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
--
========================================
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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