AMBER Archive (2008)

Subject: Re: AMBER: how to enlarge the TIP3PBOX size

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Sep 26 2008 - 11:06:37 CDT

On Fri, Sep 26, 2008, Qiuting Hong wrote:
>
> I use solvateoct 1wgg TIP3PBOX 10.0, and xleap said:
>
> solute vdw bounding box: 36.162, 30.853, 52.074

This is printed just for information -- the size of solute is clearly
independent of how many waters will eventually be added, or what the
size of the final box will be.
>
> Actually, when I prepare the sander input file, I also try solvateoct 1wgg
> TIP3PBOX 12.0. The solute vdw bounding box is also: 36.162, 30.853, 52.074
> (the density, and number of water molecules added is different). Thus,
> I decide to use TIP3PBOX 10.0 since it has less water molecules.

Well, sure, it has fewer water molecules. But if you are having trouble
getting the entire solute solvated, especially if the solute changes its
conformation, you may need more waters.

...dac

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