Hi Raghav,
If there are 11 phosphates on each strand, it means there will be 22 total
phosphates in the duplex. If one needs to neutralize the negative charge,
I should need 22 Na ions.
But it is taking 20 Na ions to do that.
Regards.
P.
> Hello Purshotam,
>
> I don't think xleap is wrong... because in case of classical pdb entries
> the DNA chains are generally missing a terminal PO2 group and because of
> that you are always short of 1 charge group so think like your DNA is a
> duplex of 12 nucleotides that means it has only 11 Phosphates on each
> backbone.
>
> LEAP is doing just fine... according to me. :)
>
> cheers
> raghav
>
> On Sat, Apr 14, 2012 at 2:52 AM, Sharma, Purshotam <
> purshotam.sharma.uleth.ca> wrote:
>
>> Hi all,
>> I am working on a DNA strand with one chemically modified guanine
>> (modified at C8-position). I actually did partial charge calculations
>> for
>> this residue using RED program, and was finally able to generate a
>> library
>> file for this modified residue.
>> Since it was a 12mer duplex, I explicitly added 22 Na+ ions into the PDB
>> file using xleap. However, when I calculated the total charge on the
>> duplex after counterion addition using xleap, it gave the charge as +2.
>> However, when I added 20 ions and calculated the charge, it gave the
>> charge as 0.
>> >From my understanding, since my new modified residue is neutral, a
>> 12mer
>> duplex with 22 anionic phosphates should need 22 Na+ counterions to
>> neutralize it. Then why does xleap show a 0 charge on addition of 20
>> ions
>> and a net +2 charge on addition of 20 ions.
>> Can anyone help me in this regard?
>>
>> Thanks in advance.
>> Purshotam.
>>
>>
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Received on Fri Apr 13 2012 - 21:00:05 PDT
