AMBER Archive (2008)

Subject: Re: AMBER: SCC-DFTB for Zinc atom

From: Jifeng Wang (wangjf_at_gmail.com)
Date: Fri Jul 18 2008 - 12:10:17 CDT

Hi, Gustavo,

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.

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?

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)

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.

Thanks,
Jifeng

On Thu, Jul 17, 2008 at 11:48 AM, Gustavo Seabra <gustavo.seabra_at_gmail.com>
wrote:

> Hi Jifeng,
>
> For licensing restrictions, the DFTB parameters cannot be distributed
> with Amber. To get the parameters you want (Zn), I'd suggest
> contacting the authors of the paper directly, since the files have not
> been added to DFTB.org yet. Try contacting Prof. Marcus Elstner
> (m.elstner ** at ** tu-bs.de).
>
> Gustavo.
>
>
> On Thu, Jul 17, 2008 at 11:33 AM, Jifeng Wang wrote:
> > Hi, there,
> >
> > I have a protein using a Zinc atom as cofactor. I want to include this
> Zinc
> > atom and other surrounding residues in the QM region for QM/MM
> calculation
> > by Amber 9. I noticed that some CHARMM people used SCC-DFTB for this kind
> of
> > system and claimed that it is better than AM1 and PM3.
> >
> > I downloaded the slko files from DFTB.org. However the files for Zinc are
> > not included in the parameter set (mio, pbc, hyb, trans3d). So my
> question
> > is: where can I get these files? Since ChARMM people are using, it should
> be
> > somewhere...
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu