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Алиса - Веретено

Saturday, April 25, 2015

QCWO


HEADER    UNCLASSIFIED                            25-Apr-15
TITLE     ALL ATOM STRUCTURE FOR MOLECULE UNK                                   
AUTHOR    GROMOS AUTOMATIC TOPOLOGY BUILDER REVISION 2015-03-06
AUTHOR   2  http://compbio.biosci.uq.edu.au/atb
HETATM    1   O3 QCWO    0      -6.629  -1.565  -1.580  1.00  0.00           O
HETATM    2   S1 QCWO    0      -7.182  -0.859  -0.079  1.00  0.00           S
HETATM    3   O1 QCWO    0      -8.883   0.153  -0.543  1.00  0.00           O
HETATM    4   O2 QCWO    0      -6.708  -2.285   1.295  1.00  0.00           O
HETATM    5   C6 QCWO    0      -5.956   0.482   0.170  1.00  0.00           C
HETATM    6   C7 QCWO    0      -6.394   1.672   0.564  1.00  0.00           C
HETATM    7   H4 QCWO    0      -7.451   1.875   0.681  1.00  0.00           H
HETATM    8   C2 QCWO    0      -5.417   2.747   0.827  1.00  0.00           C
HETATM    9   N1 QCWO    0      -5.805   3.958   1.180  1.00  0.00           N
HETATM   10   H1 QCWO    0      -5.068   4.663   1.323  1.00  0.00           H
HETATM   11   C1 QCWO    0      -7.207   4.413   1.382  1.00  0.00           C
HETATM   12   H1 QCWO    0      -7.681   3.816   2.163  1.00  0.00           H
HETATM   13   H2 QCWO    0      -7.763   4.321   0.448  1.00  0.00           H
HETATM   14   H3 QCWO    0      -7.169   5.456   1.688  1.00  0.00           H
HETATM   15   C3 QCWO    0      -3.980   2.469   0.657  1.00  0.00           C
HETATM   16   H2 QCWO    0      -3.294   3.289   0.829  1.00  0.00           H
HETATM   17   C4 QCWO    0      -3.560   1.260   0.300  1.00  0.00           C
HETATM   18   H3 QCWO    0      -2.500   1.072   0.153  1.00  0.00           H
HETATM   19   C5 QCWO    0      -4.504   0.141   0.021  1.00  0.00           C
HETATM   20   N2 QCWO    0      -4.214  -1.062  -0.354  1.00  0.00           N
HETATM   21   H5 QCWO    0      -5.735  -1.915  -1.296  1.00  0.00           H
HETATM   22   C8 QCWO    0      -2.829  -1.523  -0.371  1.00  0.00           C
HETATM   23   C9 QCWO    0      -2.342  -2.148  -1.517  1.00  0.00           C
HETATM   24   H6 QCWO    0      -2.962  -2.209  -2.403  1.00  0.00           H
HETATM   25  C13 QCWO    0      -2.048  -1.462   0.784  1.00  0.00           C
HETATM   26   H9 QCWO    0      -2.446  -1.011   1.684  1.00  0.00           H
HETATM   27  C12 QCWO    0      -0.781  -2.014   0.781  1.00  0.00           C
HETATM   28   H8 QCWO    0      -0.180  -1.980   1.681  1.00  0.00           H
HETATM   29  C11 QCWO    0      -0.272  -2.618  -0.369  1.00  0.00           C
HETATM   30  C10 QCWO    0      -1.061  -2.673  -1.518  1.00  0.00           C
HETATM   31   H7 QCWO    0      -0.671  -3.149  -2.408  1.00  0.00           H
HETATM   32   N3 QCWO    0       1.059  -3.237  -0.379  1.00  0.00           N
HETATM   33  H10 QCWO    0       1.164  -3.778   0.492  1.00  0.00           H
HETATM   34  C14 QCWO    0       2.173  -2.293  -0.450  1.00  0.00           C
HETATM   35  C15 QCWO    0       2.197  -1.269  -1.397  1.00  0.00           C
HETATM   36  H11 QCWO    0       1.357  -1.136  -2.064  1.00  0.00           H
HETATM   37  C19 QCWO    0       3.269  -2.457   0.387  1.00  0.00           C
HETATM   38  H13 QCWO    0       3.276  -3.253   1.121  1.00  0.00           H
HETATM   39  C18 QCWO    0       4.358  -1.604   0.295  1.00  0.00           C
HETATM   40   S2 QCWO    0       5.747  -1.837   1.468  1.00  0.00           S
HETATM   41   O4 QCWO    0       5.269  -0.820   3.056  1.00  0.00           O
HETATM   42   O5 QCWO    0       5.969  -3.755   1.674  1.00  0.00           O
