[gmx-users] Backbone and MainChain

[Chih-Ying Lin]

Hi
>From Gromacs Manual:

   - Backbone: all protein backbone atoms (C-alpha, N, C)
   - MainChain: backbone atoms, plus the carbonyl oxygens


The following is part of .gro file.
I listed the atom number, are those all correct ?

C-alpha: 161,170,179
N:158,163, 172
C:  ???   what does this "C" represent ?
carbonyl oxygens: 162,171,180

Thank you
Lin



   16GLY      N  158   4.365  -0.145   3.067 -0.6971 -0.0210  0.0556
   16GLY      H  159   4.280  -0.127   3.017  0.4468  0.2941 -1.8808
   16GLY     CA  160   4.377  -0.037   3.166 -0.3605  0.4870 -0.5237
   16GLY      C  161   4.250  -0.037   3.252  0.0432 -0.0265  0.0901
   16GLY      O  162   4.180  -0.137   3.266  0.2570 -0.1341  0.3963
   17LEU      N  163   4.216   0.087   3.287  0.7572  0.0242  0.6305
   17LEU      H  164   4.276   0.160   3.254  0.7410 -0.8313 -1.4811
   17LEU     CA  165   4.102   0.123   3.372 -0.0401 -0.2644 -0.2910
   17LEU     CB  166   4.156   0.220   3.477  0.1016 -0.1889 -0.4337
   17LEU     CG  167   4.275   0.181   3.566 -0.0012 -0.5604 -0.4598
   17LEU    CD1  168   4.338   0.303   3.632  1.2085 -0.9864 -0.7919
   17LEU    CD2  169   4.233   0.084   3.676  0.8349 -0.3795  0.0241
   17LEU      C  170   3.980   0.184   3.303 -0.0634  0.2558  0.2056
   17LEU      O  171   3.993   0.297   3.258 -0.2180  0.0717 -0.3035
   18ASP      N  172   3.867   0.113   3.302  0.0759  0.0338 -0.0172
   18ASP      H  173   3.855   0.036   3.364 -0.9960  1.0931  1.1466
   18ASP     CA  174   3.744   0.153   3.233 -0.1100 -0.0437  0.2680
   18ASP     CB  175   3.638   0.047   3.201 -0.1316  0.1250 -0.2304
   18ASP     CG  176   3.612  -0.052   3.315 -0.1959  0.1668 -0.2089
   18ASP    OD1  177   3.588  -0.170   3.282  0.1094  0.1194 -0.2643
   18ASP    OD2  178   3.643  -0.033   3.435 -0.2608 -0.1375 -0.1441
   18ASP      C  179   3.665   0.270   3.294  0.1485  0.2274  0.0883
   18ASP      O  180   3.660   0.382   3.245 -0.2873  0.2105  0.0864
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