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Date: Wed, 30 Sep 1998 23:04:47 -0500 (CDT)
From: Tapas Kar <root@risky3.thchem.siu.edu>
To: ComputerChemistryList <chemistry@www.ccl.net>
Subject: Risc/Silicon Graphics/multiprocessor PC/Digital  ...
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Hi Everybody,
We are planning to buy a box who shall be fully dedicated for
Gaussian94/98
jobs and can handle(in good manner) large molecules(50-100atoms) with say
300+ basis sets. How fast are the multiprocessor PC with Linux compared to
others say Risc/Silicon Graphics/Digital Alpha/ or other(???)?

Budget is within 30-35K.

Looking for your suggestion.
Thanks,
Tapas

--------------------------------------------
Tapas Kar, Ph. D                           
Asst. Scientist/Asst. Professor (Adjunct)                            
Forestry Bldg 118
Department of Chemistry
Southern Illinois University at Carbondale
Illinois 62901-4409

Fax: (618) 453 6408
Tel: (618) 453 6433(Lab) 6485(Office)
--------------------------------------------     



From chemistry-request@www.ccl.net  Thu Oct  1 12:42:41 1998
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Date: Thu, 01 Oct 1998 13:34:30 -0300
From: Gustavo - NPD <seabra@NPD.UFPE.BR>
Subject: Re: CCL:IR intensity Units
To: chemistry@www.ccl.net
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Dear all,

    I would like to take the opportunity and ask for units used in x-ray
difraction (radial distribution functions).

    Thanks very much,

    Gustavo Seabra.
-----Mensagem original-----
De: Artiben Taylor <ihtrap@hotmail.com>
Para: chemistry@www.ccl.net <chemistry@www.ccl.net>
Data: Quarta-feira, 30 de Setembro de 1998 14:58
Assunto: CCL:IR intensity Units


>
>CCLers:
>I would appreciate to receive review articles on IR Intensities,
>and in particular, i would like to know the various units used
>for IR intensities and the temperature dependance of IR intensities.
>My immediate requirement is how to convert the IR intensity value
>in cm/molecule to cm^(-2)atm^(-1) and vice versa.
>Thanks in advance
>A Taylor
>
>
>______________________________________________________
>Get Your Private, Free Email at http://www.hotmail.com
>
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From chemistry-request@www.ccl.net  Thu Oct  1 15:15:48 1998
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Subject: 3rd LAKE TAHOE SYMPOSIUM ON MOLECULAR DIVERSITY




LAKE TAHOE SYMPOSIA announces the
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January 24-29, 1999

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MaryJo Zaborowski, Roche Bioscience
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* Generation *
Jon Ellman, UC Berkeley
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* Evaluation *
Roger Tsien, UC San Diego
Nolan Sigal, Pharmacopeia

* New Technologies *
Paul Hoeprich, Hewlett-Packard


*** PROGRAM ***
* Keynote Address *
Jonathan Knowles (Hoffman-La Roche)
The molecular diversity of man and molecule

* Banquet Address *
Sydney Brenner (Molecular Sciences Institute)
Massively parallel solid phase cloning


* Informatics - Chemistry *
Jon Mason (Bristol-Myers Squibb)
New methods for diversity profiling

Peter Myers (Combichem)
Design of informative libraries

Bernd Rohde (Novartis)
Diversity mapper

Dora Schnur (Pharmacopeia)
Designing large "smart" combinatorial libraries: activity based
validations of diversity hypotheses

Bob Tilton (Arqule)
Diversity and library design

Lutz Weber (Morphochem)
Diversity of the chemistry space-fractals and genetic algorithms


* Informatics - Biodisplay *
David Haussler (UC Santa Cruz)
Hidden Markov models for biosequence analysis

Anthony Kerlavage (Celera)
Data management from high-throughput EST projects

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Bioinformatics beyond genomics

Eric Schadt (Roche Bioscience)
Quantitative analysis of gene expression arrays and linkage analysis

Jeffrey Skolnick (Scripps)
New methods for the prediction of protein structure and function from
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Robert Strausberg (NCI)
The cancer genome anatomy project


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Keith Bostian (Iconix Pharm)
Yeast surrogate screening and the activity matrix concept

Michael Conrad (Chromagen)
Novel fluorescence-based hybridization and immunoassays

George Grass (Navicyte)
Drug selection - interfacing in vitro screening and pharmacokinetic
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Michael Heller (Nanogen)
Electronically-driven DNA manipulation and hybridization on chips

Homme Hellinga (Duke)
Protein-based biosensors

Bill Hutchens (Ciphergen)
ProteinChipTM array strategies for differential protein display:
retentate maps of molecular recognition diversity

