*** ***
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 = 22112911152777313.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 22112911152777313.atom to be opened.
Openam> File opened: 22112911152777313.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 = 10
First residue number = 63
Last residue number = 101
Number of atoms found = 33
Mean number per residue = 3.3
Pdbmat> Coordinate statistics:
= -2.446364 +/- 2.528398 From: -7.781000 To: 1.084000
= 15.558242 +/- 3.535074 From: 9.294000 To: 23.872000
= 29.052667 +/- 3.544040 From: 22.370000 To: 35.979000
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 62.0000 % Filled.
Pdbmat> 3069 non-zero elements.
Pdbmat> 319 atom-atom interactions.
Pdbmat> Number per atom= 19.33 +/- 5.30
Maximum number = 29
Minimum number = 9
Pdbmat> Matrix trace = 6380.00
Pdbmat> Larger element = 122.860
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
10 non-zero elements, NRBL set to 1
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 = 22112911152777313.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 1
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 22112911152777313.atom to be opened.
Openam> file on opening on unit 11:
22112911152777313.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 33 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 1 residue(s) per block.
Blocpdb> 10 residues.
Blocpdb> 3 atoms in block 1
Block first atom: 1
Blocpdb> 5 atoms in block 2
Block first atom: 4
Blocpdb> 5 atoms in block 3
Block first atom: 9
%Blocpdb-Wn> 1 atoms in block 4 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 14th, in residue A 77
%Blocpdb-Wn> It will be merged with next block.
Blocpdb> 4 atoms in block 4
Block first atom: 14
Blocpdb> 3 atoms in block 5
Block first atom: 18
Blocpdb> 4 atoms in block 6
Block first atom: 21
Blocpdb> 3 atoms in block 7
Block first atom: 25
Blocpdb> 6 atoms in block 8
Block first atom: 27
Blocpdb> 8 blocks.
Blocpdb> At most, 6 atoms in each of them.
Blocpdb> At least, 3 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-Wn> 48 eigenvectors, only, can be determined.
Diagrtb> Memory allocation for RTB_to_modes.
Prepmat> Entering in.
Prepmat> Rewriting of the matrix begins.
Prepmat> 3077 matrix lines read.
Prepmat> Matrix order = 99
Prepmat> Matrix trace = 6380.0000
Prepmat> Last element read: 99 99 21.8402
Prepmat> 37 lines saved.
Prepmat> 6 empty lines.
Prepmat> Number of lines on output is as expected.
Prepmat> Normal end of Prepmat.
RTB> Entering in.
RTB> Number of atoms found in temporary coordinate file: 33
RTB> Total mass = 33.0000
RTB> Number of atoms found in matrix: 33
RTB> Number of blocks = 8
RTB> Projection begins.
RTB> Projected matrix is being saved.
RTB> Projected matrix trace = 2533.0585
RTB> 960 non-zero elements.
RTB> Normal end of RTB.
Diagstd> Entering in.
Openam> file on opening on unit 10:
diagrtb_work.sdijb
Diagstd> Projected matrix to be read from file: diagrtb_work.sdijb
Diagstd> CERFACS matrix format.
Diagstd> Projected matrix order = 48
Diagstd> Nb of non-zero elements: 960
Diagstd> Projected matrix trace = 2533.0585
Openam> file on opening on unit 11:
diagrtb_work.eigenfacs
Diagstd> Diagonalization.
Diagstd> 48 eigenvectors are computed.
Diagstd> 48 of them to be saved.
