From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Dec 17 2010 - 08:29:52 CST

I think you have to say
set selwater [atomselect top "name OH2 and within 10 of protein "]

(*delete the not*)

It's always best to view selections graphically.
You can put the selection string under representations -> selected atoms and
see what you have selected. I usually set the drawing method to CPK.

Regards,
Ajasja

On Fri, Dec 17, 2010 at 14:18, siddesh southekal <siddeshonline_at_gmail.com>wrote:

> Dear all,
>
> I have a pdb file (after 20 ns MD run ) with a membrane protein (GPCR)
> embeded in the lipid bilayer with buffer around .There is excess of water
> molecules in this file . I want to remove this excess buffer such that i
> have water molecules only 10 A above and below the protein .(say around 15 A
> around the lipid ) .The membrane normal is in y direction.
> I would be using the truncated file for MD simulation using AMBER.
> I tried -
> set selwater [atomselect top "name OH2 and not within 10 of protein "]
> But whn i try to save the selection the pdb file is blank.How do i exactly
> do this?
> I would appreciate any suggestions
> Thanks ,
> Siddesh
> Universitaet Bonn
>