AMBER Archive (2006)

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

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Tue Aug 08 2006 - 09:38:06 CDT

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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