From Bernd.Hartke@RUS.Uni-Stuttgart.DE  Wed Feb  8 03:37:48 1995
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Subject: CCL: looking for distance geometry program
To: chemistry@ccl.net
Date: Wed, 8 Feb 1995 08:58:24 +0100 (MEZ)
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Dear netters,
   I am interested in Distance Geometry. I have read the abstract
of the QCPE program DGEOM by Blaney, Crippen, Dearing and Dixon.
For my purposes, this program is too heavily geared towards
biochemical applications by its requirement of PDB input etc.,
plus it comes only in VAX BACKUP tape format. Are there any
alternatives out there? What I am looking for is a simple
implementation of the metric matrix method followed by some method
for triangle inequality bounds smoothing, metrization, or refinement;
without any fancy I/O options (input of just the distance bounds
would be fine); preferably in Fortran and under unix; and
obtainable via ftp. Am I asking for too much, or does someone
know of a program meeting most of these criteria?
   Thank you for your help!
      Bernd

-- 
Dr. Bernd Hartke                  e-mail: bernd.hartke@rus.uni-stuttgart.de
Dep. of Theoretical Chemistry
University of Stuttgart           
Pfaffenwaldring 55                Phone: +49-711-685-4409
70569 Stuttgart                   FAX:   +49-711-685-4442
GERMANY

From praa2@cluster1.urz.uni-halle.de  Wed Feb  8 05:37:55 1995
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Subject: CCL: Summary NBO for DFT available ?
To: chemistry@ccl.net
Date: Wed, 8 Feb 1995 11:20:37 +0100 (MEZ)
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Dear Netters,

A couple of days before I submitted the following question to CCL, but up to now
only two responses dealing with the question were received.

So, I submit my inquiry once again, desperately hoping of any additional answers.
Beside the NBO-tool I'm mainly interested in other analysing tools.


Now the original question:

Subject :  CCL:NBO for DFT available ?


>Dear netters,
>
>i was wondering if there is a customized interface of the NBO-tool
>(natural bond orbital analysis by Reed/Weinhold) for using in connection
>with 'native' DFT-codes (like DeFT, deMon, DGauss, ...) as available
>for common ab-initio/semiempirical codes (GaussianXX, GAMESS, Mopac ...).
>
>I've realized that within G92/DFT this tool is available also for dft
>calculations. Unfortunately I need this tool in connection with one of the 
>above mentioned 'native' dft codes.
>
>Though the ks-orbitals do not have the same physical meaning as the canonical
>hf-orbitals, is such a tool reliable for the description e.g. the metal-ligand
>interaction ?
>
>Are there other tools (maybe density difference maps, fragment orbital analysis, ...)
>for a qualitative and/or quantitative analysis of such interactions ?
>
>Any suggestions or hints are grateful appreciated.
>
>Many thankx in advance
>
>	Peter


The answers I got are appended:

----------------------------------------------------------------------------------------
Message-Id: <9502011724.AA17581@nylon.es.dupont.com>
Peter,

    I'm interested in the same question.  If you do not post the
substantive responses to the CCL could you please mail me a copy?

Thanks,
Paul Soper
soperpd@esvax.dnet.dupont.com

-----------------------------------------------------------------
Paul Soper                        All the usual disclaimers apply
DuPont Central Research             soperpd@esvax.dnet.dupont.com  
P.O. Box 80328                                 Tel (302)-695-1757  
Wilmington, DE 19880-0328                      FAX (302)-695-8412  
-----------------------------------------------------------------

-----------------------------------------------------------------------------------------
From: sgustaf@rhea.cray.com (Susan M. Gustafson)

Peter,

I am the main support person for UniChem (DGauss) here at Cray.
Sorry to say that at this time DGauss does not have NBO analysis.
We have considered putting it in, but have not done so to date.

