try trjconv, maybe your reference gro/tpr file is <span class="Apple-style-span" style="font-size:medium">cubic? </span><div><span class="Apple-style-span" style="font-size:medium"><br></span></div><div><span class="Apple-style-span" style="font-size:medium">make sure:</span></div>

<div><span class="Apple-style-span" style="font-size:medium">trjconv -s the_</span><span class="Apple-style-span" style="font-size:medium">dodecahedral_generated.tpr -f </span><span class="Apple-style-span" style="font-size:medium">the_</span><span class="Apple-style-span" style="font-size:medium">dodecahedral_generated.gro -o your_aim.pdb</span><br>

<br><div class="gmail_quote">On Tue, May 22, 2012 at 9:27 AM, patrick wintrode <span dir="ltr">&lt;<a href="mailto:pat_wde2@yahoo.com" target="_blank">pat_wde2@yahoo.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

<table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td valign="top" style="font:inherit">After generating my protein .gro and .top files and doing the initial energy minimization, I used the following series of commands:<br>

<br>editconf -f protein-vacuum.gro -o protein-PBC.gro -bt dodecahedron -d 1.2<br><br>genbox -cp protein-PBC.gro -cs spc216.gro -p protein.top -o protein-water.gro
<br><br>I then use editconf to convert protein-water.gro to a pdb file. When I open this<br>file in PyMol, the water box is cubic rather than dodecahedral.<br><br>Has any one else encountered this?<br><br>Thanks.<br></td>

</tr></tbody></table><br>--<br>
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