Re: charmm param ... wrong charges

From: Raghav (
Date: Thu Mar 08 2012 - 17:31:24 CST


Hey Aron, I have postulated the same that because of valence electrons and P
is available for 5 bonds but it is bound to 4 O atoms which left P with +1
as well as 2 O's are bound to P have partial double bond characters. And if
I will sum up all partial charges P + 4O atoms final would be ­1.5 but that
would be for whole species that PO4 thing not P alone.

Thanks , I just wanted to listen the same postulation from someone else. :)

From: Aron Broom <>
Date: Thu, 8 Mar 2012 14:27:49 -0500
To: Cristhian Boetsch <>
Cc: RPS S <>, <>
Subject: Re: namd-l: charmm param ... wrong charges

As already stated, that -1 should NOT be the partial charge of the P atom,
it will almost certainly be different. You should look at the partial
charges of the other atoms attached to it to convince yourself that it makes
sense (or perhaps there really is a problem). Likely the oxygens that are
attached will have negative partial charges such that the net charge from
summing all these partials will be reasonably close to -1 (you'll have to
count any hydrogens also, and any other atoms that are part of that residue,
which perhaps means the whole nucleotide, but I don't do DNA simulations, so
I'm just guessing here).


On Thu, Mar 8, 2012 at 1:49 PM, Cristhian Boetsch
<> wrote:
> -1 is the charge of the group. one atom have not net charge at least it is a
> ion as Mg++ Na+ Cl-. Take a look how charmm assign parcial charge to a
> molecule.
> 2012/3/7 raghav singh <>
>> Hello All,
>> During my simulation of a ssDNA i have found that the vmd/namd combo has
>> calculated wrong charges for the P atom of DNA backbone ... as mostly all
>> of us know that it is -1 (as per my info). but in my psf file this is +1.5
> --
> Mic. Cristhian Boetsch
> Universidad Nacional de Río Cuarto
> Río Cuarto - Argentina
> Cel.: 0358-154361332

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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