Best regards,
Susan

--------------------------------------------------------
Susan M. Gustafson, Ph.D.	Phone: (612) 683-3662
Cray Research, Inc.		e-mail: sgustaf@cray.com
--------------------------------------------------------

------------------------------------------------------------------------------------------
From: Eric Patterson <PATTERSON@chem.wisc.edu>

Peter,
	The NBO source code is available from the Quantum Chemistry Program
Exchange (QCPE) at Indiana University.  From the code, you can build a
program-specific NBO routine (i.e. for Gaussian), or you can build a
stand-alone version (GENNBO).  It is also usually possible to attach the NBO
routine to your own, non-supported ESS program with a little bit of work.  All
of this is explained in the manual that should come with the code.
	Contact QCPE by telneting to qcpe6.chem.indiana.edu (log in as
anonymous).
	Hope this helps.

Eric Patterson
University of Wisconsin-Madison

-----------------------------------------------------------------------------------------
From: kaupp@vsibm1.mpi-stuttgart.mpg.de (Martin Kaupp)

Hallo,

habe leider keine Antwort (ich verwende falls noetig eben auch
die NBO Analyse in G92/DFT), aber waere sehr interessiert zu
erfahren, was sich bei der Anfrage ergibt.

Viele Gruesse, Martin Kaupp


----------------------------------------------------------------------
|          Dr. Martin Kaupp                                          |
|          Max-Planck-Institut fuer Festkoerperforschung             |
|          Heisenbergstrasse 1                                       |
|          D-70569 Stuttgart                                         |
|          Germany                                                   |
|                                                                    |
|          Tel.: country-code+711/689-1532                           |
|          Fax.: country-code+711/689-1562                           |
|          email: kaupp@vsibm1.mpi-stuttgart.mpg.de                  |
|                                                                    |
|          and                                                       |
|                                                                    |
|          Institut fuer Theoretische Chemie                         |
|          Universitaet Stuttgart                                    |
|          Pfaffenwaldring 55                                        |
|          D-70569 Stuttgart                                         |
|          Germany                                                   |
|                                                                    |
|          Tel.: country-code+711/685-4399                           |
|          Fax.: country-code+711/685-4442                           |
|                                                                    |
----------------------------------------------------------------------

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


Many thankx in advance

	Peter

From gl@coil.mdy.univie.ac.at  Wed Feb  8 07:37:59 1995
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From: "Gerald Loeffler" <gl@coil.mdy.univie.ac.at>
Message-Id: <9502081314.ZM23845@coil.mdy.univie.ac.at>
Date: Wed, 8 Feb 1995 13:14:20 +0100
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To: CHEMISTRY@ccl.net
Subject: Books on Mix of DFT with MD, again
Content-Type: text/plain; charset=us-ascii
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Hi again,

unfortunately I got 0 (in words: zero) answers to my question on books that
cover the mix of "classical" Molecular Dynamis with Density Functional
Calculations.

Here is my original mail again - and please: Enlighten my this time!

Dear Net-chemists,

after doing "classical" Molecular Dynamics of solvated proteins I'm thinking
about treating small parts of my proteins with Density Functional Calculations,
while retaining the old MD force field for the rest of the system.

Since my background is mostly in classical MD, I'm in desparate need of GOOD
literature!

So if you have any must-reads in mind, please share your knowledge with me! I'm
thinking of books, but very thorough reviews would certainly be welcome, too!

        Thanx in advance,
        Gerald

--
Gerald Loeffler
PhD student in Theoretical Biochemistry

Email: gl@mdy.univie.ac.at
Phone: +43 1 40480 612
Fax:   +43 1 4028525
Mail:  University of Vienna
       Institute for Theoretical Chemistry
       Theoretical Biochemistry Group
       Waehringerstrasse 17/Parterre
       A-1090 Wien, Austria

#include "fancy_ASCII_picture"
#include "funny_statement"
#include "standard_disclaimer"



From herbert.homeier@rchs1.chemie.uni-regensburg.de  Wed Feb  8 08:37:59 1995
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Date: Wed, 8 Feb 95 14:03:28 +0100
From: Herbert Homeier (t4720) <Herbert.Homeier@chemie.uni-regensburg.de>
Message-Id: <9502081303.AA10506@rchs1.chemie.uni-regensburg.de>
To: CHEMISTRY@ccl.net
Subject: Re: CCL:Propose: A Hypermail conversion of the CCL



Dear CCLers,

Steven Bachrach and Soaring Bear pointed out that the 
following URL does not work. 

