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.
thanks
nahren
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