HETATM   43   O6 QCWO    0       7.182  -1.038   0.639  1.00  0.00           O
HETATM   44  C17 QCWO    0       4.397  -0.565  -0.646  1.00  0.00           C
HETATM   45  C16 QCWO    0       3.290  -0.432  -1.495  1.00  0.00           C
HETATM   46  H12 QCWO    0       3.300   0.342  -2.250  1.00  0.00           H
HETATM   47   N4 QCWO    0       5.592   0.211  -0.790  1.00  0.00           N
HETATM   48  H14 QCWO    0       6.389  -0.255  -0.196  1.00  0.00           H
HETATM   49  C20 QCWO    0       5.544   1.637  -0.714  1.00  0.00           C
HETATM   50  C25 QCWO    0       4.392   2.403  -0.536  1.00  0.00           C
HETATM   51  H18 QCWO    0       3.434   1.920  -0.421  1.00  0.00           H
HETATM   52  C21 QCWO    0       6.767   2.323  -0.824  1.00  0.00           C
HETATM   53  H15 QCWO    0       7.675   1.749  -0.951  1.00  0.00           H
HETATM   54  C22 QCWO    0       6.822   3.697  -0.763  1.00  0.00           C
HETATM   55  H16 QCWO    0       7.782   4.194  -0.845  1.00  0.00           H
HETATM   56  C23 QCWO    0       5.667   4.462  -0.594  1.00  0.00           C
HETATM   57  C24 QCWO    0       4.461   3.787  -0.482  1.00  0.00           C
HETATM   58  H17 QCWO    0       3.548   4.351  -0.339  1.00  0.00           H
HETATM   59  C26 QCWO    0       5.738   5.985  -0.542  1.00  0.00           C
HETATM   60  H11 QCWO    0       4.825   6.400  -0.125  1.00  0.00           H
HETATM   61  H21 QCWO    0       5.873   6.405  -1.537  1.00  0.00           H
HETATM   62  H31 QCWO    0       6.574   6.315   0.070  1.00  0.00           H
CONECT    1    2
CONECT    2    1    3    4    5
CONECT    3    2
CONECT    4    2
CONECT    5    2    6   19
CONECT    6    5    7    8
CONECT    7    6
CONECT    8    6    9   15
CONECT    9    8   10   11
CONECT   10    9
CONECT   11    9   12   13   14
CONECT   12   11
CONECT   13   11
CONECT   14   11
CONECT   15    8   16   17
CONECT   16   15
CONECT   17   15   18   19
CONECT   18   17
CONECT   19    5   17   20
CONECT   20   19   21   22
CONECT   21   20
CONECT   22   20   23   25
CONECT   23   22   24   30
CONECT   24   23
CONECT   25   22   26   27
CONECT   26   25
CONECT   27   25   28   29
CONECT   28   27
CONECT   29   27   30   32
CONECT   30   23   29   31
CONECT   31   30
CONECT   32   29   33   34
CONECT   33   32
CONECT   34   32   35   37
CONECT   35   34   36   45
CONECT   36   35
CONECT   37   34   38   39
CONECT   38   37
CONECT   39   37   40   44
CONECT   40   39   41   42   43
CONECT   41   40
CONECT   42   40
CONECT   43   40
CONECT   44   39   45   47
CONECT   45   35   44   46
CONECT   46   45
CONECT   47   44   48   49
CONECT   48   47
CONECT   49   47   50   52
CONECT   50   49   51   57
CONECT   51   50
CONECT   52   49   53   54
CONECT   53   52
CONECT   54   52   55   56
CONECT   55   54
CONECT   56   54   57   59
CONECT   57   50   56   58
CONECT   58   57
CONECT   59   56   60   61   62
CONECT   60   59
CONECT   61   59
CONECT   62   59
END
;----------------------------TITLE -------------------------------------------
;   None
;
; This file was generated at 15:10 on 2015-04-25 by
;
;                  Automatic Topology Builder  
;
;                   REVISION 2015-03-06
;-----------------------------------------------------------------------------
; Authors     : Alpeshkumar K. Malde, Le Zuo, Matthew Breeze, Martin Stroet, Alan E. Mark
;
; Institute   : Molecular Dynamics group, 
;               School of Chemistry and Molecular Biosciences (SCMB),
;               The University of Queensland, QLD 4072, Australia
; URL         : http://compbio.biosci.uq.edu.au/atb
; Citation    : Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.