Diagstd> Sum of eigenvalues = 2533.0585
Diagstd> Best zero-eigenvalue found : 0.000000
Diagstd> 6 zero-eigenvalues, that is, below or equal to: 0.0000000
Diagstd> Selected eigenvalues:
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
0.0000000 3.9092402 5.4947847 6.2046694 7.8566787
11.2207385 18.6006826 20.2187978 21.2285263 27.4656441
30.3111134 34.2558665 36.9677805 37.6711497 40.3908031
44.1427800 46.7340562 47.6481007 51.3217892 52.2014997
56.2448399 58.0598782 60.5940974 61.2507839 63.0562421
63.7874549 64.0433477 65.8831758 67.3114339 71.0488352
72.1831321 73.5548249 81.5974473 84.6688666 87.4161419
88.9120241 96.9557139 100.9888638 102.6536149 118.6260790
126.0656137 158.3973698 165.9139803
Diagstd> Frequencies (cm-1, if the input matrix is a hessian in CHARMM units):
0.0034339 0.0034339 0.0034339 0.0034340 0.0034340
0.0034340 214.7046547 254.5485453 270.4921109 304.3790629
363.7525121 468.3383496 488.2845073 500.3284551 569.1020817
597.8554943 635.5690768 660.2478094 666.4993305 690.1389271
721.4813689 742.3556505 749.5801499 777.9401290 784.5791636
814.3978582 827.4339582 845.2991660 849.8672738 862.3018599
867.2871611 869.0250456 881.4192739 890.9220367 915.3217059
922.5993444 931.3241471 980.9199478 999.2108780 1015.2923121
1023.9424047 1069.2567106 1091.2695155 1100.2272671 1182.7293335
1219.2523504 1366.6876288 1398.7392809
Diagstd> Normal end.
Rtb_to_modes> Entering in.
Rtb_to_modes> Number of atoms in temporary block-file = 33
Rtb_to_modes> Number of blocs = 8
Openam> file on opening on unit 10:
diagrtb_work.eigenfacs
Openam> file on opening on unit 11:
matrix.eigenrtb
Rdmodfacs> Entering in.
Rdmodfacs> Old Blzpack file format detected.
Rdmodfacs> Eigenvector number: 1
Rdmodfacs> Corresponding eigenvalue: 9.9996E-10
Rdmodfacs> Eigenvector number: 2
Rdmodfacs> Corresponding eigenvalue: 9.9998E-10
Rdmodfacs> Eigenvector number: 3
Rdmodfacs> Corresponding eigenvalue: 9.9999E-10
Rdmodfacs> Eigenvector number: 4
Rdmodfacs> Corresponding eigenvalue: 1.0000E-09
Rdmodfacs> Eigenvector number: 5
Rdmodfacs> Corresponding eigenvalue: 1.0000E-09
Rdmodfacs> Eigenvector number: 6
Rdmodfacs> Corresponding eigenvalue: 1.0000E-09
Rdmodfacs> Eigenvector number: 7
Rdmodfacs> Corresponding eigenvalue: 3.909
Rdmodfacs> Eigenvector number: 8
Rdmodfacs> Corresponding eigenvalue: 5.495
Rdmodfacs> Eigenvector number: 9
Rdmodfacs> Corresponding eigenvalue: 6.205
Rdmodfacs> Eigenvector number: 10
Rdmodfacs> Corresponding eigenvalue: 7.857
Rdmodfacs> Eigenvector number: 11
Rdmodfacs> Corresponding eigenvalue: 11.22
Rdmodfacs> Eigenvector number: 12
Rdmodfacs> Corresponding eigenvalue: 18.60
Rdmodfacs> Eigenvector number: 13
Rdmodfacs> Corresponding eigenvalue: 20.22
Rdmodfacs> Eigenvector number: 14
Rdmodfacs> Corresponding eigenvalue: 21.23
Rdmodfacs> Eigenvector number: 15
Rdmodfacs> Corresponding eigenvalue: 27.47
Rdmodfacs> Eigenvector number: 16
Rdmodfacs> Corresponding eigenvalue: 30.31
Rdmodfacs> Eigenvector number: 17
Rdmodfacs> Corresponding eigenvalue: 34.26
