[gmx-users] PDB file

[Albert Sun]

Dear Gromax users

Appreciate if you could explain to me the meaning of each column of the PDB file(as shown below in example)?  how should we create a PDB file for an epoxy polymer simulation?

ATOM      1  N   LYS      1      24.966  -0.646  22.314  1.00 32.74      1SRN  99
ATOM      2  CA  LYS     1      24.121   0.549  22.271  1.00 32.05      1SRN 100
ATOM      3  C   LYS      1      24.794   1.733  22.943  1.00 31.16      1SRN 101
ATOM      4  O   LYS      1      25.742   1.575  23.764  1.00 31.50      1SRN 102
ATOM      5  CB  LYS     1      22.812   0.323  23.047  1.00 33.09      1SRN 103
ATOM      6  CG  LYS     1      21.763   1.415  22.695  1.00 34.29      1SRN 104
ATOM      7  CD  LYS     1      20.497   1.124  23.561  1.00 34.93      1SRN 105
ATOM      8  CE  LYS     1      20.706   1.659  24.970  1.00 35.35      1SRN 106
ATOM      9  NZ  LYS      1      21.524   0.759  25.825  1.00 35.85      1SRN 107
ATOM     10  N   GLU      2      24.300   2.909  22.632  1.00 29.30      1SRN 108
ATOM     11  CA  GLU     2      24.858   4.145  23.207  1.00 27.38      1SRN 109
ATOM     12  C   GLU      2      24.567   4.201  24.693  1.00 26.12      1SRN 110
ATOM     13  O   GLU      2      23.398   4.051  25.038  1.00 26.39      1SRN 111
ATOM     14  CB  GLU     2      24.238   5.355  22.537  1.00 27.12      1SRN 112
ATOM     15  CG  GLU     2      24.775   6.731  22.894  1.00 26.16      1SRN 113
ATOM     16  CD  GLU     2      24.277   7.798  21.950  1.00 25.53      1SRN 114
ATOM     17  OE1 GLU    2      23.087   7.974  21.734  1.00 25.09      1SRN 115
ATOM     18  OE2 GLU    2      25.200   8.451  21.448  1.00 24.78      1SRN 116
ATOM     19  N   THR      3      25.608   4.399  25.499  1.00 24.80      1SRN 117
ATOM     20  CA  THR     3      25.475   4.513  26.954  1.00 23.26      1SRN 118
ATOM     21  C   THR      3      24.803   5.847  27.263  1.00 22.23      1SRN 119
ATOM     22  O   THR      3      24.805   6.756  26.419  1.00 22.26      1SRN 120
ATOM     23  CB  THR     3      26.857   4.478  27.708  1.00 23.53      1SRN 121
ATOM     24  OG1 THR    3      27.581   5.698  27.276  1.00 23.39      1SRN 122
ATOM     25  CG2 THR    3      27.750   3.260  27.496  1.00 23.71      1SRN 123
ATOM     26  N   ALA      4      24.316   6.023  28.470  1.00 20.81      1SRN 124
ATOM     27  CA  ALA     4      23.646   7.264  28.928  1.00 19.56      1SRN 125
ATOM     28  C   ALA      4      24.622   8.442  28.958  1.00 18.79      1SRN 126
ATOM     29  O   ALA      4      24.267   9.606  28.686  1.00 17.61      1SRN 127
ATOM     30  CB  ALA     4      23.015   7.064  30.281  1.00 19.62      1SRN 128


Thanks!

Albert

 

 

 



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