[gmx-users] Partial Vs Formal Charges

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 1 15:29:48 CEST 2008

nahren manuel wrote:
> 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.

The "best way out" is the one that you believe to be most defensible for 
your particular situation.  I would suggest looking up some of the 
original references for force field derivations (OPLS, GROMOS, AMBER, 
etc.) to get a sense of what types of methods are typically employed in 
deriving parameters.  If you can find similar functional groups that 
have already been parameterized, that would probably be a good resource.

> Also,  does gromacs takes formal charges automatically or is there a 
> way to define the same.

Gromacs will assign charges to each atom based on what you provide in 
the .itp file.


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


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