AMBER Archive (2006)

Subject: Re: AMBER: cutting the box after "solvatebox"

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Aug 17 2006 - 14:28:55 CDT

I just saw this email. I wrote a script before, which is removing the
water molecules after centering the solute. If u need it, let me know.

Best,

On Tue, 8 Aug 2006, Guanglei Cui wrote:

> Hi Vlad,
>
> This is probably not an immediate solution. I would try to center the
> solute, image the water molecules, and save it as a PDB file. Then you
> need a script to do the trimming (awk will do). You can load the trimmed
> PDB file into leap and use setbox command to add the box information.
>
> With a bit reading of VMD manual, you can create a selection based on
> coordinates. That would save you from writing that script.
>
> Regards,
> Guanglei
>
> Vlad Cojocaru wrote:
> > Dear Amber users,
> >
> > I created a box around a solute (loaded as pdb) using "solvatebox sol
> > TIP3PBOX {0 20 0}". However, I need to cut out from this box about 5A
> > from each side of the x and y directions and about 10A from 1 side of
> > the z direction. Is there any tool in Amber that can do that?
> >
> > Thanks
> >
> > vlad
> >
> >
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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