Rdmodfacs> Eigenvector number: 18
Rdmodfacs> Corresponding eigenvalue: 36.97
Rdmodfacs> Eigenvector number: 19
Rdmodfacs> Corresponding eigenvalue: 37.67
Rdmodfacs> Eigenvector number: 20
Rdmodfacs> Corresponding eigenvalue: 40.39
Rdmodfacs> Eigenvector number: 21
Rdmodfacs> Corresponding eigenvalue: 44.14
Rdmodfacs> Eigenvector number: 22
Rdmodfacs> Corresponding eigenvalue: 46.73
Rdmodfacs> Eigenvector number: 23
Rdmodfacs> Corresponding eigenvalue: 47.65
Rdmodfacs> Eigenvector number: 24
Rdmodfacs> Corresponding eigenvalue: 51.32
Rdmodfacs> Eigenvector number: 25
Rdmodfacs> Corresponding eigenvalue: 52.20
Rdmodfacs> Eigenvector number: 26
Rdmodfacs> Corresponding eigenvalue: 56.24
Rdmodfacs> Eigenvector number: 27
Rdmodfacs> Corresponding eigenvalue: 58.06
Rdmodfacs> Eigenvector number: 28
Rdmodfacs> Corresponding eigenvalue: 60.59
Rdmodfacs> Eigenvector number: 29
Rdmodfacs> Corresponding eigenvalue: 61.25
Rdmodfacs> Eigenvector number: 30
Rdmodfacs> Corresponding eigenvalue: 63.06
Rdmodfacs> Eigenvector number: 31
Rdmodfacs> Corresponding eigenvalue: 63.79
Rdmodfacs> Eigenvector number: 32
Rdmodfacs> Corresponding eigenvalue: 64.04
Rdmodfacs> Eigenvector number: 33
Rdmodfacs> Corresponding eigenvalue: 65.88
Rdmodfacs> Eigenvector number: 34
Rdmodfacs> Corresponding eigenvalue: 67.31
Rdmodfacs> Eigenvector number: 35
Rdmodfacs> Corresponding eigenvalue: 71.05
Rdmodfacs> Eigenvector number: 36
Rdmodfacs> Corresponding eigenvalue: 72.18
Rdmodfacs> Eigenvector number: 37
Rdmodfacs> Corresponding eigenvalue: 73.55
Rdmodfacs> Eigenvector number: 38
Rdmodfacs> Corresponding eigenvalue: 81.60
Rdmodfacs> Eigenvector number: 39
Rdmodfacs> Corresponding eigenvalue: 84.67
Rdmodfacs> Eigenvector number: 40
Rdmodfacs> Corresponding eigenvalue: 87.42
Rdmodfacs> Eigenvector number: 41
Rdmodfacs> Corresponding eigenvalue: 88.91
Rdmodfacs> Eigenvector number: 42
Rdmodfacs> Corresponding eigenvalue: 96.96
Rdmodfacs> Eigenvector number: 43
Rdmodfacs> Corresponding eigenvalue: 101.0
Rdmodfacs> Eigenvector number: 44
Rdmodfacs> Corresponding eigenvalue: 102.7
Rdmodfacs> Eigenvector number: 45
Rdmodfacs> Corresponding eigenvalue: 118.6
Rdmodfacs> Eigenvector number: 46
Rdmodfacs> Corresponding eigenvalue: 126.1
Rdmodfacs> Eigenvector number: 47
Rdmodfacs> Corresponding eigenvalue: 158.4
Rdmodfacs> Eigenvector number: 48
Rdmodfacs> Corresponding eigenvalue: 165.9
Rtb_to_modes> 48 vectors, with 48 coordinates in vector file.
Norm of eigenvectors in projected coordinates (one expected):
1.00000 0.99999 1.00002 1.00002 1.00002
0.99999 1.00000 0.99998 1.00001 0.99998
0.99997 1.00002 1.00003 0.99995 0.99998
0.99996 0.99998 1.00000 1.00003 0.99997
0.99999 1.00002 1.00001 1.00002 0.99999
0.99999 1.00002 0.99999 1.00000 1.00001
1.00002 0.99995 0.99998 0.99999 1.00000
1.00000 0.99998 1.00000 1.00002 0.99999
0.99991 0.99998 1.00001 1.00002 0.99999
1.00006 1.00002 0.99997
Rtb_to_modes> RTB block-file is being read.
Rtb_to_modes> 594 lines found in RTB file.
