AMBER Archive (2008)

Subject: Re: AMBER: Solvatebox problem

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Dec 19 2008 - 07:19:18 CST

On Fri, Dec 19, 2008, musa ?zboyac? wrote:

> Dear Amber users,I am trying to create a TIP4PEWBOX box -using solvatebox
> command- with a given size of the box and the number of water residues in
> this box. However, I couldn't find any command to construct this box with
> specific number of residues inside the box. Any help will be appreciated .

I don't think there is such a command -- you would have to adjust the
size by trial and error to get a certain number of molecules.

Note that there already is such a beast --
$AMBERHOME/dat/leap/lib/tip4pew box.off. And, the way in which leap
uses such a unit makes it relatively unimportant how may water molecles
there are -- leap just replicates the box periodically as needed.

...dac

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