<br><br><div class="gmail_quote">On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo <span dir="ltr"><<a href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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genbox calculates overlaps based on vdW radii as included in
vdwradii.dat in the topology folder. Increase the vdW radii of
carbons to avoid water to closer that you want. Other possibilities
are patiently removing undesired waters by hand after solvation or
using a "ad-hoc" script.<br>
<br>
Javier<br></div></blockquote><div><br>Thank you Javier. Can you please explain what is ad-hoc script and where I can find it?<br><br>Steven<br><br> <br></div><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>
El 17/05/12 12:25, Steven Neumann escribió:
<div><div class="h5"><blockquote type="cite">Dear Gmx users,<br>
<br>
My system consists of a tube which is representated by atoms which
are not connected via bonds.<br>
genbox somehow place water molecules overlapping my tube atoms
resulting in bad contacts.<br>
<br>
Is there anyway to add water e.g. 4A away from existing index file
of my tube?<br>
<br>
Please, help.<br>
<br>
Steven<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div><span class="HOEnZb"><font color="#888888"><div>-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tel: <a href="tel:%28%2B34%29868887434" value="+34868887434" target="_blank">(+34)868887434</a>
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</font></span></div>
<br>--<br>
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