ion concentration

From: Shirley Li (
Date: Thu Oct 06 2005 - 18:36:26 CDT

Thanks a lot.

I have some further THREE questions:

1) Should ions be added AFTER or BEFORE the protein is

2) The protein is -36e charged. I tried to add ions
after solvating the protein, using the following
command from autoionize:
autoionize -psf file_wb.psf -pdb file_wb.pdb -is 0.05
-o file_ion

I got a warning as follows, even though I tried "-is

WARNING: ion concentration too low, cannot add Cl
Adding 36 Na and 0 Cl ions, total 36 ions

Could sb tell me this is an important issue, and how
to solve it?

3)I got to know that ion concentration should be in
the range 1200 mM, is it correct?

Your help will be greatly appreciated.


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