Re: AMBER: SCC-DFTB for Zinc atom

From: Gustavo Seabra <>
Date: Fri, 18 Jul 2008 19:21:45 -0400

On Fri, Jul 18, 2008 at 1:10 PM, Jifeng Wang wrote:
> Hi, Gustavo,

Hi Jinfeng,

> Thank you. I got the parameter set for Zn from Prof Elstner. The naming for
> these files is like: znpc.spl, znph.spl... I have to change the name from
> znpc.spl to znc.spl ... to make it work. At least it apparently works well
> since no error reported. So I am wondering if I did it right.

That's great. It means you are using Amber9, right? The ones I had
were already called znc.spl, zno.spl, ..., but that should work as
well. When you are renaming it, pay attention to the order of the
names: znc.spl should be different than czn.spl, and so on.

If you can, I would really recommend upgrading to Amber10. The DFTB
code there ismuch more integrated with the rest of the Amber QM/MM,
and now it includes support for GB and PME, which wasn't present in

> However when I turn on dispersion correction by seting dftb_disper =1, it
> gives an error stating "
> WARNING: a parameter is 0.0 for atom 38
> IZP = 3
> nei = 3 ( 2 neighbors.)
> hh1 = 0.00
> hh2 = 3.50
> Ni = 0.80
> I already have the DISPERSION.INP_ONCHSP file in the slko folder. But this
> file doesnt have any information about Zn. Read from amber9 manual "
> DFTB_DISPER ... not available fro the Zn atom", does it mean I can not use
> this option?

Unfortunately, you are right. (Well, half right, at least.) The name
of that file is supposed to indicate what atoms are there, no there's
no out-of-the-box way to run DFTB+dispersion with Zn atoms. However,
in principle you can derive those parameters yourself if needed, and
add to that file. I don't have the references on me now, but it should
not be hard to find the papers about DFTB dispersion in the
literature. Or, if you've seen any publication that claims to use
DFTB+dispersion and Zn atoms, you can try contacting those authors

> Prof Elstner mentioned in his email: be aware that Zn has d-orbitals, i.e.
> you have to specify a '3' in the input! What does the "3" mean? which
> parameter should I set for this? Spin? ( I should ask Prof Elstner
> directly, but since I am writing this email, probably you or somebody else
> can help me out)

My guess is that he didn't realize you are using Amber. In Amber, this
is set automatically and you don't have to worry about that.

> At last, I have a general question. Manual says "the QM region should be
> compact... you can define an active site to be the QM region". How about TWO
> separated active sites? Since my protein is a dimer, I want to include
> both active sites in the QM region.

I would not recommend splitting the QM region. DFTB is really not
famous for it's easy convergence, and splitting the QM zone in two
will certainly not help it, and you would very likely run into
convergence problems. If you can, avoid it.

Good luck,
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Received on Sun Jul 20 2008 - 06:07:48 PDT
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