<p>Hi Jose,</p>
<p>You're not the first one to follow the tutorial, it does state which version to use (4.5, see introduction), and it does state how to fix the topology: editing the file, adding the lines, using the appropriate names. This tutorial is made to be read and to be thought over. </p>
<p>Of course time flies. The tutorial was written a few years back and ion naming has changed. You should run genion with -pname Na -nname Cl these days. And you can use -p, but one of the aims of the tutorial is familiarizing you with the files, file formats, and components of a simulation.</p>
<p>The error about the box has nothing to do with the tutorial anymore. You deviated from a well trodden path, editing the coordinate file, probably screwing it up... But please don't blame me for that.</p>
<p>But I take note of the ion issue that hadn't been brought to my attentin yet. I'll fix it soon.</p>
<p>Best,</p>
<p>Tsjerk </p>
<p><blockquote type="cite">On Dec 7, 2011 8:31 PM, "Jose Borreguero" <<a href="mailto:borreguero@gmail.com">borreguero@gmail.com</a>> wrote:<br><br><font color="#000099">This tutorial doesn't seem to be quite useful, if so many error</font><span style="color:rgb(0,0,153)">s pop up. Maybe it was implemented for Gromacs < 4.5.x but there's no info on the version it should be used.</span><br style="color:rgb(0,0,153)">
<br style="color:rgb(0,0,153)"><span style="color:rgb(0,0,153)">However, Lo and behold! I found that you have a nice page with Gromacs 4.5.x tutorials :D (<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html</a>) I'll give a try with the Lyzosyme one!</span><font color="#888888"><br style="color:rgb(0,0,153)">
<br style="color:rgb(0,0,153)"><span style="color:rgb(0,0,153)">- Jose</span></font><p><font color="#500050">
On Wed, Dec 7, 2011 at 1:29 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:
>
>
>
> Jose Borreguero ...</font></p><br>--<br>
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