Yes I m using 4.0.7 version.so for that how could I change the name accordingly.<br><br><div class="gmail_quote">On Sat, Nov 5, 2011 at 1:37 AM, 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
Anushree Tripathi wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
when i run the given command i.e,<br>
<br>
grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr<br>
It is showing fatal error:No such molecule type NA.<br>
How could I troubleshoot this problem?<br>
<br>
</blockquote>
<br></div></div>
Ion naming is listed in ions.itp - the "NA" name works for all force fields in the Gromacs 4.5.x series. Older versions had force field-specific naming so you will have to change the name accordingly if you're using one of these versions.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
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