Re: AMBER: RESP charge fitting for N-methylguanine cation

From: Kara Di Giorgio <>
Date: Thu, 12 May 2005 19:40:17 -0700

I'm trying to create a frcmod file for an organometalic compound
containing bonded nickel. I've used antechamber to help create the
files for the organic portion of the molecule and created custom atom
types for the atoms (nitrogens) attached to the nickel. I've been
modifying the frcmod file generated from this structure based on
distances/angles/dihedrals from Spartan and analogy in gaff.dat. I was
wondering where I could find info about the nonbond info for nickel
(it's my next step). Does anyone know of any frcmod info for a
transition metal bound to an organometallic compound that I could look
at? I was considering iron as a model.


Kara Di Giorgio
University of the Pacific

On May 12, 2005, at 9:50 AM, Grzegorz Jezierski wrote:

> Dear AMBER users,
> As a result of a charge fitting procedure using RESP, performed for a
> cationic form (1+) of 9N-methylguanine, I could see that calculated
> point charges strongly depend on a basis set used and the density of
> MEP points specified in Gaussian input, namely:
> 1) Increasing the 'density of points' parameter "IOp 6/42" from 1 to 6
> changed the optimized RESP charges drastically, about 0.1 e on some
> atoms. Further increase of the parameter from 6 to 8 gave the changes
> 0.05 e or lower, and in the same direction (convergence?). Should I go
> up with the parameter? What's the precise definition of IOp 6/42? Is
> it in 1/(bohr sq.)? The Gaussian manual says "density of points per
> unit area in ESP fit" - does this mean the area of one of MEP layers?
> I kept all the time the default value for IOp 6/41 (=4). Both geometry
> optmization and population analysis was calc. with HF/6-31G*.
> 2) I then changed the basis set to HF/cc-pVTZ and kept: IOp 6/41=4;
> IOp 6/42=8. Charges differed (between the two basis sets) by at most
> 0.05 e, except for the amino group, where the discrepancy was 0.1 e.
> Generally, one see more polarized charge distr. in the case of 6-31G*.
> Which basis set is more suitable as regards modeling polarization
> effects on the solvent?
> Thank you for help.
> Grzegorz
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Received on Fri May 13 2005 - 03:53:00 PDT
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