Autoionize: net charge NOT equal to zero

From: Shirley Li (
Date: Wed Oct 19 2005 - 11:44:34 CDT

Dear NAMD expert,

I'm using autoionize to neutralize the protein, which
is -33 e. The problem I have is that "System net
charge after adding ions: -0.999989831234e". The net
charge is not neutral. The command I used is:

autoionize -psf output_wb.psf -pdb output_wb.pdb -is
0.05 -o output_wbi. Could sb tell me what's wrong?

Based on what is suggested in some post of the mailing
list, I checked my protein and water box using VMD,
and the minimization output. All of them look ok.

Your help will be greatly appreciated.


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