AMBER Archive (2006)

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

From: S.Sundar Raman (sundar02_at_gmail.com)
Date: Sat Aug 26 2006 - 05:51:04 CDT

thank you for your reply. I have a cobalt 3+ complex with 6 nitrogen atom
and 14 carbon atom and 32 hydrogen atoms. I would like to interact this
complex with DNA. So what can i do.
Is it right way to do treat cobalt as the charge of 3+ ? and in Gaussian, i
can able to calculate other atoms in the molecule charges ( while nuc of
Cobalt as 0 )?
or i would like to know the exact basis set card in Gaussian for treating
this complex in amber.

On 8/25/06, Thomas Cheatham <tec3_at_utah.edu> wrote:
>
>
> > 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
> -/-
> /-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
> \-/ BPRP295A http://www.chpc.utah.edu/~cheatham
>
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-- 
S.Sundar Raman
Chemical Lab,
CLRI
Chennai-20
ph: 044-24411830

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