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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