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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="yui-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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