Fred Kramer (Pub Hlth Res Inst)
Multicolor molecular beacons for the identification of single nucleotide
polymorphisms

Alex Varshavsky (Caltech)
Co-dominant interference and multi-target drugs

K. Xanthopoulos (Aurora Bio)
Genome-wide cytometric trapping of differentially expressed genes in
live cells


* Solid & Liquid Phase Chemistry *
Shankar Balasubramanian (U Cambridge)
Solid phase chemical technologies 

Scott Berk (Merck)
A combinatorial approach to non-peptide subtype selective somatostatin
receptor agonists

Alexey Eliseev (SUNY Buffalo)
Dynamic combinatorial chemistry

Michael Foley (Harvard)
Stereoselective synthesis

Ole Hindsgaul (U Alberta)
Solid phase synthesis and screening of carbohybrid libraries

Shu Kobayashi (U Tokyo)
New methods for the synthesis of compound libraries

Wilhelm Maier (Max Planck Inst)
Combinatorial catalysis

Richard Morphy (Organon Labs)
Diversification linkers for tertiary amine synthesis

Mike Organ (York U)
Diverse solution phase libraries based upon an alkene template

Allen Reitz (Johnson & Johnson)
Sulfonate traceless linkers

Susan Rohrer (Merck)
A combinatorial approach to non-peptide subtype selective somatostatin
receptor agonists

Peter Schneider (Novartis Pharm)
Large scale solid phase synthesis: a valuable approach?

Victor Snieckus (Queen's U)
C-C bond formation: solid support-solution phase interface

Drew Thompson (Dupont)
Silica based scavengers


* New Technologies *
Tony Czarnik (Illumina)
Beads on fiber optic bundle tips: self-assembled femtoarrays

Randall King (Harvard)
Nanowell format assays for identifying inhibitors of cell division

Doug Modlin (LJL Biosystems)
Multi-assay development

Jack Owicki (LJL Biosystems)
Multi-assay development

Tom Paterson (Entelos)
Disease modeling systems

Mike Sailor (UC San Diego)
Chemical and biological sensing with nanocrystalline  porous silicon

Raymond Salemme (3-D Pharm)
Finding ligands by their effects on the thermal denaturation curves of
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Lans Taylor (Cellomics)
Integration of UHTS, HCS, and cellular informatics

Peter Wilding (U PA Med Ctr)
Microfluidic-based technologies: overcoming sample problems


Organization:  Lake Tahoe Symposia are organized by scientific
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*** 1998 Lake Tahoe Symposia Sponsors ***

* 2nd Lake Tahoe Symposium on Molecular Diversity *

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* Antiviral Therapy: Targets, Resistance, Strategies To Minimize
Resistance *

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For additional information, registration and lodging forms, contact Lake
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From chemistry-request@www.ccl.net  Thu Oct  1 15:28:30 1998
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Date: Thu, 1 Oct 1998 14:31:29 -0500
To: chemistry@www.ccl.net
From: "Jan H. Jensen" <jhjensen@blue.weeg.uiowa.edu>
Subject: EPR g-factors / Summary



Hello,

	Attached below are all the e-mail I received from the CCL regarding
ab initio evaluations of g-factors.  Thanks to all who responded.  In
addition to the programs mentioned below it seems that the program DALTON
(http://www.kjemi.uio.no/software/dalton/dalton.html#Capabilities) also has
this capability.

	Best regards,
			Jan Jensen

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Jan H. Jensen				Assistant Professor
Department of Chemistry			jan-jensen@uiowa.edu
University of Iowa			Phone:(319) 335-1108
Iowa City, IA 52242			FAX:  (319) 335-1270
http://www.uiowa.edu/~chemdept/faculty/jensen/
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

From: frisch@lorentzian.com (Mike Frisch)
Subject: Re: CCL:EPR g-factors
To: uunet!blue.weeg.uiowa.edu!jhjensen@uunet.uu.net (Jan H. Jensen)
Date: Thu, 24 Sep 1998 22:27:37 -0400 (EDT)
MIME-Version: 1.0

Jan H. Jensen writes:
>
>
> Hello,
>
> 	I am interested in calculating anisotropic EPR g-factors using ab
> initio electronic structure theory.  I would like to know what programs can
> calculate this property, and what kind of accuracy one can expect.
>
> 	Best regards,  Jan Jensen
>

Gaussian 98 can do this.  There are references in the G98 manual (and the
web site)
to papers of Barone's which make detailed comparisons with experiment.

