VMD-L Mailing List

From: nunolf_at_ci.uc.pt
Date: Thu Jan 04 2007 - 11:03:59 CST

Hi Cesar

Quoting Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar>:

> Dear all,
> I would like to remove water molecules in a box. The number of water
> molecules is huge and they are spread among several segments which
> may also contain ions. Does anyone have an efficient tcl script for
> doing this under vmd /psfgen ?
> Thanks in advance
> Cesar
>
>

Supposing that your box has protein+water+ions.
On the VMD console, if you type:

set sel [atomselect top protein]
$sel writepdb only_protein.pdb

You will get a pdb file with only protein atoms.
Is this what you want?

Cheers,
Nuno