VMD-L Mailing List

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Tue Jul 06 2010 - 14:36:20 CDT

Dear John,

My DNA system has "-20" charges from (o1p) atoms and (+1) form SOD (atom 781) in the pdb file. In order to neutralize the system, I need to add 19 SOD atoms using autoionize. I figured out that if I use 0.3 instead of 0.0001 in the command below:

"autoionize -psf file.psf -pdb file.pdb -is 0.0001"

The system net charge after adding ions is 8.53529961375e-007e while it was -18.9999991465e before adding ions. It seems that the program is adding 19 Na and 0 Cl ions, total 19 ions in this case to balance the charge. My questions are:

(1) Does 8.53529961375e-007e mean 8.53529961375810^-7? If yes, is this net charge now in neutralization by autoionize?

(2) If I use 0.28 instead of 0.3, the final net charge is -0.999999146471e which is very different from what produced by 0.3. Is it because of rounding problem as you mentioned before?

Thanks,

Parisa

(2) If yes

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Tue 7/6/2010 11:42 AM
To: Parisa Akhski
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Autoionize does not neutralize the system
 
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
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