I am trying to run grompp using a pdb file of DNA duplex, a sucessfully generated topology, and the steep.mpd from <a href="http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top">http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top</a><div>
<br class="webkit-block-placeholder"></div><div>I am getting the fatal error:</div><div><br class="webkit-block-placeholder"></div><div><div>Fatal error:</div><div>[ file spc.itp, line 37 ]:</div><div>Atom index (1) in bonds out of bounds (1-0).</div>
<div>This probably means that you have inserted topology section "bonds"</div><div>in a part belonging to a different molecule than you intended to.</div><div>In that case move the "bonds" section to the right molecule.</div>
<div><br class="webkit-block-placeholder"></div><div>I am using the amber99 force field, and have followed the notes on nucleic acids on <a href="http://chemistry.csulb.edu/ffamber/">http://chemistry.csulb.edu/ffamber/</a></div>
<div><br class="webkit-block-placeholder"></div><div>I am new to Gromacs, can anyone help me with this?</div><div><br class="webkit-block-placeholder"></div><div>Thanks,</div><div>Gunnar W.</div></div>