VMD-L Mailing List

From: Salvatore Mario Cosseddu (S.M.Cosseddu_at_warwick.ac.uk)
Date: Thu Jan 27 2011 - 10:27:32 CST

sorry if I post twice but it the first time I post and I don't know how
the mailing list works properly.

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

On 27/01/11 14:05, Dudo wrote:
> mm, sorry, i cant figure out any xxx in it, perhaps you put too much
> water on it
>
> 2011/1/27 ahmet yıldırım <ahmedo047_at_gmail.com
> <mailto:ahmedo047_at_gmail.com>>
>
>
>
> 27 Ocak 2011 15:40 tarihinde Dudo <dudomail_at_gmail.com
> <mailto:dudomail_at_gmail.com>> yazdı:
>
> Could you attach some pictures from your xxx.pdb, please?
>
> Dudo
>
>
> 2011/1/27 ahmet yıldırım <ahmedo047_at_gmail.com
> <mailto:ahmedo047_at_gmail.com>>
>
> 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
>
>
>
>
> --
> ____________________
> Ing. Dusan Racko, PhD
> Polymer Institute of the Slovak Academy of Sciences
> Dubravska cesta 3
> 845 41 Bratislava, Slovak Republic
> tel: +421 2 5477 3448
>
>
>
>
> --
> Ahmet YILDIRIM
>
>
>
>
> --
> ____________________
> Ing. Dusan Racko, PhD
> Polymer Institute of the Slovak Academy of Sciences
> Dubravska cesta 3
> 845 41 Bratislava, Slovak Republic
> tel: +421 2 5477 3448