> There is now a hypermail entry point to the Automated Archive of Mailing Lists
> (that presently mirrors new CCL messages). It works, maybe it could be improved.
> See:
> 
> http://rchs1.chemie.uni-regensburg.de/gopher/.maillist/
> 

The correct URL is

http://rchs1.chemie.uni-regensburg.de/gopher/pub/.maillist/

I am sorry for any inconvenience caused by the error.

Best regards

Herbert Homeier
--------------------------------------------------------------
Dr. Herbert H. H. Homeier
Institut fuer Physikalische und Theoretische Chemie
Universitaet Regensburg
D-93040 Regensburg, Germany
Phone: +49-941-943 4720                FAX  : +49-941-943 2305
email: na.hhomeier@na-net.ornl.gov
<A HREF="http://rchs1.uni-regensburg.de/%7Ec5008/">HOMEPAGE</A>
---------------------------------------------------------------


From moshe_o@VNET.IBM.COM  Wed Feb  8 09:37:55 1995
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	by www.ccl.net (8.6.9/930601.1506) id JAA03941; Wed, 8 Feb 1995 09:35:33 -0500
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   Wed, 08 Feb 95 09:35:10 EST
Date: Wed, 8 Feb 95 16:33:37 IST
From: "Moshe Olshansky" <moshe_o@VNET.IBM.COM>
To: chemistry@ccl.net
Subject: Moderately large example


A follow-up to my earlier request for 300 to 500 basis functions
Hartree-Fock (SCF) example - is there any data base where one can find
such examples (i.e. some list of molecules with their geometries and
"recommended" basis sets)?

Moshe Olshansky
moshe_o@vnet.ibm.com

From moshe_o@VNET.IBM.COM  Wed Feb  8 09:40:06 1995
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Date: Wed, 8 Feb 95 15:48:33 IST
From: "Moshe Olshansky" <moshe_o@VNET.IBM.COM>
To: chemistry@ccl.net
Subject: Moderately large SCF example


Dear netters!
We are looking for Hartree-Fock example containing 300 to 500 basis
functions  (we need GAMESS-like input for such an example).
We would like as many examples as possible,  since we need them to test
certain technique.
Please send such examples to moshe_o@vnet.ibm.com

Thank you in advance
Moshe Olshansky
IBM Israel Science & Technology

From palres.dnet.sandoz.com!bowlus@sandoz.com  Wed Feb  8 10:37:56 1995
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Date: Wed, 8 Feb 95 10:27:48 -0500
From: bowlus@palres.dnet.sandoz.com (Steve Bowlus)
To: "chemistry@ccl.net"@SNDZEH.dnet.sandoz.com
Cc: BOWLUS@sandoz.com
Subject: MGMS International Meeting


Can someone provide me with a pointer to the organizer for the Molecular 
Graphics and Modeling Society's conference, which is to be held in 
Australia in July or August, 1995?

