From salzner@fen.bilkent.edu.tr  Wed Oct  1 01:27:44 1997
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Date: Wed, 1 Oct 1997 08:22:13 +0300 (EET DST)
From: Ulrike Salzner <salzner@gunser.fen.bilkent.edu.tr>
To: Georg Schreckenbach <schrecke@t12.lanl.gov>
Cc: CCL <CHEMISTRY@www.ccl.net>
Subject: Re: CCL:G:summary: solid state/band structures
In-Reply-To: <v02130504b0570beece91@[128.165.22.209]>
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Dear collegues,

I read the interesting summary on polymer programs and would like to ask 
an additional question.  

There seems to be a considerable gap between the physicists and chemists 
working in this field. Following the chemical literature little meaning 
is assigned to DFT orbital energies and, to my knowledge, there is no 
physical justification do interpret them as IPs and EAs.

However, there are all these DFT band structure codes which determine 
band gaps. The band gap problem but not the fundamental question whether 
DFT eigenenergies should be used at all has been discussed. According to 
Levy, the (band) gap problem is analogous in solids and in molecules. At 
the American Physical Society Meeting in March 1997 there was a section 
on the topic and it appeared to me that DFT orbital energies have 
physical meening although the matter is by far not settled.

I am trying to obtain band gaps by extrapolating oligomer HOMO-LUMO gaps 
using DFT and run into considerable problems with reviewers (most likely 
chemists) who usually point out that DFT can not be used for this. 

As far as I understand band structure calculations, the band gaps are  
analogous to HOMO-LUMO gaps in molecules. Do I misunderstand band 
structure calculations? Is there a fundamental difference between the 
DFT eigenenergies of molecules and of solids? Any comments would be 
greatly appreciated.

Concerning the comment on ab initio codes in Georg Schreckenbach's summary: 
there is also a Hartree-Fock solid state program in Erlangen/Germany. 
This program seems to be able to do MP2 corrections. Moreover, W. 
Foerner (also formerly in Erlangen) et al. published a paper in J. Chem. 
Phys., 1997, 106, pp. 10249 on coulped cluster theory applied to polymers. 

Sincerely,
Dr. Ulrike Salzner
e-mail: salzner@fen.bilkent.edu.tr
Tel.: (312) 2664000 ext.2122

Department of Chemistry
Bilkent University
06533 Bilkent, Ankara
Turkey


From bruehwi@solar.iac.unibe.ch  Wed Oct  1 08:27:48 1997
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From: Dominik Bruehwiler <bruehwi@solar.iac.unibe.ch>
To: chemistry <chemistry@www.ccl.net>
Subject: ICON-EDiT and BICON-CEDiT
Date: Wed, 1 Oct 1997 13:55:26 +0200
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Dear CCLers

We can offer the full versions (the WindowsNT binaries along with the
FORTRAN sources) of the following TWO program packages:

   o ICON-EDiT
   o BICON-CEDiT

     ICON-EDiT performs extended Hueckel molecular orbital and oscillator
strengths (i.e. UV/VIS spectra) calculations on molecules.

s,p,d orbitals, a two-body repulsive energy term, different
Wolfsberg-Helmholz formulas, charge iteration procedures, geometry
variation and an FMO option are included.

     BICON-CEDiT performs extended Hueckel molecular and crystal orbital
as well as oscillator strengths calculations on solids. Numerous tools
such as to generate k-point sets or to transform Cartesian into fractional
coordinates and vice versa are also supplied. The energy band and density
of states plot programs make use of Tim Pearsons pgplot graphic library
freely available at http://astro.caltech.edu/~tjp/pgplot (supported on
numerous platforms).

UNIX Makefiles and a dos2unix shell script are included for those wishing
to compile and run the programs under such operating systems.

Both program packages along with extensive manuals can be downloaded at
http://iacrs1.unibe.ch/

Enjoy the programs!

Gion Calzaferri, Martin Braendle, Ruedi Rytz and Dominik Bruehwiler
Department of Chemistry and Biochemistry, University of Bern, Switzerland.


From fyawitz@mail.netvision.net.il  Wed Oct  1 09:27:47 1997
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I downloaded molgen for DOS from ccl archives, but when I tried to 
run the install program, it just gave me a blank screen (after I 
clicked on the 'continue' button) and set up a lot of empty 
directories.  What, if anything, do you recommend?
Thank you,

E. Yawitz

From malisa@nirvana.uncor.edu  Mon Sep 29 12:27:35 1997
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Date: Mon, 29 Sep 1997 12:48:26 GMT
From: Malisa Chiappero <malisa@nirvana.uncor.edu>
Message-Id: <199709291248.MAA07744@nirvana.uncor.edu>
To: chemistry@www.ccl.net, Erdem.Buyukbingol@pharmacy.ankara.edu.tr
Subject: CCL: Re: New Computational Chemistry Lab.




