Re: [AMBER] developing parameters for Zn-binding site

From: FyD <>
Date: Tue, 22 Feb 2011 23:28:47 +0100

Dear Jorgen,

I copied/cut/adapted an email sent in the Amber mailing list several days ago.

You could use "R.E.D. Server Development" for your Zn2+ complex

> I have a zinc site in my protein and I would like to develop
> parameters for this site. I have found articles where the describe
> what level of theory is used for copper ions but I have not been able
> to find any for Zn2+ and I do not presume that one can generalize
> here. So for my substrate I have used HF 6-31* but I would presume
> that DFT using either GGA or hybrid functional would get the
> geometries better as well as the Merz-Kollman charges - what is the
> level of theory for parametrizing metal sites in this case zinc so
> probably not so complicated?

We have developed a new R.E.D. Server version called "R.E.D. Server
Development" .

The new features of this server are:
- handling of ALL the elements of the periodic table (but a few elements).
- new charge models; up to 15 charge models by now; HF & DFT based
theory levels.
- handling of automatic or specific atom radius in MEP computation for
metallic atoms.
- new resp version: resp version 2.2

See the faq of R.E.D. server development:
  & in particular:

New features to come pretty soon:
- new q4md-fft charge models for all the elements of the periodic table
- Ante_R.E.D. 2.1
- new algorithm to improve SCF & geometry convergence in the geometry
optimization step.
- full integration with R.E.DD.B.

If you want to use this new RESP version 2.2 on your workstation just
let me know, and we will release it on our q4md-fft web site...

regards, Francois

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Received on Tue Feb 22 2011 - 14:30:06 PST
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