Thanks in advance,
S. Bowlus 	bowlus@sandoz.com


From ADAMO@CHEMNA.DICHI.UNINA.IT  Wed Feb  8 10:39:23 1995
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	by www.ccl.net (8.6.9/930601.1506) id JAA04050; Wed, 8 Feb 1995 09:40:21 -0500
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 (PMDF V4.3-10 #3559) id <01HMT8OKZEXS000081@CHEMNA.DICHI.UNINA.IT>; Wed,
 08 Feb 1995 15:40:58 +0100 (CET)
Date: Wed, 08 Feb 1995 15:40:57 +0100 (CET)
Subject: Hybrid DFT approach
To: chemistry@ccl.net
Message-id: <01HMT8OL23DU000081@CHEMNA.DICHI.UNINA.IT>
X-VMS-To: IN%"chemistry@ccl.net"
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Dear net-ters,
   I shold like to add something to the hybrid DFT approaches (B3LYP and so on)
and to have your advice.
The first point is (about the discussion between Johnson and Gaussian 
Inc.) that that the following references could be added to the B3LYP 
bibliografy:


[1] V. Barone, C. Adamo, "Theoretical study of direct and water assisted
isomerization of formaldehyde radical cation.  A comparison between 
density functional and post Hartree-Fock approaches" Chem. Phys. Lett.
224 (1994) 432, erratum ibid. 228 (1994) 499

[2]V. Barone " Inclusion of Hartee-Fock exchange in the density functional
approach. Benchmark computations for diatomic molecules containing H, B, 
C, N, O and F atoms, Chem. Phys. Lett. 226 (1994) 392.

[3] V. Barone " Inclusion of Hartree-Fock exchange in density functional 
methods.  Hyperfine structure of second row atoms and hydrides", J. Chem. Phys.
101 (194) 6834.

[4]V. Barone " Characterization of the potential energy surface of the HO2
molecular system by a density functional approach", J. Chem. Phys. 101 (1994) 
10666.

[5]V. Barone, C. Adamo "Proton transfer in model hydrogen-bonded systems by 
a density functional approach" Chem. Phys. Lett. 231 (1994) 295.

[6]F. Lelj, C. Adamo V. Barone " Role of the Hartree-Fock exchange in
density functional theory.  Some aspects of the conformational potential
energy surface of glycine in the gas-phase" Chem. Phys. Lett. 230 (1994) 189.

[7]V. Barone, L. Orlandini e C. Adamo, "Density functional study of
diborane, dialane and digalane", J. Phys. Chem. 98 (1994) 13185.

[8]V. Barone, C.Adamo, F. Lelj "Conformational behaviour of gaseous glycine
by a density functional approach", J. Chem. Phys. 101 (1995) 366.

[9]C. Adamo V. Barone, F. Fortunelli " Validation of self-consistent hybrid
density functionals for the study of structural and electronic characteristic 
of organic pi-radicals, J. Chem. Phys. 102 (1995) 384.

Please note that at least paper n. 2 is a systematic study.

The second point is on the nature of the hybrid approaches.  
Since there are in the B3LYP method 3 parameters fitted on experimental 
values, should B3LYP be considered a semiempirical method?  

 Ciao Carlo




-------------------------------------------------------------------------------
  Carlo Adamo                      | tel. +39-81-5476504
  Dipartimento di Chimica          | fax  +39-81-5527771
  via Mezzocannone 4               | e-mail ADAMO@CHEMNA.DICHI.UNINA.IT
  I-80134 Napoli                   |
  Italy                            |
________________________________________________________________________________







From jkl@ccl.net  Wed Feb  8 11:38:13 1995
Received:  for jkl@ccl.net
	by www.ccl.net (8.6.9/930601.1506) id LAA06486; Wed, 8 Feb 1995 11:34:56 -0500
Date: Wed, 8 Feb 1995 11:34:56 -0500
From: Jan Labanowski <jkl@ccl.net>
Message-Id: <199502081634.LAA06486@www.ccl.net>
To: bowlus@palres.dnet.sandoz.com
Subject: Re: CCL:MGMS International Meeting
In-Reply-To: Mail from 'bowlus@palres.dnet.sandoz.com (Steve Bowlus)'
      dated: Wed, 8 Feb 95 10:27:48 -0500
Cc: chemistry@ccl.net, jkl@ccl.net


> Can someone provide me with a pointer to the organizer for the Molecular 
> Graphics and Modeling Society's conference, which is to be held in 
> Australia in July or August, 1995?

