Re: vmd-l: Autoionize plugin problem

From: John Stone (
Date: Thu Dec 16 2004 - 11:30:21 CST

  The autoionize plugin has been modified to make better/safer use
of psfgen when it creates structures since VMD 1.8.2 was released,
along with that a couple of other minor changes were made. Since I didn't
write it I can't directly answer your questions, but I'd recommend that
you try replacing the version that you're running with the latest version
and see if that cures your problem. Let me know if you need help with this.

  John Stone

On Tue, Dec 14, 2004 at 01:52:03PM -0500, Gaurav Sharma wrote:
> Hi all,
> I am having problem neutralizing the charges in my system using the autoionize plugin of vmd 1.8.2 on windows xp.
> Initially the error was that the file was missing. So I renamed the top_all27_prot_lipid.inp file as and placed it in the autoionize plugin directory. After this the plugin seemed to be running fine (it calculated the total charge on the system, number of ions to be placed etc.) until in the end when the ionized file was being created it gave error messages : "unknown residue type SOD" and " unknown residue type CLA".
> I checked the topology file and found that both SOD and CLA are defined in it. A similar email was posted on the list a few months back but met with no response.
> I would really appreciate if someone can help me out with this.
> Thanks
> Gaurav
> Gaurav Sharma
> Computational BioNano Robotics Lab
> Northeastern University
> Boston, MA - 02115
> Tel: 617-373-2970

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