[gmx-users] Double vs. Charged Single bonded Oxygen in GROMOS96.1

[Justin A. Lemkul]

Peyman Yamin wrote:
> Hi again dears,
> 
> I should ask for another comment. I have a Phorphorus to which two Oxygen 
> atoms are bonded. One O is double bonded and the other has only a single bond 
> while being negatively charged. In the topology file I get from prodrg both 
> Os are denoted with OA (GROMOS96.1) atom type. both have the same charge 
> (-0.421) and mass (15.9994). I guess the charge is reasonable for the 
> double-bonded one, but not for the one with a single bond and a free 
> electron. How could I correct this?
> 

There is no true double or single bond.  Think resonance!

-Justin

> Cheers,
> Peyman
> 

-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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