[gmx-users] diketopiperazine

[Jose Tusell]

Hi,

I'm trying to construct diketopiperazine with gromacs.  The problem that I
have right now is forming the bond that unites the C and N termi to make the
cyclic peptide.  I tried using specbond.dat but so far I've been
unsucessful.  Here is my specbond.dat file and pdb file:

specbond.dat
8
CYS     SG      1       CYS     SG      1       0.2     CYS2    CYS2
CYS     SG      1       HEME    FE      2       0.25    CYS2    HEME
CYS     SG      1       HEME    CAB     1       0.18    CYS2    HEME
CYS     SG      1       HEME    CAC     1       0.18    CYS2    HEME
HIS     NE2     1       HEME    FE      1       0.2     HIS1    HEME
MET     SD      1       HEME    FE      1       0.24    MET     HEME
CYM     SG      1       CYM     SG      1       0.2     CYS2    CYS2
TRP      N      1       HISH     C      1       0.2     TRP     HISH

whdikp.pdb
REMARK       S  14 x 14 mn oif
ATOM      1  N   TRP    1       -0.813   0.594   1.164
ATOM      2  H   TRP    1       -0.249   1.064   1.843
ATOM      3  CA  TRP    1       -0.264  -0.210   0.004
ATOM      4  HA  TRP    1        0.855  -0.244   0.066
ATOM      5  CB  TRP    1       -0.633   0.484  -1.321
ATOM      6  HB1 TRP    1       -1.672   0.344  -1.531
ATOM      7  HB2 TRP    1       -0.408   1.528  -1.262
ATOM      8  CG  TRP    1        0.205  -0.166  -2.397
ATOM      9  CD1 TRP    1        0.227  -1.464  -2.727
ATOM     10  HD1 TRP    1       -0.407  -2.173  -2.195
ATOM     11  CD2 TRP    1        1.119   0.455  -3.258
ATOM     12  NE1 TRP    1        1.166  -1.607  -3.796
ATOM     13  HE1 TRP    1        1.401  -2.473  -4.259
ATOM     14  CE2 TRP    1        1.673  -0.432  -4.078
ATOM     15  CE3 TRP    1        1.485   1.803  -3.344
ATOM     16  HE3 TRP    1        1.065   2.575  -2.699
ATOM     17  CZ2 TRP    1        2.626  -0.117  -5.054
ATOM     18  HZ2 TRP    1        3.035  -0.902  -5.690
ATOM     19  CZ3 TRP    1        2.444   2.145  -4.320
ATOM     20  HZ3 TRP    1        2.741   3.190  -4.402
ATOM     21  CH2 TRP    1        2.990   1.222  -5.140
ATOM     22  HH2 TRP    1        3.727   1.540  -5.878
ATOM     23  C   TRP    1       -0.816  -1.621   0.004
ATOM     24  O   TRP    1       -0.072  -2.712   0.004
ATOM     25  N   HISH   2       -2.331  -1.621   0.004
ATOM     26  H   HISH   2       -2.895  -2.093  -0.674
ATOM     27  CA  HISH   2       -2.881  -0.816   1.162
ATOM     28  HA  HISH   2       -4.000  -0.781   1.098
ATOM     29  CB  HISH   2       -2.516  -1.510   2.488
ATOM     30  HB1 HISH   2       -1.564  -1.990   2.400
ATOM     31  HB2 HISH   2       -2.494  -0.794   3.283
ATOM     32  CG  HISH   2       -3.591  -2.538   2.747
ATOM     33  ND1 HISH   2       -3.867  -3.560   1.846
ATOM     34  HD1 HISH   2       -3.399  -3.715   0.964
ATOM     35  CD2 HISH   2       -4.447  -2.700   3.792
ATOM     36  HD2 HISH   2       -4.608  -2.157   4.723
ATOM     37  CE1 HISH   2       -4.846  -4.291   2.344
ATOM     38  HE1 HISH   2       -5.219  -5.152   1.791
ATOM     39  NE2 HISH   2       -5.203  -3.793   3.502
ATOM     40  HE2 HISH   2       -5.932  -4.166   4.093
ATOM     41  C   HISH   2       -2.329   0.595   1.164
ATOM     42  O   HISH   2       -3.089   1.710   1.164

Thanks for any suggestions,

Jose Tusell
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