VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 06 2010 - 10:42:58 CDT

Hi,
  Interestingly, in reading the current version of the code, there
are a number of checks for this kind of problem. It would seem
that this particular case is exercising a code path that either
isn't covered, or that you neglected to mention anything about warning
messages that should have appeared when running the tool?

It would be helpful to have the actual files that caused the problem,
as there's clearly a case that's not being handled here.

Which version of VMD are you running? (so I can get a rough
guess which version of autoionize you're using)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 06, 2010 at 10:16:20AM -0400, Parisa Akhski wrote:
> Dear VMD users,
>
> I am using autoionize to neutralize a DNA molecule. I am using the command
> below as posted on the VMD mailing list to make it only place enough ions
> to neutralize the system:
>
> autoionize -psf file.psf -pdb file.pdb -is 0.0001
>
> The system net charge before adding ions is -18.9999991446e and after
> adding ions is -0.999999144592e. Isn't that supposed to be zero after
> adding ions? Or is it acceptable?
>
> Thanks in advance for your help,
>
> Parisa 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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