Hi Fatima,
Unfortunately, I don't believe there is a way to do this in AMBER. Your best
bet is probably to write a short script that goes through a pdb created from
the inpcrd file. You can start by rotating the coordinates so the box aligns
with the XZ plane you want and then it is a simple matter of throwing out
any water molecules that have Y coordinates that would place them above the
plane. You probably just want to look at the oxygens so you don't break any
waters. I.e. if the oxygen lies outside the plane then you delete the
hydrogens as well.
Once you have the pdb for this then you can load that pdb file back into
Leap in order to create the inpcrd and prmtop files. Just beware that AMBER
only has a 3D concept of periodic boundaries so you will have to think
carefully about how you deal with your water layer in MD.
Good luck,
Ross
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of fatima.chami.durham.ac.uk
> Sent: Thursday, May 29, 2008 4:47 AM
> To: amber.scripps.edu
> Subject: AMBER: solvatebox
>
> Dear Amber users,
>
> From a solvated box I want to strip water molecules in the Y direction
> within a
> certain distance from the box edges (Y DIRECTION) so to create a layer...
> is there a way to do this ?
>
> best wishes
> Fatima
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Received on Sun Jun 01 2008 - 06:07:34 PDT
