[gmx-users] diketopiperazine

Jose Tusell jrta1981 at gmail.com
Fri Jan 22 23:05:54 CET 2010


Thanks Justin, I used specbond.dat with a 0.15nm searching distance to
create the bond, it seemed to work.

Ramon

On Fri, Jan 22, 2010 at 2:40 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>
>>
> --
> ========================================
>
> 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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