<div dir="ltr">Hi,<br><br>Make sure you do specify the explicit names of the topology and structure file. in the mannual they omit the suffix of the file.<br>for the purpose of rigourism - this is the line i'm using:<br>
<br> genion -pname Na+ -nname Cl- -o file_ionized.gro -conc 0.2 -p topol.top <br><br><div class="gmail_quote">On Tue, Nov 17, 2009 at 1:56 AM, Arden Perkins <span dir="ltr"><<a href="mailto:perkina2@eou.edu">perkina2@eou.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>I am an undergraduate student and I am still learning to use GROMACS. When I add my ions to the solution (using genion) by the procedure described in the funnel web spider tutorial the .gro and .top files do not match. I tried subtracting solvent molecules but they still dont match and I can't continue. What am I doing wrong?</div>
<div> </div>
<div>Thanks!</div>
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