*** modes_struct_lipids ***
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 = 22123014490835388.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 22123014490835388.atom to be opened.
Openam> File opened: 22123014490835388.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 = 761
First residue number = 1
Last residue number = 286
Number of atoms found = 45798
Mean number per residue = 60.2
Pdbmat> Coordinate statistics:
= -0.203666 +/- 27.257801 From: -55.454000 To: 55.894000
= -0.518668 +/- 27.855033 From: -55.864000 To: 55.046000
= -6.975632 +/- 32.741028 From: -126.616000 To: 76.445000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 302 residue(s) not known.
Openam> File opened: pdbmat.xyzm
Pdbmat> Coordinates and masses considered are saved.
Openam> File opened: pdbmat.sdijb
Pdbmat> Matrix statistics:
Pdbmat> The matrix is 4.1470 % Filled.
Pdbmat> 35195294 non-zero elements.
Pdbmat> 3880699 atom-atom interactions.
Pdbmat> Number per atom= 169.47 +/- 53.25
Maximum number = 316
Minimum number = 22
Pdbmat> Matrix trace = 7.761398E+07
Pdbmat> Larger element = 1244.92
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
761 non-zero elements, NRBL set to 4
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 = 22123014490835388.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 4
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 22123014490835388.atom to be opened.
Openam> file on opening on unit 11:
22123014490835388.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 45798 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 4 residue(s) per block.
Blocpdb> 761 residues.
Blocpdb> 61 atoms in block 1
Block first atom: 1
Blocpdb> 39 atoms in block 2
Block first atom: 62
Blocpdb> 65 atoms in block 3
Block first atom: 101
Blocpdb> 56 atoms in block 4
Block first atom: 166
Blocpdb> 69 atoms in block 5
Block first atom: 222
Blocpdb> 73 atoms in block 6
Block first atom: 291
Blocpdb> 60 atoms in block 7
Block first atom: 364
Blocpdb> 41 atoms in block 8
Block first atom: 424
Blocpdb> 51 atoms in block 9
Block first atom: 465
Blocpdb> 63 atoms in block 10
Block first atom: 516
Blocpdb> 52 atoms in block 11
Block first atom: 579
Blocpdb> 58 atoms in block 12
Block first atom: 631
Blocpdb> 63 atoms in block 13
Block first atom: 689
Blocpdb> 68 atoms in block 14
Block first atom: 752
Blocpdb> 51 atoms in block 15
Block first atom: 820
Blocpdb> 77 atoms in block 16
Block first atom: 871
Blocpdb> 78 atoms in block 17
Block first atom: 948
Blocpdb> 65 atoms in block 18
Block first atom: 1026
Blocpdb> 62 atoms in block 19
Block first atom: 1091
Blocpdb> 72 atoms in block 20
Block first atom: 1153
Blocpdb> 65 atoms in block 21
Block first atom: 1225
Blocpdb> 56 atoms in block 22
Block first atom: 1290
Blocpdb> 62 atoms in block 23
Block first atom: 1346
Blocpdb> 65 atoms in block 24
Block first atom: 1408
Blocpdb> 73 atoms in block 25
Block first atom: 1473
Blocpdb> 62 atoms in block 26
Block first atom: 1546
Blocpdb> 50 atoms in block 27
Block first atom: 1608
Blocpdb> 66 atoms in block 28
Block first atom: 1658
Blocpdb> 66 atoms in block 29
Block first atom: 1724
Blocpdb> 70 atoms in block 30
Block first atom: 1790
Blocpdb> 56 atoms in block 31
Block first atom: 1860
Blocpdb> 73 atoms in block 32
Block first atom: 1916
Blocpdb> 54 atoms in block 33
Block first atom: 1989
Blocpdb> 67 atoms in block 34
Block first atom: 2043
Blocpdb> 61 atoms in block 35
Block first atom: 2110
Blocpdb> 62 atoms in block 36
Block first atom: 2171
Blocpdb> 51 atoms in block 37
Block first atom: 2233
Blocpdb> 48 atoms in block 38
Block first atom: 2284
Blocpdb> 51 atoms in block 39
Block first atom: 2332
Blocpdb> 55 atoms in block 40
Block first atom: 2383
Blocpdb> 68 atoms in block 41
Block first atom: 2438
Blocpdb> 73 atoms in block 42
Block first atom: 2506
Blocpdb> 63 atoms in block 43
Block first atom: 2579
Blocpdb> 68 atoms in block 44
Block first atom: 2642
Blocpdb> 87 atoms in block 45
Block first atom: 2710
Blocpdb> 71 atoms in block 46
Block first atom: 2797
Blocpdb> 81 atoms in block 47
Block first atom: 2868
Blocpdb> 62 atoms in block 48
Block first atom: 2949