Mike Frisch

From: Jussi Eloranta <eloranta@endor.chem.jyu.fi>
Subject: Re: CCL:EPR g-factors
To: jhjensen@blue.weeg.uiowa.edu (Jan H. Jensen)
Date: Fri, 25 Sep 1998 11:33:59 +0300 (EEST)

Dear Jan,

>	I am interested in calculating anisotropic EPR g-factors using ab
>initio electronic structure theory.  I would like to know what programs can
>calculate this property, and what kind of accuracy one can expect.
>


I have been looking for the same information but have not found any program
that can do it (there are some private codes that can - as you can see from
some publications in JCP, for example). The closest I have found is GAMESS-UK
in which the g-tensor code was once in but has been commented out for some
reason. I have been trying to get Dr. M. F. Guest to put it back but I
think there has not been enough requests for it (or he is extremely busy
or something). Currently gamess-uk can calculate isotropic and anisotropic
hfc for various wavefunctions (including MR-CI too!). BTW this was the only
program I found that could do even this for MR-CI wavefunctions!

You can find more info from: http://wserv1.dl.ac.uk/CFS/
(the program is commercial but very cheap, includes very good support,
very good manuals, etc.)


Best regards,


Jussi Eloranta
University of Jyvaskyla
Finland

Hi
Im just sticking my head into this area myself so I'l share what i've found.
there is a good general review on dft with some stuff on ESR at
http://129.43.1.11/tmmec/current/CURRENT_REVIEWS/oscar_ventura/oscar5.html#120
if you can get onto it -I've had some trouble  over the past few days.
also
This is something that appeared on the list in about 1996 and refers to using
the gaussian program for computing anisotropic coupling constants.
its from Vicence Barone and his address is at the end of the item.



I have received several requests about the computation of ESR anisotropic
coupling constants by Gaussian94. Since this seems a general question I
directly post this message for the whole CCL community.
These constants are nothing else than field gradients computed with the
spin rather than the total electronic density and not including the nuclear
contribution. Furthermore the resulting tensor must be put in the zero-trace
form. In gaussian94 it is possible to force these options by setting in the
keyword list the following items:
PROP IOP(6/17=2,6/26=4)
Here follows an input and the relevant part of the output for a STO-3G
computation of H2NO
----------------------------------------------------------------------------
#UHF/PROP IOP(6/17=2) IOP(6/26=4)

H2NO

 0 2
 X
 X 1 1.0
 N 2 1.0  1 90.0
 H 3 NH   2 90.0  1   THETA
 H 3 NH   2 90.0  1  -THETA
 O 3 NO   2 ALPHA 1  180.0

 NH=1.0179
 NO=1.2778
 THETA=58.9235
 ALPHA=110.0
-----------------------------------------------------------------------------

Fermi contact analysis (atomic units).
              1
  1  N     .042923
  2  H    -.005038
  3  H    -.005038
  4  O     .098025

 **********************************************************************

            Electrostatic Properties Using The SCF Density

 **********************************************************************


 Warning!  Using spin rather than total density!

 --- Only the electronic contributions will be computed ---


 -----------------------------------------------------
    Center         ---- Electric Field Gradient ----
                     XX            YY            ZZ
 -----------------------------------------------------
    1 Atom         .119043      -.295145      -.363285
    2 Atom         .002506       .031422       .029384
    3 Atom         .002506       .031422       .029384
    4 Atom        2.130337     -1.663300     -1.698867
 -----------------------------------------------------
-----------------------------------------------------
    Center         ---- Electric Field Gradient ----
                       ( tensor representation )
                   3XX-RR        3YY-RR        3ZZ-RR
 -----------------------------------------------------
    1 Atom         .298838      -.115349      -.183489
    2 Atom        -.018598       .010318       .008280
    3 Atom        -.018598       .010318       .008280
    4 Atom        2.540947     -1.252690     -1.288257
 -----------------------------------------------------

these are the principal values of anisotropic coupling constants

-------------------------------------------------------------------------------
Since the directions of principal moments are often significant and transforma-
tion to more conventional units can be performed once for ever, I have modified
the links 601 and 602 of gaussian to obtain the following output for the same
input

-------------------------------------------------------------------------------

 ------------------------------------------------------------------------------
                       Isotropic Fermi Contact Couplings
 ------------------------------------------------------------------------------

     Atom                 a.u.       MegaHertz       Gauss       10(-4) cm-1

   1  N(14)               .04292      13.86856       4.94865       4.62605
   2  H                  -.00504     -22.51979      -8.03562      -7.51179
   3  H                  -.00504     -22.51979      -8.03562      -7.51179
   4  O(17)               .09802     -59.42481     -21.20426     -19.82198

 ------------------------------------------------------------------------------


 **********************************************************************

            Electrostatic Properties Using The SCF Density

 **********************************************************************


 Warning!  Using spin rather than total density!