Did you ever check the conferences file available in CCL archives?

It can be accessed via ftp (www.ccl.net in /pub/chemistry/info),
via gopher:
gopher gopher.ccl.net 73
  info
    conferences

WWW: http://www.ccl.net/chemistry.html
       Computational Chemistry Archive
          Information
             Conferences

or via e-mail by sending a message:
    select chemistry
    size 60kb
    limit 300kb
    cd info
    ls
    get conferences
    quit
to MAILSERV@ccl.net

-- 
Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc.
Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163
ph:(614)-292-9279,  FAX:(614)-292-7168,  E-mail: jkl@ccl.net  JKL@OHSTPY.BITNET


From mmadrid@gardel.psc.edu  Wed Feb  8 12:44:42 1995
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From: "Marcela Madrid" <mmadrid@gardel.psc.edu>
Message-Id: <9502081140.ZM12534@gardel.psc.edu>
Date: Wed, 8 Feb 1995 11:40:23 -0500
X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail)
To: chemistry@ccl.net
Subject: CCL: Nucleic Acid and Protein Sequence workshop
Content-Type: text/plain; charset=us-ascii
Mime-Version: 1.0



                   NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS
                       WORKSHOP FOR BIOMEDICAL RESEARCHERS
                              Pittsburgh, Pennsylvania
				June 4-9, 1995



Pittsburgh Supercomputing Center (PSC) is again offering a five-day workshop on
"Nucleic Acid and Protein Sequence Analysis," June 4-9, 1995.  It is
funded by a grant from the National Center for Human Genome Research of
the National Institutes of Health.

The workshop will familiarize biomedical researchers with computational
methods and provide practice in applying supercomputing resources to
problems of concern in macromolecular sequence analysis.  Emphasis will be
on alignment of and pattern extraction from multiple sequences.
Participants will gain practical experience on PSC's Cray C-90 and T3D in
(1) comparing and aligning sequences, (2) identifying informative patterns
in a set of sequences; and (3) using extracted informative patterns to
identify related sequences.  Researchers will also learn several approaches
to database searching and  multiple sequence alignment, how to use profile
analysis effectively, and how to identify patterns in their sequences.
Participants are encouraged to bring sequence analysis problems from their
current research.  Extensive documentation will be given at the outset on
the PSC computing environment as well as on the specific programs
to be employed in the workshop.  No prior supercomputing experience is
required.

Workshop leaders are Dr. Gary Churchill, Cornell University, Dr. Michael
Gribskov, San Diego Supercomputing Center, and Dr. Hugh Nicholas, PSC.

A limited number of grants to cover travel and hotel accommodations are
available for U.S. academic participants.  ALL PARTICIPANTS ARE REQUIRED
TO PAY A $135 REGISTRATION FEE, IN ADVANCE, UPON ACCEPTANCE INTO THE WORKSHOP.
The deadline for submitting applications is April 17, 1995.  Enrollment is
limited to 20 participants.

Additional information about this workshop can be found in
http://pscinfo.psc.edu/biomed/workshops95.html



				      * * * * *




			  PITTSBURGH SUPERCOMPUTING CENTER
                     NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS
                        WORKSHOP FOR BIOMEDICAL RESEARCHERS
                                June 4-9, 1995


		                   APPLICATION


Name:	       ________________________________________________________________

Affiliation:   ________________________________________________________________

Address:       ________________________________________________________________
	       (Business)
	       ________________________________________________________________

	       ________________________________________________________________
	       (Home)
	       ________________________________________________________________

Telephone:  ____________________________         ______________________________
	           (Business)				     (Home)

*Social Security Number:  _______-_____-_______	Citizenship:___________________

Electronic Mail Address:_______________________________________________________

Status: ___Graduate  ___Post-doctoral Fellow  ___Faculty  ___Other (specify)

