AMBER Archive (2009)

Subject: Re: [AMBER] how to add desired number of water

From: Simon Becker (simon.becker_at_uni-konstanz.de)
Date: Wed Dec 09 2009 - 10:09:51 CST

Hi Balaji,
you encountered the targeted-md-water-problem, I presume?

The recommended way is to write a script the tests various sets of x,y
and z values for the box size until the desired amount of water is in
your box. This can be done in the programming or scripting language of
your choice using three nested loops.

hth
simon

balaji nagarajan schrieb:
> Dear Amber !
>
>
> To put solvation box in leap ,
> suppose one give
> slovatebox model TIP3PBOX 8.0
> it adds 2800 water residues, suppose i need to add only 2000 residues of water molecule ,
> what should be done ?.
>
> thanks in advance
> balaji
>
>
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