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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Received on Wed Aug 09 2006 - 06:07:13 PDT
