AMBER Archive (2007)

Subject: Re: AMBER: AMBER hydrophobic Box : script

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 14 2007 - 09:29:47 CST

On Wed, Mar 14, 2007, Sophie Barbe wrote:
>
>
> For the next step, I need a script that goes through each solvent molecule in
> the box and calculate if any are overlapping or to close to the solute. If it
> finds an atom too close or overlapping the script shpuld then delete
> the solvent molecule.

The solvateBox (or solvateOct) command in LEaP already does this. That might
serve your purpose, or you might adapt that code to something else.

...good luck...dac

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