Re: AMBER: how to reduce box size and delete excess solvent

From: Bill Ross <>
Date: Sun, 15 May 2005 12:50:01 -0700 (PDT)

> I would like to reduce the size of the bounding box (periodic BC) and
> delete all solvents which don't fit inside new box. How to achieve it?
> Can anyone furnish a script?

You could use 'awk'.. something like

% awk '$7 < 21.4 && $8 < 30.4 && $9 < 28.2' in.pdb > out.pdb

Read up on awk or perl.. some solvent molecules would
be partial and the atoms could be replaced by leap in
places that could lead to steric problems. The solution
would be either a more complex script or iterative manual
deoletion of the problem residues.

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Received on Sun May 15 2005 - 21:53:00 PDT
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