VMD-L Mailing List

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Fri Sep 17 2010 - 16:11:50 CDT

Hi Peter,

Thanks for reply. I was looking at some MD papers working on DNA and figured out that at least the ones I have, neutralized DNA first and then added water. I am not sure whether this really is a necessity or not. In the case of autoionize, you are right. It replaces the water molecules with ions. BTW, As mentioned in "Caveats and Limitations" part of autoionize:

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

Autoionize does not work properly for DNA so I have to use cionize instead.

Thanks again for your help,
Parisa

-----Original Message-----
From: Peter Freddolino [mailto:petefred_at_ks.uiuc.edu]
Sent: Tue 9/14/2010 7:55 PM
To: Parisa Akhski
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Autoionize question for DNA molecule
 
Hi Parisa,
autoionize *works* by replacing random waters with ions, so prior
solvation is required. Why does it matter whether you add the ions first
or water first during your system setup?
Best,
Peter

On 09/14/2010 06:45 PM, Parisa Akhski wrote:
>
> Dear VMD users,
>
> I am using Autoionize on VMD 1.8.7 to neutralize a DNA system. The
> total net charge on the system is -17 and I need to add 17 Sodium ions
> to make it neutral. There is no water molecule in the system (I will
> add the water box after neutralization). After running autoionize, it
> gives me the error below:
>
>
> Error, failed to add ions after 10 tries.
> Try decreasing -form and/or between parameters,
> decreasing ion concentration or adding more water molecules....
>
>
> I tried to add the distance between the ions and also tried to
> decrease the ion concentration. None worked for me. If I add water box
> first everything seems fine. But, I want to neutralize my system first
> and then add the water molecules. I did the same thing on another DNA
> sequence with the same "total net charge" and it worked perfectly
> fine. Can anyone please help me what maybe wrong for this molecule or
> is it DNA sequence dependent?
>
> Thanks for your help,
>
> Parisa
>
>
>