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>Diana<br><br><div class="gmail_quote">On Sat, Nov 6, 2010 at 8:08 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><p>Hi Diana,</p>
<p>Yeah, my reply was a bit off, as Vitaly had already pointed out. Lazy reading, sorry. But are these holes created by genbox, or are they already present in the acn solven box? Have you already checked all intermediate structures?</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p></p><blockquote type="cite"><div class="im">On Nov 6, 2010 7:25 PM, "Diana Lousa" <<a href="mailto:dlousa@itqb.unl.pt" target="_blank">dlousa@itqb.unl.pt</a>> wrote:<br><br>Hello,<div><br></div><div>No, the hole don't correspond to parts of the protein sticking out on the other side. The protein is in the center of the box and the holes are not due to pbc issues. </div>
<div><br></div>
<div><br></div></div><div>Diana <br><br><div class="gmail_quote"><div class="im"><p><font color="#500050">On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>> wrote:
</font></p></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p><font color="#500050">>
> Hey,
>
> Do the holes match the parts of the protein sticking out on the other side?
>
> Tsjerk
...</font></p>--<p><font color="#500050">
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PhD student
Protein Modeling Laboratory
ITQB/UNL
Oeiras, Portugal
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