Norm of eigenvectors in cartesian coordinates (one expected):
1.00000 0.99999 1.00002 1.00002 1.00002
0.99999 1.00000 0.99998 1.00001 0.99998
0.99997 1.00002 1.00003 0.99995 0.99998
0.99996 0.99998 1.00000 1.00003 0.99997
0.99999 1.00002 1.00001 1.00002 0.99999
0.99999 1.00002 0.99999 1.00000 1.00001
1.00002 0.99995 0.99998 0.99999 1.00000
1.00000 0.99998 1.00000 1.00002 0.99999
0.99991 0.99998 1.00001 1.00002 0.99999
1.00006 1.00002 0.99997
Orthogonality of first eigenvectors (zero expected):
Vector 2:-0.000
Vector 3: 0.000-0.000
Vector 4:-0.000-0.000-0.000
Vector 5:-0.000-0.000-0.000-0.000
Vector 6: 0.000-0.000 0.000 0.000 0.000
Vector 7:-0.000-0.000-0.000 0.000-0.000 0.000
Vector 8: 0.000 0.000 0.000-0.000-0.000 0.000-0.000
Vector 9:-0.000-0.000-0.000-0.000-0.000-0.000 0.000-0.000
Vector 10: 0.000 0.000-0.000-0.000-0.000 0.000-0.000 0.000 0.000
Rtb_to_modes> 48 eigenvectors saved.
Rtb_to_modes> Normal end.
Diagrtb> Normal end.
B-factor analysis
Bfactors> Version 1.22, Bordeaux.
Getnam> Eigenvector filename ?
Getnam> 22112911152777313.eigenfacs
Openam> file on opening on unit 10:
22112911152777313.eigenfacs
Getnam> Corresponding pdb filename ?
Getnam> 22112911152777313.atom
Openam> file on opening on unit 11:
22112911152777313.atom
Getnum> Number of skipped eigenvectors ?
Getnum> 0
Getnum> Number of usefull eigenvectors ?
Getnum> 10000
%Getnum-Err: number larger than 106 This is not allowed. Sorry.
Rdatompdb> Reading pdb file.
Rdatompdb> End of file reached.
Rdatompdb> Number of I/O errors: 0
Rdatompdb> Number of residues found = 10
First residue number = 63
Last residue number = 101
Number of atoms found = 33
Mean number per residue = 3.3
Rdmodfacs> Old Blzpack file format detected.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 1
Rdmodfacs> Valeur propre du vecteur en lecture: 9.9996E-10
Rdmodfacs> Numero du vecteur CERFACS en lecture: 2
Rdmodfacs> Valeur propre du vecteur en lecture: 9.9998E-10
Rdmodfacs> Numero du vecteur CERFACS en lecture: 3
Rdmodfacs> Valeur propre du vecteur en lecture: 9.9999E-10
Rdmodfacs> Numero du vecteur CERFACS en lecture: 4
Rdmodfacs> Valeur propre du vecteur en lecture: 1.0000E-09
Rdmodfacs> Numero du vecteur CERFACS en lecture: 5
Rdmodfacs> Valeur propre du vecteur en lecture: 1.0000E-09
Rdmodfacs> Numero du vecteur CERFACS en lecture: 6
Rdmodfacs> Valeur propre du vecteur en lecture: 1.0000E-09
Rdmodfacs> Numero du vecteur CERFACS en lecture: 7
Rdmodfacs> Valeur propre du vecteur en lecture: 3.909
Rdmodfacs> Numero du vecteur CERFACS en lecture: 8
Rdmodfacs> Valeur propre du vecteur en lecture: 5.495
Rdmodfacs> Numero du vecteur CERFACS en lecture: 9
Rdmodfacs> Valeur propre du vecteur en lecture: 6.205
Rdmodfacs> Numero du vecteur CERFACS en lecture: 10
Rdmodfacs> Valeur propre du vecteur en lecture: 7.857
Rdmodfacs> Numero du vecteur CERFACS en lecture: 11
Rdmodfacs> Valeur propre du vecteur en lecture: 11.22
Rdmodfacs> Numero du vecteur CERFACS en lecture: 12
Rdmodfacs> Valeur propre du vecteur en lecture: 18.60
Rdmodfacs> Numero du vecteur CERFACS en lecture: 13
Rdmodfacs> Valeur propre du vecteur en lecture: 20.22
Rdmodfacs> Numero du vecteur CERFACS en lecture: 14
Rdmodfacs> Valeur propre du vecteur en lecture: 21.23
Rdmodfacs> Numero du vecteur CERFACS en lecture: 15
Rdmodfacs> Valeur propre du vecteur en lecture: 27.47
Rdmodfacs> Numero du vecteur CERFACS en lecture: 16
Rdmodfacs> Valeur propre du vecteur en lecture: 30.31