;               An Automated force field Topology Builder (ATB) and repository: version 1.0.
;               Journal of Chemical Theory and Computation, 2011, 7(12), 4026-4037.
;               http://pubs.acs.org/doi/abs/10.1021/ct200196m
;
; Disclaimer  : 
;      While every effort has been made to ensure the accuracy and validity of parameters provided below
;      the assignment of parameters is being based on an automated procedure combining data provided by a
;      given user as well as calculations performed using third party software. They are provided as a guide.
;      The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided
;      are appropriate for use in any specific application. Users are advised to treat these parameters with discretion
;      and to perform additional validation tests for their specific application if required. Neither the authors
;      of the ATB or The University of Queensland except any responsibly for how the parameters may be used.
;
; Release notes and warnings: 
;  (1) The topology is based on a set of atomic coordinates and other data provided by the user after
;      after quantum mechanical optimization of the structure using different levels of theory depending on
;      the nature of the molecule.
;  (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.
;      In these cases alternative type codes are provided at the end of the line.
;  (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral
;      type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard"
;      or "uncertain" in comments.
;  (4) In some cases it is not possible to assign an appropriate parameter automatically. "%" is used as a place holder
;      for those fields that could not be determined automatically. The parameters in these fields must be assigned manually
;      before the file can be used.
;-----------------------------------------------------------------------------
; Input Structure : QCWO
; Output          : ALL ATOM topology
; Use in conjunction with the corresponding all atom PDB file.
;----------------------------------------------------------------------------
; Initial Guess Topology Generation: 
; The topology was guessed from HF/STO-3G level in implicit water optimized geometry
; and MULLIKEN charges.
; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.
;
; Topology file generated at 15:04 on 25 Apr 2015 for molecule
; None (IUPAC: [5-(methylamino)-2-{[4-({4-[(4-methylphenyl)amino]-3-(trihydroxy-$l^{4}-sulfanyl)phenyl}amino)phenyl]amino}phenyl]-$l^{4}-sulfanetriol, database identifier: QCWO)
; by Automatic Topology Builder(revision 2015-03-06).
;
[ moleculetype ]
; Name   nrexcl
QCWO     3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1    OM    1    QCWO     O3    1   -0.249  15.9994 
    2 SDmso    1    QCWO     S1    1    0.248  32.0600 
    3    OM    1    QCWO     O1    1   -0.249  15.9994 
    4    OM    1    QCWO     O2    1   -0.249  15.9994 
    5     C    1    QCWO     C6    1    0.040  12.0110      ; -0.459
    6     C    1    QCWO     C7    2   -0.094  12.0110 
    7    HC    1    QCWO     H4    2    0.094   1.0080      ;  0.000
    8     C    1    QCWO     C2    3    0.289  12.0110 
    9    NT    1    QCWO     N1    3   -0.230  14.0067 
   10     H    1    QCWO     H1    3    0.315   1.0080 
   11     C    1    QCWO     C1    3   -0.053  12.0110 
   12    HC    1    QCWO     H1    3    0.120   1.0080 
   13    HC    1    QCWO     H2    3    0.120   1.0080 
   14    HC    1    QCWO     H3    3    0.120   1.0080      ;  0.681
   15     C    1    QCWO     C3    4   -0.059  12.0110 
   16    HC    1    QCWO     H2    4    0.122   1.0080 
