<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span><font face="Courier New, courier, monaco, monospace, sans-serif">Will you please tell me where can I find the <font>ions.itp file?</font></font></span></div><div><span><font face="Courier New, courier, monaco, monospace, sans-serif"></font></span> </div><div><span><font face="Courier New, courier, monaco, monospace, sans-serif">I am looking forward to getting your reply.</font></span></div><div><span><font face="Courier New, courier, monaco, monospace, sans-serif"></font></span> </div><div><span><font face="Courier New, courier, monaco, monospace, sans-serif">Wholly</font></div></span><div><br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2"
face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="hr" contentEditable="false" readonly="true"></div> <b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, 17 March 2012 3:55 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] genion -pname no NA molecule (sodium) type<br> </font> </div> <br><meta content="off" http-equiv="x-dns-prefetch-control"><div id="yiv1286870782">
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On 17/03/2012 4:48 PM, Wholly Peach wrote:
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<span><font face="Arial">Dear All,
<pre> </pre>
<pre>I use the following to neutralize the charge</pre>
<pre> </pre>
<pre>"genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8",</pre>
<pre> </pre>
<pre>Then I do the following "<font face="Arial">grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr"</font>".<var id="yiv1286870782yui-ie-cursor"></var></pre>
<pre> </pre>
<pre>However the feedback says there is no Na (sodium) moleculetype.</pre>
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Your force field defines [moleculetype] sections for ions in its
ions.itp file. Go and look at it, compare with your .top and see
what the problem is. Atom names, residue names and moleculetype
names are all different things, and each part of your .top must
match the right name at the right time.<br>
<br>
Mark<br>
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