 --- Only the electronic contributions will be computed ---
       Atomic Center    1 is at   -.021142   .543231   .000000
       Atomic Center    2 is at    .158563  1.036966   .871810
       Atomic Center    3 is at    .158563  1.036966  -.871810
       Atomic Center    4 is at   -.021142  -.734569   .000000
 -----------------------------------------------------
    Center         ----  Spin Dipole Couplings  ----
                   3XX-RR        3YY-RR        3ZZ-RR
 -----------------------------------------------------
    1 Atom         .298838      -.115349      -.183489
    2 Atom        -.018598       .010318       .008280
    3 Atom        -.018598       .010318       .008280
    4 Atom        2.540947     -1.252690     -1.288257
 -----------------------------------------------------
    Center         ----  Spin Dipole Couplings  ----
                     XY            XZ            YZ
 -----------------------------------------------------
    1 Atom        -.074772       .000000       .000000
    2 Atom         .004800       .007098       .035617
    3 Atom         .004800      -.007098      -.035617
    4 Atom        -.099769       .000000       .000000


 ------------------------------------------------------------------------------
           Anisotropic Spin Dipole Couplings in Principal Axis System
 ------------------------------------------------------------------------------

     Atom            a.u.   MegaHertz   Gauss  10(-4) cm-1        Axes

            Baa     -.1835    -7.077    -2.525    -2.361   .0000   .0000
1.0000
            Baa     -.1835    -7.077    -2.525    -2.361   .0000   .0000
1.0000
   1 N(14)  Bbb     -.1284    -4.953    -1.767    -1.652   .1724   .9850
 .0000
            Bcc      .3119    12.030     4.293     4.013   .9850  -.1724
 .0000
           1/R**3   -.5394   -20.803    -7.423    -6.939

            Baa     -.0268   -14.276    -5.094    -4.762  -.2361  -.6571
 .7158
   2 H      Bbb     -.0193   -10.278    -3.667    -3.428   .9631  -.2560
 .0828
            Bcc      .0460    24.554     8.762     8.190   .1288   .7090
 .6933
           1/R**3    .0633    33.780    12.053    11.268

            Baa     -.0268   -14.276    -5.094    -4.762   .2361   .6571
 .7158
   3 H      Bbb     -.0193   -10.278    -3.667    -3.428   .9631  -.2560
-.0828
            Bcc      .0460    24.554     8.762     8.190   .1288   .7090
-.6933
           1/R**3    .0633    33.780    12.053    11.268

            Baa    -1.2883    93.221    33.264    31.095   .0000   .0000
1.0000
   4 O(17)  Bbb    -1.2553    90.837    32.413    30.300   .0263   .9997
 .0000
            Bcc     2.5436  -184.059   -65.677   -61.395   .9997  -.0263
 .0000
           1/R**3  -1.2318    89.138    31.807    29.733


 ------------------------------------------------------------------------------

-------------------------------------------------------------------------------
  Vincenzo Barone                          |
  Professor of Theoretical Chemistry       |
  Dipartimento di Chimica                  | tel. +39-81-5476503
  Universita' Federico II                  | fax  +39-81-5527771
  via Mezzocannone 4                       | e-mail ENZO@CHEMNA.DICHI.UNINA.IT
  I-80134 Napoli                           |
  Italy

 you might also want to read  some of his papers i.e.
 V. Barone and C. Adamo Theor. Chim. Acta 91 (1995) 129
     ..           ..    Chem. Phys. Letters 224 (1994) 432
     ..      J. Chem Phys 101 (1994) 10666
 or posibly
 Leif A Eriksson Internationa Journal of Quantum Chemistry vol52 879-901
(1994)

 The impresion I get -so far- is that good acuracy can be got for
anistropic constants
 with most ab-initio methods. For isortopic ones you need good basis sets
with split
 cores and DFT b3lyp seems to do particularily well.  If not using DFT meed big
 CC or CI calculations which mean V Small molecules only
 hope this all helps

 Larry Cuffe
 Chemistry Dept
 U.C.D
 Dublin


 From: gaussian.com!fox@lorentzian.com (Doug Fox)
Subject: Re: CCL:EPR g-factors
To: uunet!blue.weeg.uiowa.edu!jhjensen%lorentzian.com@uunet.uu.net (Jan H.
Jensen)
Date: Fri, 25 Sep 1998 15:56:23 -0400 (EDT)
MIME-Version: 1.0


   Dr. Jensen,

   Gaussian 98 includes anisotropic hyperfine couplings for HF, DFT etc.
Anything which can create a UHF style density.

