Re: Autoionize error: spontaneously quits

From: dora guzman (
Date: Fri Jun 23 2006 - 12:18:02 CDT

I figured this out by using another script from the previous version of
VMD (1.8.3). I'm not sure why the newest script didn't work though.


dora guzman wrote:

> I'm experiencing some difficulty with the autoionize function in VMD
> 1.8.4. I've tried adding ions to a solvated protein (~60K atoms) with
> a concentration range of 0.05 to 0.5, and it continuously displays the
> following error:
> Warning: ion concentration too low, cannot add Cl ions!
> Error: failed to add ions from 10 tries
> Try decreasing -from and/or -between parameters (which are
> set at 5A)
> or decreasing ion concentration, or adding more water
> molecules...
> I've tried everything it recommends, but continue to get the same error.
> The size of the protein is 95 residues, and I've added 20,420 water
> molecules. I can't afford to make the water box too large because it
> will be more time consuming to equilibrate and the perform SMD.
> Any advice would be greatly appreciated.
> -dora

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