<div>The problem I was facing earlier: in the force field files (I am ussing ffG53a6) the ions are named NA+, CL-, for example, so with capital letters. Genion will add to the topology the ions named by default Na or Cl, unless you use the options -pname and/or -nname to name the ions. I do so and I have no mismatch of ionsname in different files. I hope this helps.</div>
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<div>Regards</div>
<div>Andrea<br><br></div>
<div class="gmail_quote">2009/11/17 Arden Perkins <span dir="ltr"><<a href="mailto:perkina2@eou.edu">perkina2@eou.edu</a>></span><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<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>
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<div>Thanks!</div><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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