Re: charmm param ... wrong charges

From: Aron Broom (
Date: Thu Mar 08 2012 - 13:27:49 CST

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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