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***  modes_struct_lipids  ***

LOGs for ID: 22123014490835388

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




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It was developed by Karsten Suhre.
Between 2003 and 2014, it was hosted by IGS (Marseille).
Last modification: October 18th, 2018.