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

From: FyD <>
Date: Wed, 23 Feb 2011 09:16:58 +0100


I would start by RESP-A1A & then RESP-X1.

Create an accurate initial structure for geometry optimization in a
P2N file; this will save lot of cpu time...

We will release new charge models with new theory levels and new
charge fitting approaches for complexes with such a metal atom.

regards, Francois

> Thanks for the reply. I will try to use it but as I understand you
> have to specify level of theory there as well and here I am quite
> confused what level to use woth Zn2+
> Thanks,
> On Tue, Feb 22, 2011 at 11:28 PM, FyD <> wrote:
>> 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
>> parametrization.
>>> 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.
>> See
>> - handling of automatic or specific atom radius in MEP computation for
>> metallic atoms.
>> See
>> - 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

AMBER mailing list
Received on Wed Feb 23 2011 - 00:30:06 PST
Custom Search