Re: [AMBER] How to unsolvate solvated protein?

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Tue, 23 Feb 2010 21:34:52 -0800 (PST)

> I would like to unsolvate already solvated=2C EM-zed protein.

Easiest way I know is

% egrep -v WAT solvated.pdb > unsolvated.pdb

This removes all lines containing WAT. If you want to get rid of
ions too, and your ion is Na,

% egrep -v 'WAT|Na' solvated.pdb > unsolvated.pdb

> I am thinking to do it in xleap=2C but don't know how.

xleap is not designed for it.. manual deletion of each water
is the only way I know.

Bill

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Received on Tue Feb 23 2010 - 22:00:02 PST
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