If you have one instance of your modified residue in each strand,
the below results would suggest that the phosphate on the modified
residue is uncharged.
Bill
"Sharma, Purshotam" <purshotam.sharma.uleth.ca> wrote:
> Dear all,
> I wish to add one more thing to what I said earlier. On a similar DNA
> strand without guanine modification, 22 Na ions neutralize the total
> system, whereas for the modified one, 20 Na ions are required for
> neutralization as indicated by xleap.
> That is the reason for confusion.
> Regards.
> P.
>
> > On Fri, Apr 13, 2012, Sharma, Purshotam wrote:
> >
> >> 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.
> >
> > Run ambpdb with the -pqr flag. This will produce a file showing all of
> > the
> > charges you have, and you can see where any of the assumptions you are
> > making
> > above might be wrong. Without knowing exactly what you did (or even how
> > many
> > modified guanines you have[!] or even if the problem has anything to do
> > with
> > the chemical modifications], those on the list can't help you very much.
> >
> > ....dac
> >
> >
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>
>
>
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Received on Fri Apr 13 2012 - 22:30:03 PDT
