Hi,<br><br>You can try "packmol" (<a href="http://www.ime.unicamp.br/~martinez/packmol/download.html">http://www.ime.unicamp.br/~martinez/packmol/download.html</a>) to create any starting configuration of your interest. I found it very useful for random initial configurations.<br>
<br>Hope this help.<br><br><br>Esteban Gabriel Vega Hissi<br>Área de Química Física<br>Departamento de Química<br>Universidad Nacional de San Luis<br>Argentina<br><br><div class="gmail_quote">On Wed, Apr 13, 2011 at 10:48 AM, Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Olga Ivchenko skrev 2011-04-13 15.20:<div><div></div><div class="h5"><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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<br>
Dear Gromacs Users,<br>
<br>
I want to add a sphere of water molecules around a ligand. I know I need to use -shell option in genbox. But first I I need to create a sphere. Please could you guide me?<br>
<br>
best,<br>
Olga<br>
</blockquote></div></div>
Just fill the box with water, then run trjorder to sort the solvent according to their distance to the ligand. Having done that, you can just edit away the bottom part of the sorted gro-file to have your ligand in a ball of water.<br>
<br>
-- <br>
-----------------------------------------------<br>
Erik Marklund, PhD student<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: +46 18 471 4537 fax: +46 18 511 755<br>
<a href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a><br><font color="#888888">
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