packmol comes to mind: http://www.ime.unicamp.br/~martinez/packmol/ . Then
all you need is a library file for urea. There's a related OFF file in
amber right now (8Mureabox.off), but I attached one to an email in a
previous post to the mailing list that just has urea (URE) taken from this
OFF file. This is what you'll need to use if you generate your own
structure with packmol or something of the like.
That previous post is here: http://archive.ambermd.org/201001/0389.html
Hope this helps,
Jason
On Thu, Jan 20, 2011 at 2:09 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> PS -
>
> I wonder if there is some non-Amber tool to do this?
> If so, you could loadpdb in leap and setbox to create
> a periodic system.
>
> Bill
>
> > 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?
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jan 20 2011 - 12:30:02 PST
