nucleic acids - total charge

From: raghav singh (
Date: Mon Apr 30 2012 - 04:55:38 CDT

Hi All,

I have a question about total charge of nucleic acid system... no matter
what I have tried it does not sum up to an integer value... for a double
stranded helix of 24 bp ...i is like 45.9999 .......!! something like this
(with terminal patch).
during ionization it tells me that I have to add 46 ions to neutralize the
system... but it come up with some positive value?

while if I understand it right it should be -48 with terminal patch or -47
with terminal patch. (gromacs, amber ).

and after solvation and ionization it comes up with some positive value of
1.23446 ... !!

if someone have any idea abt it.. please tell me how can solve this one.

Thank You


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