AMBER Archive (2006)

Subject: Re: AMBER: Details about Gaussian basis set for Cobalt complex

From: Thomas Cheatham (
Date: Fri Aug 25 2006 - 13:21:07 CDT

> I would like to compute the RESP charge for Cobalt 3+ complex. I had gone
> through the following article which calculates the RESP charge for the
> cobalt hex amine complex and used those values in Amber simulation.
> *Insight into the stabilization of A-DNA by specific ion association:
> **Structure, Volume 5, Issue 10, 15 October 1997, Pages 1297-1311 *
> Thomas E Cheatham, III and Peter A Kollman
> I would like to calculate Co 3+ complex ESP charges using Gaussian
> package. I tried with Hf/6-31G** basis set. It failed with an error "*GetVDW:
> no radius for atom 1 atomic number 27*". Therefore i would like to know

If you look carefully through the methods of that paper at the end of the
article, you will see that the cobalt hexammine complex charges were not
calculated with "RESP" at the 6-31G* level but with an "ESP" fit to an
electrostatic potential from the DGAUSS program at the double zeta plus
polarization level on the main terms with the A1 auxiliary basis set
applying the Becke non-local correction in the SCF.

Likely you cannot treat a metal like cobalt at the HF/6-31G** level...

(related: are the current charges from the Structure paper incorrect such
that new charges are needed from a RESP approach? In general, molecular
mechanics does a terrible job of treating metals such that we only really
provide a very approximate representation of the cobalt hexammine as a
highly charged "ion".)

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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