In order to attend the workshop, will you need funds for travel?___ lodging?___

Please indicate specifically any special housing, transportation or dietary
arrangements you will need: __________________________________________

How did you learn about this workshop:_________________________________________

REQUIREMENTS:

Applicants must submit a completed application form and a cover letter.  The
letter should describe, in one or two paragraphs, the sequence analysis
problems encountered in your research, and how participating in the workshop
will enhance this research.  Please include a brief statement describing your
level of experience with computers.  Faculty members, staff and post-docs
should provide a curriculum vita.  Graduate students must have a letter
of recommendation from a faculty member. If you have requested travel funds,
please include the cost of roundtrip air fare from your home to Pittsburgh and
indicate the amount of travel funds you will need. ALL PARTICIPANTS WILL BE
REQUIRED TO PAY A $135 ADVANCE REGISTRATION FEE UPON ACCEPTANCE INTO THE
WORKSHOP.

Please return all application materials by APRIL 17, 1995 to:

  Biomedical Workshop Applications Committee
  Pittsburgh Supercomputing Center
  4400 Fifth Avenue, Suite 230C
  Pittsburgh, PA 15213

Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960.

*Disclosure of Social Security Number is voluntary.

PSC does not discriminate on the basis of race, color, religion, sex, age,
creed, national or ethnic origin, or handicap.






From bonvoisi@cemes.cemes.fr  Wed Feb  8 13:38:59 1995
Received: from cix.cict.fr  for bonvoisi@cemes.cemes.fr
	by www.ccl.net (8.6.9/930601.1506) id NAA09014; Wed, 8 Feb 1995 13:14:03 -0500
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Received: by cemes.cemes.fr; Wed, 8 Feb 95 19:13:54 EST
From: bonvoisi@cemes.cemes.fr (Bonvoisin Jacques)
Message-Id: <9502081813.AA07117@cemes.cemes.fr>
Subject: POVRAY file ?
To: chemistry@ccl.net (CCL Computational Chemistry)
Date: Wed, 8 Feb 95 19:13:53 EST
X-Mailer: ELM [version 2.3 PL11]


Dear Netters,
Does anyone have a tool to translate a MOPAC, XYZ, ALCHEMY ...file
into a POVRAY type file.
Thank you for the answer.
Sincerely.
-- 
+----------------------------------------------------------------+
|     Jacques  BONVOISIN                                         |
|       CNRS/CEMES-LOE           Tel  :  +33 62 25 78 52         |
|     29 , rue Jeanne Marvig     Fax  :  +33 62 25 79 99         |
|     F-31055 Toulouse Cedex     Email: bonvoisi@cemes.fr        |
+----------------------------------------------------------------+

From steckler@sdsc.edu  Wed Feb  8 13:41:50 1995
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Date: Wed, 8 Feb 1995 10:34:09 -0800
To: chemistry@ccl.net
From: steckler@sdsc.edu (Rozeanne Steckler)
Subject: West Coast Theoretical Chemistry Conference
Cc: steckler@sdsc.edu


The 1995 West Coast Theoretical Chemistry conference will be held on March
29 - March 31, 1995 in San Diego, CA.  The 3-day conference will feature
invited talks, short lectures, and poster sessions.  As usual, postdoctoral
associates and graduate students are encouraged to give talks and posters.
The invited speakers are Dr. David Gange, American Cyanamid, Dr. K.C.
Nicolaou, The Scripps Research Clinic, and Prof. M. Bowers, UC Santa
Barbara.  For more information on the conference or to receive registration
materials contact Holly Boyce at boyce@sdsc.edu



From LIBRANDO%ICTUNIV.BITNET@phem3.acs.ohio-state.edu  Wed Feb  8 14:38:32 1995
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Date: Wed, 08 Feb 1995 19:19:45 +0039
From: "Prof. Vito Librando" <LIBRANDO%ICTUNIV.BITNET@phem3.acs.ohio-state.edu>
Subject: Duplicate messages
To: CCL Administrator <chemistry@ccl.net>
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Frequently I receive duplicate or triplicate messages.
It is possible to reduce or elimitate this occurence?                        Si
cerely Yours.                                                              Prof
 Vito Librando

