From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Nov 01 2013 - 13:52:54 CDT
The CGenFF program at paramchem.org infers the formal charge from the
molecule's connectivity; if you give it a nitrogen atom with 3 bonds, it
will be formally neutral, while a nitrogen atom with 4 bonds will be
formally positive.
Note that a positive formal charge does not automatically imply a positive
partial charge. In the QM, charge is known to smear out over adjacent
atoms, and in the force field, this effect is exaggerated, to the extent
that the partial charge on a positive nitrogen is sometimes negative, with
all the positive charge moved to adjacent atoms. This is done deliberately
to better reproduce the molecule's electrostatic potential within the
limitation of an atom-centered point charge model.
More information about how charges are assigned in...
..additive force fields in general: K. Vanommeslaeghe, O. Guvench, A. D.
MacKerell Jr., Curr. Pharm. Des. 2013, in press.
..the CGenFF *force field* in particular: K. Vanommeslaeghe, E. Hatcher,
C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes,
I. Vorobyov, A. D. MacKerell Jr., J. Comput. Chem. 2010, 31, 671-690.
..the CGenFF *program* (formal charges): K. Vanommeslaeghe, A. D.
MacKerell Jr., J. Chem. Inf. Model. 2012, 52, 3144-3154.
..the CGenFF *program* (partial charges): K. Vanommeslaeghe, E. P. Raman,
A. D. MacKerell Jr., J. Chem. Inf. Model. 2012, 52, 3155-3168.
On 11/01/2013 01:28 AM, Peterson J wrote:
> Hi all,
>
> I am planning to simulate neutral and positively charged forms of a drug
> bound with a protein. How do cgenff parameters obtained from Paramchem
> deal with charge distribution when it comes to positively charged molecule?
>
> Thanks
>
> Peterson
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