Hi
 If you want to work with unix system and you have not much money, the answer to question is, I believe, use Pentium Pro with Linux , this configuration have good performance and low cost.

Best Regards

			Malisa S. Chiappero

E-mail:malisa@nirvana.uncor.edu
Dpto Fisicoquimica - Fac. Ciencias Quimicas
Universidad Nacional de Cordoba. ARGENTINA.


From ccl@www.ccl.net  Mon Sep 29 14:37:52 1997
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 Mon, 29 Sep 1997 13:02:20 CST
Date: Mon, 29 Sep 1997 13:02:31 -0600
From: tcundari@cc.memphis.edu (Tom Cundari)
Subject: computational organometallic chemistry
To: chemistry@ccl.net
Message-id: <v01530503b055a9cbd576@[141.225.145.9]>
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Fellow Comp Chemists,

        Just recently, an editor has contacted me about the feasibility of
putting together
a volume on Computational Organometallic Chemistry.  Since much of the
discussion in
computational often surrounds research with organic, biological and medicinal
applications, the idea of focusing on organometallic complexes is somewhat
intriguing
(to me anyway).

Thus, I was wondering if there would be any interest in the computational
chemistry
community in such a volume?  And if so, what topics in computational
organometallic
chemistry would be of interest?

Please feel free to respond directly to the list or to me, and I will
summarize the
responses if there is sufficient interest.

Sincerely,

Tom Cundari
Associate Professor of Chemistry

=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+
Tom Cundari                                           Department of Chemistry
Associate Professor                                The University of Memphis
e-mail:tcundari@cc.memphis.edu           Memphis, TN 38152-6060
phone: 901-678-2629
FAX: 901-678-3447
http://www.chem.memphis.edu/umchem.html

****  U of Memphis is searching for an Asst. Prof. of Computational
           Chemistry,  contact me by email for details or see these URLs
          www.chem.memphis.edu/ccad.html
          www.chem.memphis.edu/ccletter.html         ****
 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+




From gmercier@mail.med.upenn.edu  Mon Sep 29 16:27:37 1997
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From: "Gustavo A. Mercier Jr" <gmercier@mail.med.upenn.edu>
Message-Id: <199709291931.PAA22689@mail.med.upenn.edu>
Subject: Supercomputers Grants?
To: chemistry@www.ccl.net
Date: Mon, 29 Sep 1997 15:31:51 -0400 (EDT)
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Hi!

Sorry for sending this again, but the message got fragmented...

 .......................
Hi!

I have a project that is a candidate for supercomputer
level computer power. Although  I did use the Cornell Center while
a graduate student (in the early days when centers where not saturated!),
I would like info on the status of the currently active centers.

The goal is to obtain long term trajectories (ca. 5ns) using rigid body dynamic 
simulations as implemented in Moldy. The molecules of interest are the
metalloporphyrins. This is part of an ongoing project on the
structure - relaxivity relationship of these molecules that are potential
MRI contrast agents.

>From the web I can see that Cornell goes on emphasizing KSR & IBM,

Pittsburgh and San Diego move on with Crays, and NCSA...

I have the following specific questions:

1) Overall work load of the centers? It is sad that you get a job to
run in several hours but after waiting in a queue for several days.
I am interested in actual wall clock time for the turn around of jobs.

2) Any center with special interest or resources on molecular dynamics?

3) Do centers prefer that users make upgrades to their local
resources first, even if these cost several $10K, before granting
time?

4) Are there any centers with special considerations for initial
applicants (although not first time supercomputer users) with pilot projects?

Thanks in advance for your replies.


-- 
                                      ("`-/")_.-'"``-._
Gustavo A. Mercier,Jr.,MD,PhD         (. . `) -._    )-;-,_() 
Division of Nuclear Medicine          (v_,)'  _  )`-.\  ``-
Dept. of Radiology                    _;- _,-_/ / ((,'
University of Pennsylvania           ((,.-'  ((,/
3400 Spruce St.                  gmercier@mail.med.upenn.edu
Philadelphia, PA 19104         215-662-3069/3091 fax: 215-349-5843




From Steve.Bowlus@sandoz.com  Mon Sep 29 19:27:28 1997
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From: <Steve.Bowlus@sandoz.com>
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To: <CHEMISTRY@www.ccl.net>
Subject: Presentation graphics
Date: Tue, 30 Sep 1997 00:09:27 +0100



I'm looking for a converter program which will take a screen capture image (e.g.
an RGB file from the SGI snapshot utility, or a postscript file generated from
it) and generate a high quality postscript file.  By high quality, I mean with
the jaggies removed from letters and edges of smooth curves, and some color/
pattern dithering for shaded surfaces, etc.

