Blocpdb> 143 atoms in block 186
Block first atom: 25967
Blocpdb> 140 atoms in block 187
Block first atom: 26110
Blocpdb> 120 atoms in block 188
Block first atom: 26250
Blocpdb> 140 atoms in block 189
Block first atom: 26370
Blocpdb> 139 atoms in block 190
Block first atom: 26510
Blocpdb> 139 atoms in block 191
Block first atom: 26649
Blocpdb> 135 atoms in block 192
Block first atom: 26788
Blocpdb> 157 atoms in block 193
Block first atom: 26923
Blocpdb> 152 atoms in block 194
Block first atom: 27080
Blocpdb> 133 atoms in block 195
Block first atom: 27232
Blocpdb> 106 atoms in block 196
Block first atom: 27365
Blocpdb> 119 atoms in block 197
Block first atom: 27470
Blocpdb> 197 blocks.
Blocpdb> At most, 177 atoms in each of them.
Blocpdb> At least, 106 atoms in each of them.
Blocpdb> Normal end of Blocpdb.
Diagrtb> Memory allocation for Prepmat.
Diagrtb> Memory allocation for RTB.
Diagrtb> Memory allocation for Diagstd.
Diagrtb> Memory allocation for RTB_to_modes.
%Diagrtb-Er> IRWKMX up to: 44231239 Maximum allowed is LRWORK= 32000000
%Diagrtb-Er> Not enough memory allowed for working arrays. Sorry.
Lower the number of blocks, the sizes of the largest ones...
Or recompile DIAGRTB with larger WORKing arrays.
STDERR:
STOP *Working arrays allocation error*
real 0m0.135s
user 0m0.135s
sys 0m0.000s
If you find results from this site helpful for your research, please cite one of our papers:
elNémo
is maintained by Yves-Henri Sanejouand.
It was developed
by Karsten Suhre.
Between 2003 and 2014, it was hosted by IGS (Marseille).
Last modification: April 25th, 2023.
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