Rdmodfacs> Numero du vecteur CERFACS en lecture: 17
Rdmodfacs> Valeur propre du vecteur en lecture: 34.26
Rdmodfacs> Numero du vecteur CERFACS en lecture: 18
Rdmodfacs> Valeur propre du vecteur en lecture: 36.97
Rdmodfacs> Numero du vecteur CERFACS en lecture: 19
Rdmodfacs> Valeur propre du vecteur en lecture: 37.67
Rdmodfacs> Numero du vecteur CERFACS en lecture: 20
Rdmodfacs> Valeur propre du vecteur en lecture: 40.39
Rdmodfacs> Numero du vecteur CERFACS en lecture: 21
Rdmodfacs> Valeur propre du vecteur en lecture: 44.14
Rdmodfacs> Numero du vecteur CERFACS en lecture: 22
Rdmodfacs> Valeur propre du vecteur en lecture: 46.73
Rdmodfacs> Numero du vecteur CERFACS en lecture: 23
Rdmodfacs> Valeur propre du vecteur en lecture: 47.65
Rdmodfacs> Numero du vecteur CERFACS en lecture: 24
Rdmodfacs> Valeur propre du vecteur en lecture: 51.32
Rdmodfacs> Numero du vecteur CERFACS en lecture: 25
Rdmodfacs> Valeur propre du vecteur en lecture: 52.20
Rdmodfacs> Numero du vecteur CERFACS en lecture: 26
Rdmodfacs> Valeur propre du vecteur en lecture: 56.24
Rdmodfacs> Numero du vecteur CERFACS en lecture: 27
Rdmodfacs> Valeur propre du vecteur en lecture: 58.06
Rdmodfacs> Numero du vecteur CERFACS en lecture: 28
Rdmodfacs> Valeur propre du vecteur en lecture: 60.59
Rdmodfacs> Numero du vecteur CERFACS en lecture: 29
Rdmodfacs> Valeur propre du vecteur en lecture: 61.25
Rdmodfacs> Numero du vecteur CERFACS en lecture: 30
Rdmodfacs> Valeur propre du vecteur en lecture: 63.06
Rdmodfacs> Numero du vecteur CERFACS en lecture: 31
Rdmodfacs> Valeur propre du vecteur en lecture: 63.79
Rdmodfacs> Numero du vecteur CERFACS en lecture: 32
Rdmodfacs> Valeur propre du vecteur en lecture: 64.04
Rdmodfacs> Numero du vecteur CERFACS en lecture: 33
Rdmodfacs> Valeur propre du vecteur en lecture: 65.88
Rdmodfacs> Numero du vecteur CERFACS en lecture: 34
Rdmodfacs> Valeur propre du vecteur en lecture: 67.31
Rdmodfacs> Numero du vecteur CERFACS en lecture: 35
Rdmodfacs> Valeur propre du vecteur en lecture: 71.05
Rdmodfacs> Numero du vecteur CERFACS en lecture: 36
Rdmodfacs> Valeur propre du vecteur en lecture: 72.18
Rdmodfacs> Numero du vecteur CERFACS en lecture: 37
Rdmodfacs> Valeur propre du vecteur en lecture: 73.55
Rdmodfacs> Numero du vecteur CERFACS en lecture: 38
Rdmodfacs> Valeur propre du vecteur en lecture: 81.60
Rdmodfacs> Numero du vecteur CERFACS en lecture: 39
Rdmodfacs> Valeur propre du vecteur en lecture: 84.67
Rdmodfacs> Numero du vecteur CERFACS en lecture: 40
Rdmodfacs> Valeur propre du vecteur en lecture: 87.42
Rdmodfacs> Numero du vecteur CERFACS en lecture: 41
Rdmodfacs> Valeur propre du vecteur en lecture: 88.91
Rdmodfacs> Numero du vecteur CERFACS en lecture: 42
Rdmodfacs> Valeur propre du vecteur en lecture: 96.96
Rdmodfacs> Numero du vecteur CERFACS en lecture: 43
Rdmodfacs> Valeur propre du vecteur en lecture: 101.0
Rdmodfacs> Numero du vecteur CERFACS en lecture: 44
Rdmodfacs> Valeur propre du vecteur en lecture: 102.7
Rdmodfacs> Numero du vecteur CERFACS en lecture: 45
Rdmodfacs> Valeur propre du vecteur en lecture: 118.6
Rdmodfacs> Numero du vecteur CERFACS en lecture: 46
Rdmodfacs> Valeur propre du vecteur en lecture: 126.1
Rdmodfacs> Numero du vecteur CERFACS en lecture: 47
Rdmodfacs> Valeur propre du vecteur en lecture: 158.4
Rdmodfacs> Numero du vecteur CERFACS en lecture: 48
Rdmodfacs> Valeur propre du vecteur en lecture: 165.9
Bfactors> 48 vectors, 99 coordinates in file.
