<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Hi,<div><br></div><div>After searching though gmxuserlist I found the relevant thread for ED... I followed the following steps :-</div>
<div>1) g_covar - to generate a covariance matrix and diagonalize it (for c-alpha atoms only)</div><div>2) g_anaeig - to generate eigen vectors</div><div>3)g_rmsf - for calculating RMSD of first 8 eigen vectors , I got an error at this step that -</div>
<div><br></div><div><div>Fatal error:</div><div>Molecule in topology has atom numbers below and above natoms (230).</div><div>You are probably trying to use a trajectory which does not match the first 230 a</div><div>toms of the run input file.</div>
<div>You can make a matching run input file with tpbconv.</div><div>-------------------------------------------------------</div><div><br></div><div>"California, R.I.P." (Red Hot Chili Peppars)</div></div><div><br>
</div><div>4) then I used make_ndx - for generating an index file containing only c-alpha atoms..which was done successfully</div><div>5) Further I used tpbconv - to generate a .tpr file for calculating the rmsf ... but I am getting the following error at this step ..</div>
<div><br></div><div><div>Fatal error:</div><div>Molecule in topology has atom numbers below and above natoms (230).</div><div>You are probably trying to use a trajectory which does not match the first 230 a</div><div>toms of the run input file.</div>
<div>You can make a matching run input file with tpbconv.</div><div>-------------------------------------------------------</div><div><br></div><div>"California, R.I.P." (Red Hot Chili Peppars)</div></div><div><br>
</div><div><br></div><div>Pls help what has to be done in order to generate the .tpr file ...</div><div><br></div></span>