Hi.<div>I am trying to run this command on a solvated DNA</div><div><br class="webkit-block-placeholder"></div><div><div>grompp -f mini_sol.mdp -p topol.top -c DNAneutral.pdb -n DNAneutral.ndx</div><div><br class="webkit-block-placeholder">
</div><div>and I get this fatal error:</div><div><div>-------------------------------------------------------</div><div>Program grompp, VERSION 4.0.5</div><div>Source code file: toppush.c, line: 1641</div><div><br class="webkit-block-placeholder">
</div><div>Fatal error:</div><div>No such moleculetype Na+</div><div>-------------------------------------------------------</div><div><br class="webkit-block-placeholder"></div><div>I have added to the file ions.itp :</div>
<div><div><div>[ moleculetype ]</div><div>; molname nrexcl</div><div>Na+ 1</div><div><br class="webkit-block-placeholder"></div><div>[ atoms ]</div><div>; id at type res nr residu name at name cg nr charge</div>
<div>1 amber99_31 1 Na+ Na 1 1</div><div><br class="webkit-block-placeholder"></div></div><div><br></div><div>because this is how the Na ion is in ffamber99.rtp</div><div><br class="webkit-block-placeholder">
</div><div><div><br class="webkit-block-placeholder"></div><div>[ Na+ ]</div><div> [ atoms ]</div><div> Na amber99_31 1.00000 1</div><div><br class="webkit-block-placeholder"></div><div>And this I have done according to the amber website:</div>
<div><a href="http://chemistry.csulb.edu/ffamber/#aadat">http://chemistry.csulb.edu/ffamber/#aadat</a><br class="webkit-block-placeholder"></div><div><br class="webkit-block-placeholder"></div><div><br class="webkit-block-placeholder">
</div><div>The last part of the topol.top file is:</div><div><div>SOL 13651</div><div>Na+ 38</div><div>Cl 0</div><div><br class="webkit-block-placeholder"></div><div>and the structure file contains:</div>
<div>ATOM 55905 Na Na+ 3729 77.070 47.215 21.822 1.00 0.00<br class="webkit-block-placeholder"></div><div><br class="webkit-block-placeholder"></div><div>Does anyone know what could be wrong?</div><div><br class="webkit-block-placeholder">
</div><div>Thanks.</div></div></div></div></div></div>