Re: [AMBER] Urea box: artifacts or just a special distribution?

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Wed, 20 Jul 2011 16:12:42 -0700

> When I check the pdb file in Chimera, there are crossed gaps in the middle
> sections of the protein-urea box

The solvent box unit is placed according to a box drawn around the vdw
extent of the atoms to avoid initial steric clashes. This creates alleys
between the boxes when the atoms are seen as points. In the case of
solvent boxes that are equilibrated, a closer fit is possible, but
given that it needs equilibration anyway (in order to form-fit around
the solute and to undo the periodicity of the repeating solvent box),
the (my) decision was to use the general approach that you see.


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Received on Wed Jul 20 2011 - 16:30:03 PDT
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