   17     C    1    QCWO     C4    4    0.003  12.0110 
   18    HC    1    QCWO     H3    4    0.131   1.0080 
   19     C    1    QCWO     C5    4    0.126  12.0110      ;  0.323
   20    NT    1    QCWO     N2    5   -0.195  14.0067 
   21     H    1    QCWO     H5    5    0.269   1.0080 
   22     C    1    QCWO     C8    5    0.073  12.0110 
   23     C    1    QCWO     C9    5   -0.057  12.0110 
   24    HC    1    QCWO     H6    5    0.089   1.0080      ;  0.179
   25     C    1    QCWO    C13    6   -0.057  12.0110 
   26    HC    1    QCWO     H9    6    0.089   1.0080 
   27     C    1    QCWO    C12    6   -0.061  12.0110 
   28    HC    1    QCWO     H8    6    0.086   1.0080      ;  0.057
   29     C    1    QCWO    C11    7    0.104  12.0110 
   30     C    1    QCWO    C10    7   -0.061  12.0110 
   31    HC    1    QCWO     H7    7    0.086   1.0080 
   32    NT    1    QCWO     N3    7   -0.336  14.0067 
   33     H    1    QCWO    H10    7    0.179   1.0080 
   34     C    1    QCWO    C14    7    0.081  12.0110 
   35     C    1    QCWO    C15    7   -0.078  12.0110 
   36    HC    1    QCWO    H11    7    0.069   1.0080      ;  0.044
   37     C    1    QCWO    C19    8   -0.076  12.0110 
   38    HC    1    QCWO    H13    8    0.076   1.0080      ;  0.000
   39     C    1    QCWO    C18    9   -0.045  12.0110 
   40 SDmso    1    QCWO     S2    9    0.057  32.0600 
   41    OM    1    QCWO     O4    9   -0.249  15.9994 
   42    OM    1    QCWO     O5    9   -0.249  15.9994 
   43    OM    1    QCWO     O6    9   -0.249  15.9994      ; -0.735
   44     C    1    QCWO    C17   10    0.094  12.0110 
   45     C    1    QCWO    C16   10   -0.078  12.0110 
   46    HC    1    QCWO    H12   10    0.069   1.0080 
   47    NT    1    QCWO     N4   10   -0.409  14.0067 
   48     H    1    QCWO    H14   10    0.253   1.0080 
   49     C    1    QCWO    C20   10    0.100  12.0110 
   50     C    1    QCWO    C25   10   -0.099  12.0110 
   51    HC    1    QCWO    H18   10    0.057   1.0080      ; -0.013
   52     C    1    QCWO    C21   11   -0.099  12.0110 
   53    HC    1    QCWO    H15   11    0.057   1.0080 
   54     C    1    QCWO    C22   11   -0.070  12.0110 
   55    HC    1    QCWO    H16   11    0.058   1.0080      ; -0.054
   56     C    1    QCWO    C23   12   -0.013  12.0110 
   57     C    1    QCWO    C24   12   -0.070  12.0110 
   58    HC    1    QCWO    H17   12    0.058   1.0080 
   59     C    1    QCWO    C26   12   -0.187  12.0110 
   60    HC    1    QCWO    H11   12    0.063   1.0080 
   61    HC    1    QCWO    H21   12    0.063   1.0080 
   62    HC    1    QCWO    H31   12    0.063   1.0080      ; -0.023
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0         c1
    1    2    2   0.1740   2.6700e+06
    2    3    2   0.2040   5.0300e+06
    2    4    2   0.2040   5.0300e+06
    2    5    2   0.1830   5.6200e+06
    5    6    2   0.1330   1.1800e+07
    5   19    2   0.1520   5.4300e+06
    6    7    2   0.1090   1.2300e+07
    6    8    2   0.1480   5.7300e+06
    8    9    2   0.1320   1.2000e+07
    8   15    2   0.1470   8.7100e+06
    9   10    2   0.1000   1.8700e+07
    9   11    2   0.1480   5.7300e+06
   11   12    2   0.1090   1.2300e+07
   11   13    2   0.1090   1.2300e+07
   11   14    2   0.1090   1.2300e+07
   15   16    2   0.1090   1.2300e+07
   15   17    2   0.1330   1.1800e+07
   17   18    2   0.1090   1.2300e+07
   17   19    2   0.1520   5.4300e+06
   19   20    2   0.1320   1.2000e+07
   20   21    2   0.1980   6.4000e+05
   20   22    2   0.1470   8.7100e+06
   22   23    2   0.1390   8.6600e+06
   22   25    2   0.1390   8.6600e+06
