From: Salvatore Mario Cosseddu (S.M.Cosseddu_at_warwick.ac.uk)
Date: Thu Jan 27 2011 - 09:14:40 CST

load your pdb file on VMD

open the tkcon from the extension menu.

write there

set selection [atomselect top "not water"]
$selection writepdb newfile.pdb

done!

with the first command you select all but the water molecules, (see in
the manual the atomselect command), with the second one you write the
new file

Regards

Salvatore Cosseddu

--------------------------------
Centre for Scientific Computing
University of Warwick
UK
 

On 27/01/11 12:51, ahmet yıldırım wrote:
> Dear users,
>
> I want to remove all waters from the xxx.pdb file. Then, I want to
> save the pdb file (new pdb) without waters because I need to simulate
> without water. I looked at mail list but I could not find the answer I
> wanted.
>
> What should I do?
>
> Thanks in advance
>
>
> --
> Ahmet YILDIRIM