VMD-L Mailing List

From: Lixia Jin Day (ljin12_at_asu.edu)
Date: Fri Dec 21 2007 - 10:52:42 CST

I am modifying the autoionize.tcl
the equation to calculate the number of SOD ions:
set nNa [expr (-$netCharge + 0.0187 * $ionConc * $nWater)/2.0]

can you explain how to get this equation? Thank!

On Dec 19, 2007 2:37 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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
>