[gmx-users] diketopiperazine

[Justin A. Lemkul]

Jose Tusell wrote:
> 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:
> 

I believe there is a fundamental limitation with pdb2gmx - it doesn't deal with 
cyclic species.  Every post I've seen about this issue has been along the lines 
of "generate the normal topology and add the missing bonded parameters manually."

I also think the specbond.dat file could never work anyway.  The distance 
between your C and N atoms appears to be right about 0.15 nm, so a 0.2-nm 
criterion (+/- 10%) will never detect that a bond should be created between 
these two atoms anyway.  Just FYI for the future.

-Justin

> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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