[gmx-users] Partial Vs Formal Charges

nahren manuel meetnahren at yahoo.com
Tue Jul 1 15:13:03 CEST 2008

Dear Gromacs USERs,
My ligand, which contains a piperazine ring & needs to be positively charged (+1). 
When I assign Gasteiger charges, it comes out to be -0.336 on the Nitrogen. 
But When I do a SEMI-EMPIRICAL PM3 to place my partial charge , it puts +0.733 on this atom. So does it mean it has put partial charge as (F.Charge - P. Charge). When I use InsightII (cff91 FF), the partial charge on this ligand was -0.556 and also it had a formal charge of +1.   So kindly suggest me the best way out.
Also,  does gromacs takes formal charges automatically or is there a way to define the same. 

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