<font class="Apple-style-span" face="Verdana, sans-serif" size="4"><span class="Apple-style-span" style="font-size: 14px; line-height: 17px;"><div><span style=""></span><br></div>Hi <br></span></font><div><font class="Apple-style-span" face="Verdana, sans-serif" size="4"><span class="Apple-style-span" style="font-size: 14px; line-height: 17px;">From Gromacs Manual:</span></font></div>
<div><font class="Apple-style-span" face="Verdana, sans-serif" size="4"><span class="Apple-style-span" style="font-size: 14px; line-height: 17px;"><span class="Apple-style-span" style="line-height: normal; "><ul style="margin-top: 1.5em; margin-bottom: 0px; list-style-type: disc; ">
<li style="line-height: 1.25; "><span class="highlight" style="background-color: yellow; ">Backbone</span>: all protein <span class="highlight" style="background-color: yellow; ">backbone</span> atoms (C-alpha, N, C)</li>
<li style="line-height: 1.25; ">MainChain: <span class="highlight" style="background-color: yellow; ">backbone</span> atoms, plus the carbonyl oxygens</li></ul><div><span class="Apple-style-span" style="line-height: 17px;"><br>
</span></div><div><span class="Apple-style-span" style="line-height: 17px;">The following is part of .gro file.</span></div><div><span class="Apple-style-span" style="line-height: 17px;">I listed the atom number, are those all correct ?</span></div>
<div><span class="Apple-style-span" style="line-height: 17px;"><br></span></div><div><span class="Apple-style-span" style="line-height: 17px;"><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">C-alpha: 161,170,179</span></span></div>
<div><span class="Apple-style-span" style="line-height: 17px;">N:158,163, 172</span></div><div><span class="Apple-style-span" style="line-height: 17px;"><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">C: ??? what does this "C" represent ? </span></span></div>
<div><span class="Apple-style-span" style="line-height: 17px;">carbonyl oxygens: 162,171,180</span></div><div><span class="Apple-style-span" style="line-height: 17px;"><br></span></div><div><span class="Apple-style-span" style="line-height: 17px;">Thank you</span></div>
<div><span class="Apple-style-span" style="line-height: 17px;">Lin</span></div><div><span class="Apple-style-span" style="line-height: 17px;"><br></span></div><div><span class="Apple-style-span" style="line-height: 17px;"><br>
</span></div><div><span class="Apple-style-span" style="line-height: 17px;"><br></span></div><div><span class="Apple-style-span" style="line-height: 17px;"><div> 16GLY <span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">N 158</span> 4.365 -0.145 3.067 -0.6971 -0.0210 0.0556</div>
<div> 16GLY H 159 4.280 -0.127 3.017 0.4468 0.2941 -1.8808</div><div> 16GLY CA 160 4.377 -0.037 3.166 -0.3605 0.4870 -0.5237</div><div> 16GLY <span class="Apple-style-span" style="background-color: rgb(255, 255, 0);">C 161 </span> 4.250 -0.037 3.252 0.0432 -0.0265 0.0901</div>
<div> 16GLY <span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">O 162</span> 4.180 -0.137 3.266 0.2570 -0.1341 0.3963</div><div> 17LEU <span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">N 163</span> 4.216 0.087 3.287 0.7572 0.0242 0.6305</div>
<div> 17LEU H 164 4.276 0.160 3.254 0.7410 -0.8313 -1.4811</div><div> 17LEU CA 165 4.102 0.123 3.372 -0.0401 -0.2644 -0.2910</div><div> 17LEU CB 166 4.156 0.220 3.477 0.1016 -0.1889 -0.4337</div>
<div> 17LEU CG 167 4.275 0.181 3.566 -0.0012 -0.5604 -0.4598</div><div> 17LEU CD1 168 4.338 0.303 3.632 1.2085 -0.9864 -0.7919</div><div> 17LEU CD2 169 4.233 0.084 3.676 0.8349 -0.3795 0.0241</div>
<div> 17LEU <span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">C 170</span> 3.980 0.184 3.303 -0.0634 0.2558 0.2056</div><div> 17LEU <span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">O 171</span> 3.993 0.297 3.258 -0.2180 0.0717 -0.3035</div>
<div><div> 18ASP <span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">N 172</span> 3.867 0.113 3.302 0.0759 0.0338 -0.0172</div><div> 18ASP H 173 3.855 0.036 3.364 -0.9960 1.0931 1.1466</div>
<div> 18ASP CA 174 3.744 0.153 3.233 -0.1100 -0.0437 0.2680</div><div> 18ASP CB 175 3.638 0.047 3.201 -0.1316 0.1250 -0.2304</div><div> 18ASP CG 176 3.612 -0.052 3.315 -0.1959 0.1668 -0.2089</div>
<div> 18ASP OD1 177 3.588 -0.170 3.282 0.1094 0.1194 -0.2643</div><div> 18ASP OD2 178 3.643 -0.033 3.435 -0.2608 -0.1375 -0.1441</div><div> 18ASP <span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">C 179</span> 3.665 0.270 3.294 0.1485 0.2274 0.0883</div>
<div> 18ASP <span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">O 180</span> 3.660 0.382 3.245 -0.2873 0.2105 0.0864</div><div> </div></div></span></div></span></span></font></div>