VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 06 2009 - 14:48:09 CDT

Hi,
  I've posted a MacOS X binary of cionize for you here:
http://www.ks.uiuc.edu/Research/vmd/alpha/cionize/

To run it, gunzip it, then see the README file that I put
in that directory as well. Let me know if you need help
using it or if you run into any problems.

I should mention that VMD is beginning to incorporate the
computation routines used by cionize, and we'll probably completely
replace cionize with VMD scripts in the next 6 months or so.
All that remains is to write new VMD routines to do the electrostatic
map "update" steps that cionize does after placing each ion. Once
that's in place, you'll be able to write a short VMD script that does
everything that cionize does.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 05, 2009 at 09:46:10PM -0400, daniel aguayo wrote:
> Tks John, I'll be waiting for it.
> Cheers
> DAV
>
> On Wed, Aug 5, 2009 at 9:43 PM, John Stone<johns_at_ks.uiuc.edu> wrote:
> >
> > Hi,
> >  I will be compiling updated versions of catdcd and cionize based
> > on the latest VMD plugins.  I should be able to provide CUDA-enabled
> > Mac builds of cionize shortly.
> >
> > Cheers,
> >  John Stone
> >  vmd_at_ks.uiuc.edu
> >
> > On Wed, Aug 05, 2009 at 09:29:07PM -0400, daniel aguayo wrote:
> >> I want to use de cionize plugin on vmd 1.8.7, but I can't find de
> >> cionize executable?
> >> I tried to compile it from the source version on my mac leopard, but I can't.
> >> Anyone can help me.
> >>
> >> Tks a lot
> >>
> >> Daniel Aguayo V.
> >> Centro de Bionformatica y Simulacion Molecular
> >> Universidad de Talca
> >> Chile
> >>
> >> --
> >> saludos desde el fin del mundo
> >
> > --
> > 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
> >
>
>
>
> --
> saludos desde el fin del mundo 

-- 
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