VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 19 2007 - 15:37:16 CST

The autoionize.tcl file is actually in the plugins/autoionize...
directory in the VMD installation on your computer. You can just
(backup first!) edit that file and change the script to use your
favorite ion type. Someone else on VMD-L may have already done this
or have a simpler method, but this was the quickest suggestion that
came to mind at the time.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 19, 2007 at 02:27:04PM -0700, Lixia Jin Day wrote:
> John,
> Thank you. I searched the folder and the web, where can I find
> autoionize.tcl or cionize?
>
> Lixia
>
> On Dec 19, 2007 1:09 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Hi,
> > At present you could either edit the autoionize.tcl script to
> > use other ion types, or use one of the other ion placement tools like
> > cionize to do this. If you need help, let us know. We'll be
> > changing the ion placement plugins in VMD to be much more flexible
> > as time goes on...
> >
> > Cheers,
> > John
> >
> > On Thu, Dec 13, 2007 at 10:19:06AM -0700, Lixia Jin Day wrote:
> > > I used autoionize to add NA+ and CL- in the solvent by using plugin
> > > autoionize before. Now I want to add mg2+ ions instead of NA+. How can I
> > do
> > > this? Thanks!
> > >
> > > Lixia
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078