Re: [AMBER] : wrong charge calculation by xleap

From: case <>
Date: Fri, 13 Apr 2012 23:26:50 -0400

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.


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Received on Fri Apr 13 2012 - 20:30:06 PDT
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