%Bfactors-Wn> All vectors required were not found in vector file.
Openam> file on opening on unit 12:
bfactors.pred
Bfactors> Best zero-eigenvalue found : 0.000000
Bfactors> 6 eigenvalues less than : 0.000000
Bfactors> Lowest non-zero eigenvalue : 3.909000
Bfactors> 42 eigenvectors will be considered.
Bfactors> Rotation-Tranlation modes are skipped.
Bfactors> Mass-weighted B-factors are computed.
(CHARMM units assumed for eigenvalues)
%Bfactors-Wn> Experimental B-factors are nearly constant !
Bfactors> = 0.615 +/- 0.33
Bfactors> = 0.000 +/- 0.00
Bfactors> Shiftng-fct= -0.615
Bfactors> Scaling-fct= 0.000
Bfactors> Predicted, Scaled and Experimental B-factors are saved.
Bfactors> Normal end.
check_modes
Chkmod> Version 1.00, Bordeaux.
Getnam> Eigenvector filename ?
Getnam> 22112911152777313.eigenfacs
Openam> file on opening on unit 10:
22112911152777313.eigenfacs
Rdmodfacs> Old Blzpack file format detected.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 1
Rdmodfacs> Frequence du vecteur en lecture: 3.4337E-03
Rdmodfacs> Numero du vecteur CERFACS en lecture: 2
Rdmodfacs> Frequence du vecteur en lecture: 3.4338E-03
Rdmodfacs> Numero du vecteur CERFACS en lecture: 3
Rdmodfacs> Frequence du vecteur en lecture: 3.4338E-03
Rdmodfacs> Numero du vecteur CERFACS en lecture: 4
Rdmodfacs> Frequence du vecteur en lecture: 3.4338E-03
Rdmodfacs> Numero du vecteur CERFACS en lecture: 5
Rdmodfacs> Frequence du vecteur en lecture: 3.4338E-03
Rdmodfacs> Numero du vecteur CERFACS en lecture: 6
Rdmodfacs> Frequence du vecteur en lecture: 3.4338E-03
Rdmodfacs> Numero du vecteur CERFACS en lecture: 7
Rdmodfacs> Frequence du vecteur en lecture: 214.7
Rdmodfacs> Numero du vecteur CERFACS en lecture: 8
Rdmodfacs> Frequence du vecteur en lecture: 254.5
Rdmodfacs> Numero du vecteur CERFACS en lecture: 9
Rdmodfacs> Frequence du vecteur en lecture: 270.5
Rdmodfacs> Numero du vecteur CERFACS en lecture: 10
Rdmodfacs> Frequence du vecteur en lecture: 304.4
Rdmodfacs> Numero du vecteur CERFACS en lecture: 11
Rdmodfacs> Frequence du vecteur en lecture: 363.7
Rdmodfacs> Numero du vecteur CERFACS en lecture: 12
Rdmodfacs> Frequence du vecteur en lecture: 468.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 13
Rdmodfacs> Frequence du vecteur en lecture: 488.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 14
Rdmodfacs> Frequence du vecteur en lecture: 500.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 15
Rdmodfacs> Frequence du vecteur en lecture: 569.1
Rdmodfacs> Numero du vecteur CERFACS en lecture: 16
Rdmodfacs> Frequence du vecteur en lecture: 597.8
Rdmodfacs> Numero du vecteur CERFACS en lecture: 17
Rdmodfacs> Frequence du vecteur en lecture: 635.6
Rdmodfacs> Numero du vecteur CERFACS en lecture: 18
Rdmodfacs> Frequence du vecteur en lecture: 660.2
Rdmodfacs> Numero du vecteur CERFACS en lecture: 19
Rdmodfacs> Frequence du vecteur en lecture: 666.5
Rdmodfacs> Numero du vecteur CERFACS en lecture: 20
Rdmodfacs> Frequence du vecteur en lecture: 690.1
Rdmodfacs> Numero du vecteur CERFACS en lecture: 21
Rdmodfacs> Frequence du vecteur en lecture: 721.4
Rdmodfacs> Numero du vecteur CERFACS en lecture: 22
Rdmodfacs> Frequence du vecteur en lecture: 742.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 23
