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

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 27 18:08:30 CET 2008

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!


> Cheers,
> Peyman


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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