From: Ajasja Ljubetič (
Date: Wed Mar 17 2010 - 09:31:12 CDT

To select only the protein in VMD you can just type "protein" in the
selection box, which you can also save to a separate file.
You can select all ions using "ions" :)
For separate ions you have the wrong name. I think Cl+ are named CLA and Na+
as SOD.
You can double check the name by pressing 0 (pr clicking on Mouse->Query)
and then clicking on the ion of interest. On the console you will get
extended information about that atom.

Best regards,

On Wed, Mar 17, 2010 at 12:42, DimitryASuplatov <> wrote:

> Hello,
> I am running NAMD simulation in AMBER ff and eventually I want to make an
> index file excluding water and ion molecules in VMD.
> The problem is that selecting RESNAME NA+ CL- always throws en error. I
> guess VMD does not like "+" and "-" signs. I`ve tried to mask them with \\,
> {}, (), "", '' though it did not help.
> Does anyone know how to make a selection of resname Cl- and Na+ in VMD?
> Thank you.