Rdmodfacs> Frequence du vecteur en lecture: 749.6
Rdmodfacs> Numero du vecteur CERFACS en lecture: 24
Rdmodfacs> Frequence du vecteur en lecture: 777.9
Rdmodfacs> Numero du vecteur CERFACS en lecture: 25
Rdmodfacs> Frequence du vecteur en lecture: 784.5
Rdmodfacs> Numero du vecteur CERFACS en lecture: 26
Rdmodfacs> Frequence du vecteur en lecture: 814.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 27
Rdmodfacs> Frequence du vecteur en lecture: 827.4
Rdmodfacs> Numero du vecteur CERFACS en lecture: 28
Rdmodfacs> Frequence du vecteur en lecture: 845.2
Rdmodfacs> Numero du vecteur CERFACS en lecture: 29
Rdmodfacs> Frequence du vecteur en lecture: 849.8
Rdmodfacs> Numero du vecteur CERFACS en lecture: 30
Rdmodfacs> Frequence du vecteur en lecture: 862.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 31
Rdmodfacs> Frequence du vecteur en lecture: 867.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 32
Rdmodfacs> Frequence du vecteur en lecture: 869.0
Rdmodfacs> Numero du vecteur CERFACS en lecture: 33
Rdmodfacs> Frequence du vecteur en lecture: 881.4
Rdmodfacs> Numero du vecteur CERFACS en lecture: 34
Rdmodfacs> Frequence du vecteur en lecture: 890.9
Rdmodfacs> Numero du vecteur CERFACS en lecture: 35
Rdmodfacs> Frequence du vecteur en lecture: 915.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 36
Rdmodfacs> Frequence du vecteur en lecture: 922.5
Rdmodfacs> Numero du vecteur CERFACS en lecture: 37
Rdmodfacs> Frequence du vecteur en lecture: 931.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 38
Rdmodfacs> Frequence du vecteur en lecture: 980.9
Rdmodfacs> Numero du vecteur CERFACS en lecture: 39
Rdmodfacs> Frequence du vecteur en lecture: 999.2
Rdmodfacs> Numero du vecteur CERFACS en lecture: 40
Rdmodfacs> Frequence du vecteur en lecture: 1015.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 41
Rdmodfacs> Frequence du vecteur en lecture: 1024.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 42
Rdmodfacs> Frequence du vecteur en lecture: 1069.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 43
Rdmodfacs> Frequence du vecteur en lecture: 1091.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 44
Rdmodfacs> Frequence du vecteur en lecture: 1100.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 45
Rdmodfacs> Frequence du vecteur en lecture: 1183.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 46
Rdmodfacs> Frequence du vecteur en lecture: 1219.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 47
Rdmodfacs> Frequence du vecteur en lecture: 1367.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 48
Rdmodfacs> Frequence du vecteur en lecture: 1399.
Chkmod> 48 vectors, 99 coordinates in file.
Chkmod> That is: 33 cartesian points.
Openam> file on opening on unit 11:
Chkmod.res
Chkmod> Collectivity=f(frequency) to be written in this file.
%Chkmod-Wn> Norm of vector 3 is: 1.0001 (instead of 1.0000).
%Chkmod-Wn> Norm of vector 15 is: 0.9999 (instead of 1.0000).
%Chkmod-Wn> Norm of vector 18 is: 1.0001 (instead of 1.0000).
%Chkmod-Wn> Norm of vector 19 is: 1.0001 (instead of 1.0000).
%Chkmod-Wn> Norm of vector 32 is: 0.9998 (instead of 1.0000).
%Chkmod-Wn> Norm of vector 41 is: 0.9999 (instead of 1.0000).
%Chkmod-Wn> Norm of vector 48 is: 0.9999 (instead of 1.0000).
