[AMBER] : wrong charge calculation by xleap

From: Sharma, Purshotam <purshotam.sharma.uleth.ca>
Date: Fri, 13 Apr 2012 18:52:02 -0600 (MDT)

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.

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Received on Fri Apr 13 2012 - 18:00:03 PDT
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