   23   24    2   0.1090   1.2300e+07
   23   30    2   0.1390   8.6600e+06
   25   26    2   0.1090   1.2300e+07
   25   27    2   0.1390   8.6600e+06
   27   28    2   0.1090   1.2300e+07
   27   29    2   0.1390   8.6600e+06
   29   30    2   0.1390   8.6600e+06
   29   32    2   0.1470   8.7100e+06
   30   31    2   0.1090   1.2300e+07
   32   33    2   0.1000   1.8700e+07
   32   34    2   0.1470   8.7100e+06
   34   35    2   0.1390   8.6600e+06
   34   37    2   0.1390   8.6600e+06
   35   36    2   0.1090   1.2300e+07
   35   45    2   0.1390   8.6600e+06
   37   38    2   0.1090   1.2300e+07
   37   39    2   0.1390   8.6600e+06
   39   40    2   0.1830   5.6200e+06
   39   44    2   0.1390   8.6600e+06
   40   41    2   0.1940   1.3300e+06
   40   42    2   0.1940   1.3300e+06
   40   43    2   0.1840   1.0600e+06
   44   45    2   0.1390   8.6600e+06
   44   47    2   0.1400   8.5400e+06
   45   46    2   0.1090   1.2300e+07
   47   48    2   0.1100   1.2100e+07
   47   49    2   0.1400   8.5400e+06
   49   50    2   0.1390   8.6600e+06
   49   52    2   0.1390   8.6600e+06
   50   51    2   0.1090   1.2300e+07
   50   57    2   0.1390   8.6600e+06
   52   53    2   0.1090   1.2300e+07
   52   54    2   0.1390   8.6600e+06
   54   55    2   0.1090   1.2300e+07
   54   56    2   0.1390   8.6600e+06
   56   57    2   0.1390   8.6600e+06
   56   59    2   0.1530   7.1500e+06
   57   58    2   0.1090   1.2300e+07
   59   60    2   0.1090   1.2300e+07
   59   61    2   0.1090   1.2300e+07
   59   62    2   0.1090   1.2300e+07
[ pairs ]
;  ai   aj  funct  ;  all 1-4 pairs but the ones excluded in GROMOS itp
    1    6    1
    1   19    1
    3    6    1
    3   19    1
    4    6    1
    4   19    1
    5   21    1
    5   22    1
    6   10    1
    6   11    1
    8   12    1
    8   13    1
    8   14    1
   10   12    1
   10   13    1
   10   14    1
   10   15    1
   11   15    1
   17   21    1
   17   22    1
   19   23    1
   19   25    1
   21   23    1
   21   25    1
   27   33    1
   27   34    1
   29   35    1
   29   37    1
   30   33    1
   30   34    1
   33   35    1
   33   37    1
   37   41    1
   37   42    1
   37   43    1
   39   48    1
   39   49    1
   41   44    1
   42   44    1
   43   44    1
   44   50    1
   44   52    1
   45   48    1
   45   49    1
   48   50    1
   48   52    1
   54   60    1
   54   61    1
   54   62    1
   57   60    1
   57   61    1
   57   62    1
[ angles ]
;  ai   aj   ak  funct   angle     fc
    1    2    3    2    106.00   848.00
    1    2    4    2    103.00   420.00
    1    2    5    2    102.00   969.00
    3    2    4    2    134.00  2590.00
    3    2    5    2    106.75   503.00
    4    2    5    2    106.75   503.00
    2    5    6    2    118.00  1330.00
    2    5   19    2    113.00   545.00
    6    5   19    2    120.00   560.00
    5    6    7    2    120.00   505.00
    5    6    8    2    120.00   560.00
    7    6    8    2    120.00   505.00
    6    8    9    2    120.00   560.00
    6    8   15    2    120.00   560.00
    9    8   15    2    120.00   560.00
    8    9   10    2    116.00   465.00
    8    9   11    2    124.00   730.00
   10    9   11    2    116.00   465.00
    9   11   12    2    110.00  1270.00
    9   11   13    2    109.60   450.00
    9   11   14    2    107.57   484.00
   12   11   13    2    110.30   524.00
   12   11   14    2    109.60   450.00
   13   11   14    2    110.00  1270.00
    8   15   16    2    120.00   505.00
    8   15   17    2    120.00   560.00
   16   15   17    2    120.00   505.00
   15   17   18    2    120.00   505.00
   15   17   19    2    120.00   560.00
