From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Tue Sep 14 2010 - 17:45:52 CDT

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