Re: [AMBER] how to neutralized my system with Na+ ions

From: Jason Swails <>
Date: Tue, 25 Aug 2015 10:16:01 -0400

On Tue, Aug 25, 2015 at 2:53 AM, Martina Devi <>

> Hello
> Despite adding the Na ions the charge is not integral.

​Adding Na ions would do nothing to solve a non-integer charge. Sodium
ions have a net charge of +1, so there is no integer number of ions you can
add to neutralize a non-integer charge :).

> When I use a
> standard base the whole system gets neutralizes. Is it due to the presence
> of a non-standard base?

​Yes, but the issue is a little more subtle than that.​ All nucleic acid
residues have a net charge of -1... EXCEPT for terminal residues. All
3'-terminal RNA residues have a net charge of -0.6919 electrons (-0.6921
for DNA), while all 5'-terminal RNA residues have a net charge of -0.3081
electrons (-0.3079 for DNA). Since each strand needs both a 3'- and
5'-terminus, the net charge of a complete RNA or DNA strand is always an
exact integer... which is good.

But this can trip people up. If you make a custom 3'-terminal residue or
custom 5'-terminal residue and constrain its charge to be an integer rather
than the same as the charges I listed above, then when you pair it with a
standard terminus on the other end, you will end up with a net charge of
either -0.6919 (or 0.6921 for DNA) *or* -0.3081 (or -0.3079 for DNA) after
you add "neutralizing" ions.

This is exactly what happened to you -- your net charge after
neutralization is -0.6919 (which tells me you are doing RNA). You will
need to go back to your charge derivation for your custom 5'-terminal
residue (which you called "OAU" per your latest email) and constrain the
charge to be -0.3081 instead of 0 or -1.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 25 2015 - 07:30:04 PDT
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