You were right Justin. I had to include the lines:<div><br class="webkit-block-placeholder"></div><div>#ifdef _FF_AMBER</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 mass</div><div>1 amber99_31 1 Na+ Na 1 1 22.98977</div>
<div><br class="webkit-block-placeholder"></div><div>#endif</div><div>int the ions.itp</div><div><br class="webkit-block-placeholder"></div><div>And there were no errors</div><div><br class="webkit-block-placeholder"></div>
<div><br class="webkit-block-placeholder"></div><div>Thanks again.</div><div><br class="webkit-block-placeholder"></div><br><div class="gmail_quote">On Sun, Sep 20, 2009 at 11:59 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Gunnar Widtfeldt Reginsson wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi.<br>
I am trying to run this command on a solvated DNA<br>
<br>
grompp -f mini_sol.mdp -p topol.top -c DNAneutral.pdb -n DNAneutral.ndx<br>
<br>
and I get this fatal error:<br>
-------------------------------------------------------<br>
Program grompp, VERSION 4.0.5<br>
Source code file: toppush.c, line: 1641<br>
<br>
Fatal error:<br>
No such moleculetype Na+<br>
-------------------------------------------------------<br>
<br>
I have added to the file ions.itp :<br>
[ moleculetype ]<br>
; molname nrexcl<br>
Na+ 1<br>
<br>
[ atoms ]<br>
; id at type res nr residu name at name cg nr charge<br>
1 amber99_31 1 Na+ Na 1 1<br>
<br>
</blockquote>
<br></div>
Is this section contained in an appropriate #ifdef _FF_AMBER block?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
because this is how the Na ion is in ffamber99.rtp<br>
<br>
<br>
[ Na+ ]<br>
[ atoms ]<br>
Na amber99_31 1.00000 1<br>
<br>
And this I have done according to the amber website:<br>
<a href="http://chemistry.csulb.edu/ffamber/#aadat" target="_blank">http://chemistry.csulb.edu/ffamber/#aadat</a><br>
<br>
<br>
The last part of the topol.top file is:<br>
SOL 13651<br>
Na+ 38<br>
Cl 0<br>
<br>
and the structure file contains:<br>
ATOM 55905 Na Na+ 3729 77.070 47.215 21.822 1.00 0.00<br>
<br>
Does anyone know what could be wrong?<br>
<br>
Thanks.<br>
<br>
<br></div><div class="im">
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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