I know I can generate high quality images from molscript and/or Raster3D.  I
wish, however, specifically to process screen images (grabbed at screen
resolution) and upgrade them to printer resolution.

I'll summarize if I am not the only person who doesn't know how to do this.

sb

===========================================================================
  Stephen B. Bowlus, Ph.D.                Computer-Aided Molecular Design
  Principal Scientist
                                          Novartis Crop Protection, Inc.
  e-mail: Steve.Bowlus@cp.novartis.com    Palo Alto Research Center
  Phone:  + 1 650 354 3904                975 California Ave.
  Fax:    + 1 650 857 1125                Palo Alto, CA 94304
===========================================================================


From chmigorn@leonis.nus.sg  Mon Sep 29 22:27:28 1997
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Dear Netters,
can someone kindly tell me how to convert Stuttgart ECP basis set format to
standard G94 format. I remember the point being mentioned before, but I did
not keep a record of that communication.
Many thanks!

Dr I.Novak, Dept.of Chemistry, NUS, Singapore 119260
chmigorn@nus.sg



From roth@organik.uni-erlangen.de  Wed Oct  1 11:27:53 1997
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From: Henryette Roth <roth@organik.uni-erlangen.de>
Message-Id: <199710011452.QAA01615@derioc1.organik.uni-erlangen.de>
Subject: Survey: Publishing in Chemistry
To: chemistry@www.ccl.net
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This messages was cross-posted


Dear colleague!

Scientific publishing is changing in a world that is dominated
by the Internet. As a part of my PhD-thesis I am studying
the influence of electronic media on publishing in chemistry.

I would be very grateful, if you would take time to fill in my
survey, which I am using to gain an understanding of current
trends dealing with scientific publishing.

On average to read and complete the form will take you 15 minutes.
Feel free to tell a colleague about this survey as well.

The survey is accessible via World Wide Web at:

	<http://www.ccc.uni-erlangen.de/clark/survey.html>

No record will be made of your identity. Your specific answers 
will not be shared with other organizations. You will not be put 
on any mailing lists or offered any products.

Thank you for your interest in this survey. Your participation 
is greatly appreciated.

All the best,

Henryette Roth




********************************************************************************
*   Henryette Roth                     *                                       *
*   Computer Chemie Centrum            *  All opinions expressed by this user  **   Inst. f. Org. Chemie I             *  are well-reasoned and insightful.    **   Universitaet Erlangen              *  Needless to say, they are not those  **   Naegelsbachstr. 25                 *  of his advisor or university.        *
*   91052 Erlangen                     *                                       *
********************************************************************************
*   roth@organik.uni-erlangen.de                                               *********************************************************************************

From rn11@phy.cam.ac.uk  Wed Oct  1 12:27:53 1997
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	(Smail3.1.28.1 #8) id m0xGR3F-0014XHC; Wed, 1 Oct 97 16:51 BST
Date: Wed, 1 Oct 1997 16:50:58 +0100 (BST)
From: Richard Needs <rn11@phy.cam.ac.uk>
To: chemistry@www.ccl.net
Subject: Gaussian-95
Message-ID: <Pine.OSF.3.96.971001164947.11901A-100000@tcm25.phy.cam.ac.uk>
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII


I am using Gaussian-95 for atomic CI calculations, with the 
eventual aim of constructing pseudopotentials.
Could somebody kindly explain the following to me:

What is the precise definition of the "valence charge density" 
given by such a CI calculation?  

Dr Richard Needs, Department of Physics, University of Cambridge,
UK, rn11@phy.cam.ac.uk


From hinsen@lmspc1.ibs.fr  Wed Oct  1 13:27:52 1997
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	Wed, 1 Oct 1997 18:46:33 +0200
Date: Wed, 1 Oct 1997 18:46:33 +0200
Message-Id: <199710011646.SAA21738@lmspc1.ibs.fr>
From: Konrad Hinsen <hinsen@ibs.ibs.fr>
To: chemistry@www.ccl.net
Subject: Update: The Molecular Modeling Toolkit, version 1.1b1


Update: The Molecular Modeling Toolkit, version 1.1b1
=====================================================

The Molecular Modelling Toolkit (MMTK) is a program library for
molecular modelling applications. Its aim is to provide researchers,
especially those working on the development of new modelling methods,
with a code basis that can be easily extended and modified to deal
with standard and non-standard problems in molecular modelling.
MMTK is free software.


