[gmx-users] pdb file

[He, Yang]

Hi all users,

I just encountered a problem about the DNA model when I set the coordinate in the pdb file . It always shows very strange figure about the DNA model.

My pdb file is like this:

ATOM      1  Ab1  DNA      1     0.051    0.575     0.516   1.0  0.0
ATOM      2  Tb1  DNA      1     0.191    0.159     2.344   1.0  0.0
ATOM      3  S1   DNA      1     1.280    2.365     6.568   1.0  0.0
ATOM      4  S2   DNA      1     1.280   -2.365    -6.568   1.0  0.0
ATOM      5  P1   DNA      1     2.186   -0.628     8.896   1.0  0.0
ATOM      6  P2   DNA      1     2.186   -0.628    -8.896   1.0  0.0
ATOM      7  S3   DNA      1     4.660   -1.947     6.704   1.0  0.0
ATOM      8  S4   DNA      1     4.660    1.947    -6.704   1.0  0.0
ATOM      9  Cb1  DNA      1     3.431    0.162     0.756   1.0  0.0
ATOM     10  Gb1  DNA      1     3.571   -1.249     1.989   1.0  0.0
ATOM     11  P3   DNA      1     5.556   -5.737     6.828   1.0  0.0
ATOM     12  P4   DNA      1     5.556    5.737    -6.828   1.0  0.0
ATOM     13  S5   DNA      1     8.040   -5.516     4.279   1.0  0.0
ATOM     14  S6   DNA      1     8.040    5.516    -4.279   1.0  0.0
ATOM     15  Gb2  DNA      1     6.811   -1.814     1.407   1.0  0.0
ATOM     16  Cb2  DNA      1     6.951   -0.319     0.764   1.0  0.0
ATOM     17  P5   DNA      1     8.936   -8.655     2.152   1.0  0.0
ATOM     18  P6   DNA      1     8.936    8.655    -2.152   1.0  0.0
ATOM     19  S7   DNA      1     11.42    6.978     0.220   1.0  0.0
ATOM     20  S8   DNA      1     11.42   -6.978    -0.220   1.0  0.0
ATOM     21  Tb2  DNA      1     10.191  -0.707     0.430   1.0  0.0
ATOM     22  Ab2  DNA      1     10.331  -2.237    -0.518   1.0  0.0
CONECT  1  3
CONECT  2  4
CONECT  3  1  5
CONECT  4  2  6
CONECT  5  3  7
CONECT  6  4  8
CONECT  7  5  9  11
CONECT  8  6 10  12
CONECT  9  7
CONECT 10  8
CONECT 11  7  13
CONECT 12  8  14
CONECT 13  11  15  17
CONECT 14  12  16  18
CONECT 15  13
CONECT 16  14
CONECT 17  13  19
CONECT 18  14  20
CONECT 19  17  21
CONECT 20  18  22
CONECT 21  19
CONECT 22  20
MASTER        0    0    0    0    0    0    0    0   22    0    22     0
END

Can anyone of you tell me whether there is something wrong with my pdb file?

Thank you.

Yang