VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Wed Mar 17 2010 - 09:22:57 CDT

I use amber ff too and
this is what I use in my VMD scripts

atomselect top {not (water or name "Cl\-" "Na\+" ) }
will select the solute

In the gui I also put in
name "Cl\-" "Na\+"
and it works.

I recently started some sims w/ K+ and thought I should use charge to catch
all ions but this did not work as expected (other atoms get picked up) so I'll
stick w/ names

Cheers.
Tom

On Wednesday 17 March 2010 06:42:41 am 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.
>

*******************************
   Thomas C. Bishop
    Tel: 504-862-3370
    Fax: 504-862-8392
http://dna.ccs.tulane.edu
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