[gmx-users] script to remove water

Kai Zhuang kai.zhuang at gmail.com
Tue Aug 23 20:58:55 CEST 2005

easier way to do this without script: use VMD

open the pdb/gro file with VMD, use atomselect command to select
everything that's NOT water.  then use writepdb command to write your
selection to a pdb file.

look at VMD's tutorial/reference for usage of atomselect and writepdb
command. if i remember right, tutorial go through a exact same senario
like yours, to remove all waters from a system.

On 8/23/05, Ramachandra Rao Gullapalli <rrg142 at psu.edu> wrote:
> Dear Group
> As per the advice of Dr Bostick, i have tried to build my own bilayers and
> introduce the molecule of my choice into the same. However, when i try to
> hydrate the bilayer, there are water molecules everywhere. I have read on the
> groups that we need to write our own script to remove them. I tried to search
> for such a script in vain.I was wondering if anyone could lend me such a script
> as i am not familiar with scripting languages. I would be really thankful for
> such a file.
> Sincerely
> Regards
> Rama
> The important thing is not to stop questioning. Curiosity has its own reason for existing...
> -Einstein
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Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com

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