   18   17   19    2    120.00   505.00
    5   19   17    2    111.00   530.00
    5   19   20    2    115.00   610.00
   17   19   20    2    126.00   640.00
   19   20   21    2    109.50   425.00
   19   20   22    2    121.00   685.00
   21   20   22    2    123.00   415.00
   20   22   23    2    120.00   560.00
   20   22   25    2    120.00   560.00
   23   22   25    2    120.00   560.00
   22   23   24    2    120.00   505.00
   22   23   30    2    120.00   560.00
   24   23   30    2    120.00   505.00
   22   25   26    2    120.00   505.00
   22   25   27    2    120.00   560.00
   26   25   27    2    120.00   505.00
   25   27   28    2    120.00   505.00
   25   27   29    2    120.00   560.00
   28   27   29    2    120.00   505.00
   27   29   30    2    120.00   560.00
   27   29   32    2    120.00   560.00
   30   29   32    2    120.00   560.00
   23   30   29    2    120.00   560.00
   23   30   31    2    120.00   505.00
   29   30   31    2    120.00   505.00
   29   32   33    2    109.50   425.00
   29   32   34    2    116.00   620.00
   33   32   34    2    109.50   425.00
   32   34   35    2    120.00   560.00
   32   34   37    2    120.00   560.00
   35   34   37    2    120.00   560.00
   34   35   36    2    120.00   505.00
   34   35   45    2    120.00   560.00
   36   35   45    2    120.00   505.00
   34   37   38    2    120.00   505.00
   34   37   39    2    120.00   560.00
   38   37   39    2    120.00   505.00
   37   39   40    2    118.00  1330.00
   37   39   44    2    120.00   560.00
   40   39   44    2    125.00   750.00
   39   40   41    2    106.75   503.00
   39   40   42    2    106.75   503.00
   39   40   43    2    106.75   503.00
   41   40   42    2    117.20   636.00
   41   40   43    2    109.50   285.00
   42   40   43    2    113.00   545.00
   39   44   45    2    120.00   560.00
   39   44   47    2    120.00   560.00
   45   44   47    2    120.00   560.00
   35   45   44    2    120.00   560.00
   35   45   46    2    120.00   505.00
   44   45   46    2    120.00   505.00
   44   47   48    2    109.50   425.00
   44   47   49    2    121.00   685.00
   48   47   49    2    115.00   460.00
   47   49   50    2    126.00   640.00
   47   49   52    2    115.00   610.00
   50   49   52    2    120.00   560.00
   49   50   51    2    120.00   505.00
   49   50   57    2    120.00   560.00
   51   50   57    2    120.00   505.00
   49   52   53    2    120.00   505.00
   49   52   54    2    120.00   560.00
   53   52   54    2    120.00   505.00
   52   54   55    2    120.00   505.00
   52   54   56    2    120.00   560.00
   55   54   56    2    120.00   505.00
   54   56   57    2    120.00   560.00
   54   56   59    2    120.00   560.00
   57   56   59    2    120.00   560.00
   50   57   56    2    120.00   560.00
   50   57   58    2    120.00   505.00
   56   57   58    2    120.00   505.00
   56   59   60    2    111.00   530.00
   56   59   61    2    111.00   530.00
   56   59   62    2    111.00   530.00
   60   59   61    2    108.00   465.00
   60   59   62    2    108.53   443.00
   61   59   62    2    107.57   484.00
[ dihedrals ]
; GROMOS improper dihedrals
;  ai   aj   ak   al  funct   angle     fc
    8    6    5   19    2      0.00   167.36
    6    5   19   17    2      0.00   167.36
    5   19   17   15    2      0.00   167.36
   19   17   15    8    2      0.00   167.36
   17   15    8    6    2      0.00   167.36
   15    8    6    5    2      0.00   167.36
   22   23   30   29    2      0.00   167.36
   23   30   29   27    2      0.00   167.36
   30   29   27   25    2      0.00   167.36
   29   27   25   22    2      0.00   167.36