Blocpdb> 57 atoms in block 49
Block first atom: 3011
Blocpdb> 61 atoms in block 50
Block first atom: 3068
Blocpdb> 64 atoms in block 51
Block first atom: 3129
Blocpdb> 70 atoms in block 52
Block first atom: 3193
Blocpdb> 65 atoms in block 53
Block first atom: 3263
Blocpdb> 87 atoms in block 54
Block first atom: 3328
Blocpdb> 67 atoms in block 55
Block first atom: 3415
Blocpdb> 75 atoms in block 56
Block first atom: 3482
Blocpdb> 45 atoms in block 57
Block first atom: 3557
Blocpdb> 79 atoms in block 58
Block first atom: 3602
Blocpdb> 70 atoms in block 59
Block first atom: 3681
Blocpdb> 62 atoms in block 60
Block first atom: 3751
Blocpdb> 59 atoms in block 61
Block first atom: 3813
Blocpdb> 53 atoms in block 62
Block first atom: 3872
Blocpdb> 74 atoms in block 63
Block first atom: 3925
Blocpdb> 57 atoms in block 64
Block first atom: 3999
Blocpdb> 68 atoms in block 65
Block first atom: 4056
Blocpdb> 62 atoms in block 66
Block first atom: 4124
Blocpdb> 79 atoms in block 67
Block first atom: 4186
Blocpdb> 56 atoms in block 68
Block first atom: 4265
Blocpdb> 75 atoms in block 69
Block first atom: 4321
Blocpdb> 64 atoms in block 70
Block first atom: 4396
Blocpdb> 56 atoms in block 71
Block first atom: 4460
Blocpdb> 67 atoms in block 72
Block first atom: 4516
Blocpdb> 46 atoms in block 73
Block first atom: 4583
Blocpdb> 77 atoms in block 74
Block first atom: 4629
Blocpdb> 60 atoms in block 75
Block first atom: 4706
Blocpdb> 70 atoms in block 76
Block first atom: 4766
Blocpdb> 69 atoms in block 77
Block first atom: 4836
Blocpdb> 53 atoms in block 78
Block first atom: 4905
Blocpdb> 62 atoms in block 79
Block first atom: 4958
Blocpdb> 67 atoms in block 80
Block first atom: 5020
Blocpdb> 49 atoms in block 81
Block first atom: 5087
Blocpdb> 48 atoms in block 82
Block first atom: 5136
Blocpdb> 86 atoms in block 83
Block first atom: 5184
Blocpdb> 59 atoms in block 84
Block first atom: 5270
Blocpdb> 65 atoms in block 85
Block first atom: 5329
Blocpdb> 54 atoms in block 86
Block first atom: 5394
Blocpdb> 56 atoms in block 87
Block first atom: 5448
Blocpdb> 85 atoms in block 88
Block first atom: 5504
Blocpdb> 67 atoms in block 89
Block first atom: 5589
Blocpdb> 53 atoms in block 90
Block first atom: 5656
Blocpdb> 72 atoms in block 91
Block first atom: 5709
Blocpdb> 48 atoms in block 92
Block first atom: 5781
Blocpdb> 71 atoms in block 93
Block first atom: 5829
Blocpdb> 58 atoms in block 94
Block first atom: 5900
Blocpdb> 69 atoms in block 95
Block first atom: 5958
Blocpdb> 68 atoms in block 96
Block first atom: 6027
Blocpdb> 62 atoms in block 97
Block first atom: 6095
Blocpdb> 64 atoms in block 98
Block first atom: 6157
Blocpdb> 69 atoms in block 99
Block first atom: 6221
Blocpdb> 61 atoms in block 100
Block first atom: 6290
Blocpdb> 48 atoms in block 101
Block first atom: 6351
Blocpdb> 52 atoms in block 102
Block first atom: 6399
Blocpdb> 65 atoms in block 103
Block first atom: 6451
Blocpdb> 62 atoms in block 104
Block first atom: 6516
Blocpdb> 63 atoms in block 105
Block first atom: 6578
Blocpdb> 60 atoms in block 106
Block first atom: 6641
Blocpdb> 60 atoms in block 107
Block first atom: 6701
Blocpdb> 56 atoms in block 108
Block first atom: 6761
Blocpdb> 49 atoms in block 109
Block first atom: 6817
Blocpdb> 68 atoms in block 110
Block first atom: 6866
Blocpdb> 55 atoms in block 111
Block first atom: 6934
Blocpdb> 69 atoms in block 112
Block first atom: 6989
Blocpdb> 58 atoms in block 113
Block first atom: 7058
Blocpdb> 72 atoms in block 114
Block first atom: 7116
Blocpdb> 63 atoms in block 115
Block first atom: 7188
Blocpdb> 52 atoms in block 116
Block first atom: 7251
Blocpdb> 60 atoms in block 117
Block first atom: 7303
Blocpdb> 66 atoms in block 118
Block first atom: 7363
Blocpdb> 46 atoms in block 119
Block first atom: 7429
Blocpdb> 536 atoms in block 120
Block first atom: 7475
Blocpdb> 536 atoms in block 121
Block first atom: 8011
Blocpdb> 536 atoms in block 122
Block first atom: 8547
Blocpdb> 536 atoms in block 123
Block first atom: 9083
Blocpdb> 536 atoms in block 124
Block first atom: 9619
Blocpdb> 536 atoms in block 125
Block first atom: 10155
