[gmx-users] pdb file

[Mark Abraham]

He, Yang wrote:
> 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?

Your atom names look more like you have a bizarre cluster of sulfur and 
heavy atoms, not DNA. Also possible is that you have a united-atom model 
with about one site per nucleic acid residue. I've no idea whether any 
united-atom models of DNA exist.

Mark