Chkmod> Normal end.
0.0034 0.7148
0.0034 0.8841
0.0034 0.8877
0.0034 0.7478
0.0034 0.7687
0.0034 0.9607
214.6888 0.4170
254.5426 0.3401
270.4877 0.6126
304.3722 0.5550
363.7249 0.3020
468.3097 0.7113
488.2781 0.2801
500.3243 0.1199
569.1228 0.4246
597.8189 0.6425
635.5801 0.6209
660.2393 0.5504
666.4605 0.4947
690.1024 0.3951
721.4277 0.5284
742.2916 0.6577
749.5629 0.5771
777.8932 0.5138
784.5342 0.3251
814.3279 0.5797
827.3993 0.6824
845.2343 0.3606
849.8254 0.3877
862.2905 0.6275
867.2672 0.4323
868.9650 0.6013
881.3602 0.4050
890.8743 0.5841
915.2899 0.4252
922.5397 0.5183
931.2536 0.5276
980.8932 0.6171
999.1747 0.5680
1015.2711 0.6448
1023.8868 0.5960
1069.2344 0.4465
1091.2828 0.4611
1100.4286 0.4508
1182.5486 0.6877
1219.3663 0.5191
1366.6403 0.5221
1398.6203 0.6514
getting mode 7
running: ../../bin/get_modes.sh 22112911152777313 7 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 7
calculating perturbed structure for DQ=-100
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-80
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-60
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-40
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-20
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=0
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=20
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=40
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=60
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=80
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=100
22112911152777313.eigenfacs
22112911152777313.atom
making animated gifs
11 models are in 22112911152777313.7.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 22112911152777313.7.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 22112911152777313.7.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
getting mode 8
running: ../../bin/get_modes.sh 22112911152777313 8 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 8
calculating perturbed structure for DQ=-100
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-80
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-60
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-40
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-20
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=0
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=20
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=40
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=60
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=80
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=100
22112911152777313.eigenfacs
22112911152777313.atom
making animated gifs
11 models are in 22112911152777313.8.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 22112911152777313.8.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 22112911152777313.8.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
getting mode 9
running: ../../bin/get_modes.sh 22112911152777313 9 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 9
calculating perturbed structure for DQ=-100
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-80
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-60
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-40
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-20
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=0
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=20
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=40
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=60
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=80
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=100
22112911152777313.eigenfacs
22112911152777313.atom
making animated gifs
11 models are in 22112911152777313.9.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 22112911152777313.9.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 22112911152777313.9.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
getting mode 10
running: ../../bin/get_modes.sh 22112911152777313 10 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 10
calculating perturbed structure for DQ=-100
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-80
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-60
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-40
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-20
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=0
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=20
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=40
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=60
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=80
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=100
22112911152777313.eigenfacs
22112911152777313.atom
making animated gifs
11 models are in 22112911152777313.10.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 22112911152777313.10.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 22112911152777313.10.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
getting mode 11
running: ../../bin/get_modes.sh 22112911152777313 11 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 11
calculating perturbed structure for DQ=-100
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-80
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-60
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-40
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=-20
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=0
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=20
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=40
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=60
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=80
22112911152777313.eigenfacs
22112911152777313.atom
calculating perturbed structure for DQ=100
22112911152777313.eigenfacs
22112911152777313.atom
making animated gifs
11 models are in 22112911152777313.11.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 22112911152777313.11.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 22112911152777313.11.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
22112911152777313.10.pdb
22112911152777313.11.pdb
22112911152777313.7.pdb
22112911152777313.8.pdb
22112911152777313.9.pdb
STDERR:
real 0m0.031s
user 0m0.024s
sys 0m0.004s
pstopnm: Writing ppmraw file
pstopnm: Writing ppmraw file
pstopnm: Writing ppmraw file
pstopnm: Writing ppmraw file
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pstopnm: Writing ppmraw file
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pstopnm: Writing ppmraw file
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pstopnm: Writing ppmraw file
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pstopnm: Writing ppmraw file
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pstopnm: Writing ppmraw file
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pstopnm: Writing ppmraw file
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pstopnm: Writing ppmraw file
pstopnm: Writing ppmraw file
pstopnm: Writing ppmraw file
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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