   You can check Chem.Phys. Lett, vol 262. pp 201 (1996) and J.Chem.Phys
vol 105 pp 11060 (1996) for details on implementation and some examples.

Mime-Version: 1.0
Date: Tue, 29 Sep 1998 16:39:26 -0600
To: "Jan H. Jensen" <jhjensen@blue.weeg.uiowa.edu>
From: schrecke@t12.lanl.gov (Georg Schreckenbach)
Subject: Re: CCL:EPR g-factors

Dear Jan:
>
>        I am interested in calculating anisotropic EPR g-factors using ab
>initio electronic structure theory.  I would like to know what programs can
>calculate this property, and what kind of accuracy one can expect.
>
It seems to me that the g-tensor is currently a "hot" field, and various
groups seem to work on it. This means, on the other hand, that no approach
is well-established yet. Also, I would doubt that any standard program can
do the g-tensor yet.
   We have developed a DFT based method that seems to work reasonably well
for first-row radicals with one unpaired electron. Cf. our paper in J.
Phys. Chem. A 1997, 101, 3388; the program is currently not publicly
available. The DFT results were not too bad. One real difficulty turned out
to be the extremely strong influence of the host matrix on experimental
g-tensors.
   Another DFT g-tensor paper is J. Chem. Phys. 1997, 107, 2488. For ab
initio, cf. J. Chem. Phys. 1998, 108, 7587 and, in particular, various
papers by Lushington and Grein; they are referenced in the papers cited.

Best regards, Georg

P.S. I am very interested in your summary!

--
==============================================================
Dr. Georg Schreckenbach           Tel:     (USA)-505-667 7605
Theoretical Chemistry T-12        FAX:     (USA)-505-665 3909
M.S. B268, Los Alamos National      E-mail:  schrecke@t12.lanl.gov
Laboratory, Los Alamos, New Mexico, 87545, USA
Internet:    http://www.t12.lanl.gov/~schrecke/
==============================================================


Your best best for decent results without a facing a huge learning curve is to
use DFT level treatments implemented in conjunction with ADF (Amsterdam Density
Functional).  In terms of methodology you have two choices, as outlined in each
of the following:

AUTHOR(s):       Schreckenbach, Georg
                 Ziegler, Tom
TITLE(s):        Calculation of the G-Tensor of Electron Paramagnetic
                   Resonance Spectroscopy Using Gauge-Including Atomic
                   Orbitals and Density Functional Theory.

           In:   The journal of physical chemistry.  a,  molecule
                 MAY 01 1997 v 101 n 18
         Page:   3388

AUTHOR(s):       van Lenthe, Erik
                 Wormer, Paul E.S.
                 van der Avoird, Ad
TITLE(s):        Density functional calculations of molecular g-tensors in
                   the zero-order regular approximation for relativistic
                   effects.

           In:   The journal of chemical physics.
                 AUG 15 1997 v 107 n 7
         Page:   2488

In general one can expect to reproduce experimental trends fairly well for most
systems and get within a 20-30% error in comparing with experimental values for
deviations from the free electron g-value (with the exception of very small
deviations).  One usually does better with multi-reference CI calculations
(see: J. Chem. Phys. 106 (1997) 3292 and Int. J. Quantum Chem. 60 (1996) 467)
but these are very labor intensive.

                                   - Gerry


On Wed, 23 Sep 1998, Jan H. Jensen wrote:

>
> Hello,
>
> 	I am interested in calculating anisotropic EPR g-factors using ab
> initio electronic structure theory.  I would like to know what programs can
> calculate this property, and what kind of accuracy one can expect.
>
> 	Best regards,  Jan Jensen
>
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> Jan H. Jensen				Assistant Professor
> Department of Chemistry			jan-jensen@uiowa.edu
> University of Iowa			Phone:(319) 335-1108
> Iowa City, IA 52242			FAX:  (319) 335-1270
> http://www.uiowa.edu/~chemdept/faculty/jensen/
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>
>
>
>
> ---
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Gerry Lushington
Ohio Supercomputer Center
1224 Kinnear Rd.
Columbus OH 43212-1163
Ph. 614-292-6036
Fax 614-292-7168




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Dear all,

	I am interested in obtaining the S (overlap) matrix from MOPAC6.0 output.
Does anyone know how I can accomplish this task? I have tried several
keywords but none of them produce me the S matrix. It appears only as a
component of 1Electron matrix, but I would like to have the S elements, not
the Hcore elements.

Thanks in advance,
Marcio.


