Subject: Summary: ONIOM/AMBER in Gaussian

From: Dami�n Scherlis <[email-masked]>
Date: Wed, 10 Jan 2001 16:42:53 +0100 (MET)

I want to thank Stefan Fau, Nicolas Ferre, Ivan Rossi
 and Douglas Fox, their answers have been of help.
   Following are the original question and the answers:

 Hi,
    I have done some test calculations using
 the ONIOM method (Gaussian98) to combine DFT with
 either AM1 or AMBER. I assumed that the ONIOM
 procedure will solve the High and Low regions
 of the system in a self consistent way, so that
 the electron density of one part is affected by the density
 of the other. Instead I noticed that the energy
 of the High and Low layers did not depend on each other,
 as if each subsystem were isolated. As you see, I have
 probably a wrong idea of what ONIOM is, or I can't manage
 to interpret the results. I will appreciate
 any comment to clarify this question.

    Let me ask another question: when I try to run AMBER
 the computation is interrupted with the following message,
 though I included all atom types in the input:

 Stretching parameters undefined for    1 (O ) -    2 (O )
 Stretching parameters undefined for    3 (HC) -    6 (CC)
 Stretching parameters undefined for    4 (CW) -   10 (HC)
 Stretching parameters undefined for    5 (CR) -   11 (HC)
 Bending parameters undefined for    3 (HC) -    6 (CC) -    4 (CW)
 Bending parameters undefined for    3 (HC) -    6 (CC) -    7 (NA)
 Bending parameters undefined for    6 (CC) -    4 (CW) -   10 (HC)
 Bending parameters undefined for    7 (NA) -    5 (CR) -   11 (HC)
 Bending parameters undefined for    8 (NA) -    4 (CW) -   10 (HC)
 Bending parameters undefined for    8 (NA) -    5 (CR) -   11 (HC)
 Not enough parameters to run AMBER
 Error termination via Lnk1e in /usr/bin/g98/l402.exe.

    Should I provide all these parameters in an additional file?
 How is this done?
     
   Thanks in advance

-- 

Hi Damian,

ONIOM works by calculating the whole
molecule at the low level. Then the high-level
zone is saturated with hydrogens and calculated
at both the high and the low level. The final
energy is:
E(low,all) - E(low,part) + E(high,part)

There is a paper by Stefan Dapprich et al
explaining all this in detail. It is about three
or four years old.

Yours,
             Stefan
______________________________________________________________________
Dr. Stefan Fau                    |      [email-masked]
Quantum Theory Project     |     (352) 392-6714
University of Florida
Gainesville, FL 32611-8435

_______________________________________________________________________
Hi,

In your case, the energy of the whole system is given by :
            E = E(DFT in High)  + E(AM1 or Amber  in Low) - E(AM1 or
Amber in Low)
The DFT calculation is performed on a cluster builded from the High
region saturated with hydrogens. So the electronic density is not
affected by the environment. However, this effect is taken into account
at the low level with a calculation on the whole system (only with AM1 as
Amber is not a polarizable forcefield). Double counting of interactions
is avoided by substracting the energy of the whole system at the low
level of theory.

Second part of the question (about AMBER):       

You can't do this. Maybe you have to modify the Gaussian code to include
those cases. But before doing this, did you check the connectivity of
your system ?If you let G98 generating the connectivity in an automatic
way, maybe it can be wrong.
You can define this connectivity in the input file. Use the IOP(1/57=2).
Then, after the geometry specifications, you can write the connectivity
as following. For every atom:
"Bonded atom number 1" "Type of bond 1" "Bonded atom number 2" "Type of
bond 2" ... and so on
The atom number is an integer, the type of bond is a real (1.00 for a
single bond, 2.00 for a double bond ...).

Hope this helps.

Nicolas

 -- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nicolas FERRE                        Tel : (33)3.83.91.20.00. poste 35.52.
                                     Fax : (33)3.83.91.25.30.
Laboratoire de Chimie Theorique
Universite Henri Poincare - Nancy 1
BP 239                               mailto:[email-masked]
54506 VANDOEUVRE-LES-NANCY Cedex
FRANCE

      http://www.lctn.uhp-nancy.fr/Etudiants/Nicolas.Ferre.html/
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