Re: [AMBER] concentration

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Thu, 20 Jan 2011 11:01:19 -0800

> I am new in amber10. I want to simualte 1-6M urea with water . But I don't
> know how make 1-6 M concentration of urea in amber 10.
> How i make the system in different concentration?

I think you will have to use trial and error, e.g. you could solvate
a single urea with single urea's, then iteratively solvate that box
with water until you get the right ratio. In pseudocode using leap:

x = copy UREA
solvatebox x UREA 5
y = copy x
solvatebox y TIP3BOX 15

Knowing the total urea's in x, calculate the required number of
waters, and keep making new y's and solvating with different radii
until you get close enough to the desired result. Note that after
a while, leap will eat up a lot of memory (the discarded cases),
so it may be useful or necessary to stop leap and restart the process.


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Received on Thu Jan 20 2011 - 11:30:02 PST
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