   27   25   22   23    2      0.00   167.36
   25   22   23   30    2      0.00   167.36
   34   37   39   44    2      0.00   167.36
   37   39   44   45    2      0.00   167.36
   39   44   45   35    2      0.00   167.36
   44   45   35   34    2      0.00   167.36
   45   35   34   37    2      0.00   167.36
   35   34   37   39    2      0.00   167.36
   49   50   57   56    2      0.00   167.36
   50   57   56   54    2      0.00   167.36
   57   56   54   52    2      0.00   167.36
   56   54   52   49    2      0.00   167.36
   54   52   49   50    2      0.00   167.36
   52   49   50   57    2      0.00   167.36
    9    8   10   11    2      0.00   167.36
    8    6    9   15    2      0.00   167.36
   15    8   16   17    2      0.00   167.36
   17   15   18   19    2      0.00   167.36
   19    5   17   20    2      0.00   167.36
    5    2    6   19    2      0.00   167.36
    6    5    7    8    2      0.00   167.36
   20   19   21   22    2      0.00   167.36
   22   20   23   25    2      0.00   167.36
   23   22   24   30    2      0.00   167.36
   30   23   29   31    2      0.00   167.36
   29   27   30   32    2      0.00   167.36
   27   25   28   29    2      0.00   167.36
   25   22   26   27    2      0.00   167.36
   34   32   35   37    2      0.00   167.36
   35   34   36   45    2      0.00   167.36
   45   35   44   46    2      0.00   167.36
   44   39   45   47    2      0.00   167.36
   39   37   40   44    2      0.00   167.36
   37   34   38   39    2      0.00   167.36
   49   47   50   52    2      0.00   167.36
   52   49   53   54    2      0.00   167.36
   54   52   55   56    2      0.00   167.36
   56   54   57   59    2      0.00   167.36
   57   50   56   58    2      0.00   167.36
   50   49   51   57    2      0.00   167.36
[ dihedrals ]
;  ai   aj   ak   al  funct    ph0      cp     mult
    3    2    5   19    1      0.00     1.00    6
   15    8    9   11    1    180.00    33.50    2
    8    9   11   12    1    180.00     1.00    6
   17   19   20   22    1    180.00    33.50    2
   19   20   22   23    1      0.00     0.42    2
   30   29   32   34    1      0.00     0.42    2
   29   32   34   35    1      0.00     0.42    2
   44   39   40   41    1      0.00     1.00    6
   45   44   47   49    1      0.00     0.42    2
   44   47   49   52    1    180.00    33.50    2
   54   56   59   60    1      0.00     1.00    6
[ exclusions ]
;  ai   aj  funct  ;  GROMOS 1-4 exclusions
    2    7
    2    8
    2   17
    2   20
    5    9
    5   15
    5   18
    6   16
    6   17
    6   20
    7    9
    7   15
    7   19
    8   18
    8   19
    9   16
    9   17
   15   20
   16   18
   16   19
   18   20
   20   24
   20   26
   20   27
   20   30
   22   28
   22   29
   22   31
   23   26
   23   27
   23   32
   24   25
   24   29
   24   31
   25   30
   25   32
   26   28
   26   29
   27   31
   28   30
   28   32
   31   32
   32   36
   32   38
   32   39
   32   45
   34   40
   34   44
   34   46
   35   38
   35   39
   35   47
   36   37
   36   44
   36   46
   37   45
   37   47
   38   40
   38   44
   39   46
   40   45
   40   47
   46   47
   47   51
   47   53
   47   54
   47   57
   49   55
   49   56
   49   58
   50   53
   50   54
   50   59
   51   52
   51   56
   51   58
   52   57
   52   59
   53   55
   53   56
   54   58
   55   57
   55   59
   58   59

Friday, April 24, 2015

A general chemical structure of polyaniline and its repeating units





A general chemical structure of polyaniline and its repeating units.
(a) A general chemical structure of polyaniline,
(b) Reduced repeating unit, and
(c) oxidized repeating unit