<p>Hi Diana,</p>
<p>Does it also happen if you solvate the box without the protein? And are the holes close to the protein or just anywhere? And what makes it difficult to analyze the structure output by genbox directly, perhaps specifying that the output be .pdb? It's what I usually do.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Nov 6, 2010 9:15 PM, "Diana Lousa" <<a href="mailto:dlousa@itqb.unl.pt">dlousa@itqb.unl.pt</a>> wrote:<br><br>Hi,<div><br></div><div>It seems to me that the holes are created by genbox because I don't have them in the original solvent box. The intermediate box (outputed by trjconv) with the protein solvated but not converted is difficult to analyze, because the box doesn't have the right shape and of pbc issues, but it seems to me that the holes are present in this box, i.e. I don't think they are an artifact of trjconv.</div>
<div><br></div><div>Thanks for the help </div><div><br></div><div><font color="#888888">Diana</font><p><font color="#500050">
On Sat, Nov 6, 2010 at 8:08 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:
>
> Hi Diana,
>
> Yeah...</font></p></div>
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