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

Date: Tue, 25 Aug 2015 21:55:44 +0530

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 <martinadevi2011.gmail.com>
>> 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
>>
>> 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
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Aug 25 2015 - 09:30:03 PDT
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