Re: [AMBER] : wrong charge calculation by xleap

From: raghav singh <>
Date: Sat, 14 Apr 2012 04:48:55 +0200

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

LEAP is doing just fine... according to me. :)


On Sat, Apr 14, 2012 at 2:52 AM, Sharma, Purshotam <> 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.
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Fri Apr 13 2012 - 20:00:03 PDT
Custom Search