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

From: Hai Nguyen <nhai.qn.gmail.com>
Date: Tue, 25 Aug 2015 13:19:14 -0400

Like Jason said, you can use RED server to derive charge.

You just need upload 1 or few pdb files (follow its instruction), let RED
takes care of charge fitting and download output in next day (which was
what I did).

Hai

On Tue, Aug 25, 2015 at 12:25 PM, Martina Devi <martinadevi2011.gmail.com>
wrote:

> May I know how to constrain the charge using charge derivation,as I have
> been suggested to constrain the charge to -0.3081. Should I follow the
> tutorial for charge derivation for non-standard residue?
>
> On Tue, Aug 25, 2015 at 8:03 PM, Martina Devi <martinadevi2011.gmail.com>
> wrote:
>
> > Thank you for your suggestion.
> >
> >
> > On Tue, Aug 25, 2015 at 7:46 PM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> >> On Tue, Aug 25, 2015 at 2:53 AM, Martina Devi <
> >> wrote:
> >>
> >> > 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.
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> BioMaPS,
> >> Rutgers University
> >> Postdoctoral Researcher
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
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Received on Tue Aug 25 2015 - 10:30:06 PDT
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