From: Eduard Schreiner (eduard.schreiner_at_gmail.com)
Date: Mon Jul 12 2010 - 11:08:02 CDT

take a look into the cionize plugin:

http://www.ks.uiuc.edu/Research/vmd/plugins/cionize/

eddi

On Mon, Jul 12, 2010 at 10:10 AM, Parisa Akhski
<Parisa.Akhshi_at_chem.queensu.ca> wrote:
>
> Dear all,
>
> I have been using "Autoionize" in VMD 1.8.7 to neutralize a DNA molecule by
> adding 20 sodium ions. I just figured out that in the "Caveats and
> Limitations" part in the link below, it mentioned that for the systems with
> big electric charge such as DNA (my molecule has 20 negative charges), one
> needs to place ions with regard to the electrostatic potential of the
> molecule since the "Autoionize" is not acceptable in the big electric charge
> cases.
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/autoionize/
>
> Does this mean I should add the ions manually? If yes, how do I know there
> is no overlap between the ions and the solvent molecules?
>
> Thanks for your time,
>
> Parisa

-- 
--
=============================================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================================================