From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Mar 08 2012 - 18:58:01 CST
Hmm, I think you need to be careful here. If you are expecting the sum of
partial charges for P + 4O to be -1, it won't be. Two of those oxygens are
connected to carbons, so they will withdraw extra electron density. In
this case it could easily be -0.25 for each oxygen which would account for
the -1.5 (rather than -1 you were expecting, or maybe I'm not understanding
what you were expecting). You could sum up the charges on the sugar for
instance and you might find that it comes out to +0.5.
Basically, since the phosphate group is not an isolated molecule/species,
but covalently bonded to other groups, you need to be careful about
comparing net and sum-of-partial-charges.
~Aron
On Thu, Mar 8, 2012 at 6:31 PM, Raghav <raghavbioinfo_at_gmail.com> wrote:
> Hello,
>
> 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 <broomsday_at_gmail.com>
> Date: Thu, 8 Mar 2012 14:27:49 -0500
> To: Cristhian Boetsch <cristhian.boetsch_at_gmail.com>
> Cc: RPS S <raghavbioinfo_at_gmail.com>, <namd-l_at_ks.uiuc.edu>
> 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).
>
> ~Aron
>
> On Thu, Mar 8, 2012 at 1:49 PM, Cristhian Boetsch <
> cristhian.boetsch_at_gmail.com> 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 <raghavbioinfo_at_gmail.com>
>>
>>> 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
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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