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On 18/11/2011 7:40 AM, Anushree Tripathi wrote:
<blockquote
cite="mid:CAAx43BzQ3hApSLc++ui1umpvrsBmL0wgo7pBHJWtG-f1cKB_VA@mail.gmail.com"
type="cite">Yes I m using 4.0.7 version.so for that how could I
change the name accordingly.<br>
</blockquote>
<br>
You used it in your [molecules] section. Change it to what it should
be, per ions.itp.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAAx43BzQ3hApSLc++ui1umpvrsBmL0wgo7pBHJWtG-f1cKB_VA@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Sat, Nov 5, 2011 at 1:37 AM, Justin A.
Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
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<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>
========================================<br>
<br>
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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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