VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Thu Jan 27 2011 - 08:24:09 CST

Hi Ahmet,

Load the pdb into vmd and then in the tcl console:

set A [atomselect top "not water"]
$A writepdb newpdb.pdb

"not water" may be replaced with "protein" or some other atomselection string, depending exactly on what you want to extract from the pdb.

You can also do something in via the GUI using the menu item File > Save Coordinates.

Best of luck,
Josh

On Jan 27, 2011, at 7:51 AM, 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