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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>
<br>
El 17/05/12 12:25, Steven Neumann escribió:
<blockquote
cite="mid:CAKZJqQGJ3KAyaF_tuk2f+p0HA0a79tnsqrVOf7EAVyv2JJUtBA@mail.gmail.com"
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>
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<br>
</blockquote>
<br>
<div class="moz-signature">-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tel: (+34)868887434
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