Re: [AMBER] : wrong charge calculation by xleap

From: Sharma, Purshotam <>
Date: Fri, 13 Apr 2012 21:46:29 -0600 (MDT)

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.

> 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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Received on Fri Apr 13 2012 - 21:00:03 PDT
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