Blocpdb> 536 atoms in block 126
Block first atom: 10691
Blocpdb> 536 atoms in block 127
Block first atom: 11227
Blocpdb> 536 atoms in block 128
Block first atom: 11763
Blocpdb> 536 atoms in block 129
Block first atom: 12299
Blocpdb> 536 atoms in block 130
Block first atom: 12835
Blocpdb> 536 atoms in block 131
Block first atom: 13371
Blocpdb> 536 atoms in block 132
Block first atom: 13907
Blocpdb> 536 atoms in block 133
Block first atom: 14443
Blocpdb> 536 atoms in block 134
Block first atom: 14979
Blocpdb> 536 atoms in block 135
Block first atom: 15515
Blocpdb> 536 atoms in block 136
Block first atom: 16051
Blocpdb> 536 atoms in block 137
Block first atom: 16587
Blocpdb> 536 atoms in block 138
Block first atom: 17123
Blocpdb> 536 atoms in block 139
Block first atom: 17659
Blocpdb> 536 atoms in block 140
Block first atom: 18195
Blocpdb> 536 atoms in block 141
Block first atom: 18731
Blocpdb> 536 atoms in block 142
Block first atom: 19267
Blocpdb> 536 atoms in block 143
Block first atom: 19803
Blocpdb> 536 atoms in block 144
Block first atom: 20339
Blocpdb> 536 atoms in block 145
Block first atom: 20875
Blocpdb> 536 atoms in block 146
Block first atom: 21411
Blocpdb> 536 atoms in block 147
Block first atom: 21947
Blocpdb> 536 atoms in block 148
Block first atom: 22483
Blocpdb> 536 atoms in block 149
Block first atom: 23019
Blocpdb> 536 atoms in block 150
Block first atom: 23555
Blocpdb> 536 atoms in block 151
Block first atom: 24091
Blocpdb> 536 atoms in block 152
Block first atom: 24627
Blocpdb> 536 atoms in block 153
Block first atom: 25163
Blocpdb> 536 atoms in block 154
Block first atom: 25699
Blocpdb> 536 atoms in block 155
Block first atom: 26235
Blocpdb> 536 atoms in block 156
Block first atom: 26771
Blocpdb> 536 atoms in block 157
Block first atom: 27307
Blocpdb> 536 atoms in block 158
Block first atom: 27843
Blocpdb> 536 atoms in block 159
Block first atom: 28379
Blocpdb> 536 atoms in block 160
Block first atom: 28915
Blocpdb> 536 atoms in block 161
Block first atom: 29451
Blocpdb> 536 atoms in block 162
Block first atom: 29987
Blocpdb> 536 atoms in block 163
Block first atom: 30523
Blocpdb> 536 atoms in block 164
Block first atom: 31059
Blocpdb> 536 atoms in block 165
Block first atom: 31595
Blocpdb> 536 atoms in block 166
Block first atom: 32131
Blocpdb> 536 atoms in block 167
Block first atom: 32667
Blocpdb> 536 atoms in block 168
Block first atom: 33203
Blocpdb> 536 atoms in block 169
Block first atom: 33739
Blocpdb> 536 atoms in block 170
Block first atom: 34275
Blocpdb> 536 atoms in block 171
Block first atom: 34811
Blocpdb> 536 atoms in block 172
Block first atom: 35347
Blocpdb> 536 atoms in block 173
Block first atom: 35883
Blocpdb> 536 atoms in block 174
Block first atom: 36419
Blocpdb> 536 atoms in block 175
Block first atom: 36955
Blocpdb> 536 atoms in block 176
Block first atom: 37491
Blocpdb> 536 atoms in block 177
Block first atom: 38027
Blocpdb> 536 atoms in block 178
Block first atom: 38563
Blocpdb> 536 atoms in block 179
Block first atom: 39099
Blocpdb> 536 atoms in block 180
Block first atom: 39635
Blocpdb> 536 atoms in block 181
Block first atom: 40171
Blocpdb> 536 atoms in block 182
Block first atom: 40707
Blocpdb> 536 atoms in block 183
Block first atom: 41243
Blocpdb> 536 atoms in block 184
Block first atom: 41779
Blocpdb> 536 atoms in block 185
Block first atom: 42315
Blocpdb> 536 atoms in block 186
Block first atom: 42851
Blocpdb> 536 atoms in block 187
Block first atom: 43387
Blocpdb> 536 atoms in block 188
Block first atom: 43923
Blocpdb> 536 atoms in block 189
Block first atom: 44459
Blocpdb> 536 atoms in block 190
Block first atom: 44995
Blocpdb> 268 atoms in block 191
Block first atom: 45530
Blocpdb> 191 blocks.
Blocpdb> At most, 536 atoms in each of them.
Blocpdb> At least, 39 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> IIWKMX up to: 5271329 Maximum allowed is LIWORK= 5000000
%Diagrtb-Er> IRWKMX up to: 223515217 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 0m0.232s
user 0m0.228s
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: October 18th, 2018.
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