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

From: Na Le Dang <>
Date: Thu, 21 Jul 2011 10:53:23 -0400

Thank you Bill for the detailed explanation.

On Wed, Jul 20, 2011 at 7:12 PM, Bill Ross <> wrote:

> > 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.
> Bill
> _______________________________________________
> AMBER mailing list

Lena Dang' 11
"Every morning in Africa, a gazelle wakes up. It knows it must run faster
than the fastest lion, or it will be killed. Every morning a lion wakes up.
It knows it must outrun the slowest gazelle, or it will starve to death. It
doesn't matter whether you are a lion or a gazelle. When the sun comes up,
you better start running" [African proverb]
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Received on Thu Jul 21 2011 - 08:00:03 PDT
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