The new release 1.1b1, adds new features and improvements. Some
highlights:

- More visualization options for VRML.
- More flexibility for trajectories, e.g. trajectories for subsystems.
- Trajectories in DCD format (CHARMM/Xplor) can be read.
- Molecular surface calculations.
- Improved protein handling (more flexible construction and analysis)


For details and for downloading, check the MMTK home page:

     http://starship.skyport.net/crew/hinsen/mmtk.html

-- 
-------------------------------------------------------------------------------
Konrad Hinsen                          | E-Mail: hinsen@ibs.ibs.fr
Laboratoire de Dynamique Moleculaire   | Tel.: +33-4.76.88.99.28
Institut de Biologie Structurale       | Fax:  +33-4.76.88.54.94
41, av. des Martyrs                    | Deutsch/Esperanto/English/
38027 Grenoble Cedex 1, France         | Nederlands/Francais
-------------------------------------------------------------------------------

From rkrocha@dedalus.lcc.ufmg.br  Wed Oct  1 15:27:53 1997
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          id AA39092; Wed, 1 Oct 1997 15:30:58 -0300
Organization: Universidade Federal de Minas Gerais - LCC - Brasil
Date: Wed, 1 Oct 1997 15:30:58 -0300 (BSC)
From: ramon kleber da rocha <rkrocha@dedalus.lcc.ufmg.br>
To: Computational Chemistry Mailing List <chemistry@www.ccl.net>
Subject: Parameters for sulfones, sulfoxides and allyl groups.
Message-Id: <Pine.A32.3.96.971001152815.32434A-100000@dedalus.lcc.ufmg.br>
Mime-Version: 1.0
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	Does anybody knows some references about parameters for sulfones,
sulfoxides and allyl groups for Amber forcefield. 
	Thanks in advance.

____________________________________________________________________________
Ramon Kleber da Rocha                                  VOICE +55-31-499-5765
e-mail rkrocha@dedalus.lcc.ufmg.br                     FAX   +55-31-499-5700

Laboratorio de Espectroscopia e Modelagem Molecular 
Nucleo de Estudos em Quimica Medicinal - NEQUIM
Departamento de Quimica - Instituto de Ciencias Exatas
Universidade Federal de Minas Gerais
Av. Presidente Antonio Carlos, 6627 Campus Pampulha
CEP 31-270-901 - Belo Horizonte - Minas Gerais - Brasil
____________________________________________________________________________



From campagne@incm.u-nancy.fr  Wed Oct  1 16:27:54 1997
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Date: Wed, 01 Oct 1997 22:14:04 +0100
From: Fabien Campagne <campagne@incm.u-nancy.fr>
Organization: Lab. Chimie theorique Nancy
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 Dear all,

Those of you interested in Computational Chemistry Software (CCS)
development, possibly followed the OO discussion that occurred
on CCL last summer.
Advantages of object-oriented programming methods, compared to
traditional fortran programming style were discussed. At some point
of the discussion, I proposed to create and maintain a resource that
would help people interested in CCS development, find information
about methods useful to achieve maximum software reuse. i.e. how
could you design and propose interfaces to your code so that others
won't need to spend weeks understanding all the details, before they
can use it (safely!). More details are available from the original post.

This resource is now available and provides:

 - a discussion area focused on the design of reusable CCS
    components (computational chemistry algorithms, tools),
 - background information and pointers about useful design and
    programming techniques (including mixed programming portable
    solutions),
 - a repository of well designed Object Oriented public interfaces
    to common CCS algorithm/method implementations,
 - proposals for APIs (Application programming Interface) around
    aspects of CCS that are common to many implementations: molecular
    information storage, optimization algorithms.

and more. The resource is freely available through the WWW in the hope
it will help promote design and reuse ideas around the CCS development
community.

http://www.lctn.u-nancy.fr/design/

Feel free to contribute.

--

Fabien Campagne -- campagne@incm.u-nancy.fr | Lab. de Chimie Theorique
phone: +33 (0)3 83 91 20 00  extension 3236 | Nancy, France.
           http://www.lctn.u-nancy.fr/viseur/FC.html




From seabra@NPD.UFPE.BR  Wed Oct  1 18:27:54 1997
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 1 Oct 1997 19:24:37 GMT-3
Date: Wed, 01 Oct 1997 19:34:22 -0300
From: Gustavo de Miranda Seabra <seabra@NPD.UFPE.BR>
Subject: Ab-Initio potentials
To: Computational Chemistry Letters <chemistry@www.ccl.net>
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Dear All,

    I would appreciate very much if someone could indicate me any
references about
using ab-inito calculations to parametrize interatomic pair potentials.
Thanks in advance.

--

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

                            Gustavo de Miranda Seabra
MSc Student in Chemistry                     E-Mail: seabra@npd.ufpe.br
Universidade Federal de Pernambuco - Recife - Pernambuco - Brazil
-----------------------------------------------------------------------------------