SINCERELY YOURS.
PROF. VITO LIBRANDO

------CHEMISTRY DEPARTMENT OF CATANIA UNIVERSITY-----------------
------V.LE A.DORIA, 6 - 95126 CATANIA - ITALY

------LIBRANDO@ICTUNIV.UNICT.IT
-- TEL. +39 95 330424
__ FAX: +39 95 330424
-------------------------------------------------------------------

From 6031SCHRADER@VMS.CSD.MU.EDU  Wed Feb  8 14:40:06 1995
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	by www.ccl.net (8.6.9/930601.1506) id OAA10908; Wed, 8 Feb 1995 14:32:48 -0500
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 id <01HMT45TE7GG91WTF0@VMS.CSD.MU.EDU>; Wed, 08 Feb 1995 13:31:50 -0600 (CST)
Date: Wed, 08 Feb 1995 13:31:50 -0600 (CST)
From: "David M. Schrader" <6031SCHRADER@VMS.CSD.MU.EDU>
Subject: Correlation energy of 3-electron systems
To: chemistry@ccl.net
Message-id: <01HMT45TEQR691WTF0@VMS.CSD.MU.EDU>
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I need to know the electronic correlation energy of the following
three-electron systems:  LiH+, He2+, and H3.  Can you direct me to RHF
calculations and accurate ab initio?

Thanks.

Dave Schrader

===============================================================================
                              David M. Schrader
                           Professor of Chemistry
Department of Chemistry		      |  Telephone numbers:
Marquette University                  |		(414) 288-3332 (office)
Milwaukee, WI 53233                   |		(414) 288-7066 (FAX)
USA                                   |         (414) 288-3515 (secretary)
                    Internet: 6031schrader@vms.csd.mu.edu
===============================================================================

From lwalsh@aries.scs.uiuc.edu  Wed Feb  8 15:38:05 1995
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Date: Wed, 8 Feb 1995 14:01:53 -0600 (CST)
From: Laura Walsh <lwalsh@aries.scs.uiuc.edu>
Subject: Extended Huckel Calculations
To: Computational Chemistry List Server <chemistry@ccl.net>
Message-Id: <Pine.3.89.9502081451.A18812-0100000@aries.scs.uiuc.edu>
Mime-Version: 1.0
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What programs are there for an SGI which would do Extended Huckel MO 
calculations?

Thanks.
Laura

Laura Lynn Walsh, School of Chemical Sciences Computer Center, 
Box 66-1, 152 Noyes Lab, 505 South Mathews Ave., 
University of Illinois, Urbana, IL  61801-3364
lwalsh@aries.scs.uiuc.edu                       (217) 244-0560



From michael@bch48.bch.ncsu.edu  Wed Feb  8 16:38:27 1995
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From: "Michael R Rothwell" <michael@bch48.bch.ncsu.edu>
Message-Id: <9502081541.ZM16264@bch48.bch.ncsu.edu>
Date: Wed, 8 Feb 1995 15:41:28 -0500
In-Reply-To: bonvoisi@cemes.cemes.fr (Bonvoisin Jacques)
        "CCL:POVRAY file ?" (Feb  8,  7:13pm)
References: <9502081813.AA07117@cemes.cemes.fr>
X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail)
To: bonvoisi@cemes.cemes.fr (Bonvoisin Jacques),
        chemistry@ccl.net (CCL Computational Chemistry)
Subject: Re: CCL:POVRAY file ?
Content-Type: text/plain; charset=us-ascii
Mime-Version: 1.0


I would also be interested in a PDB (or other format) - to - POVRAY converter.
POVRAY is a cheap (free) fast raytracer available on almost any platform. It
uses ASCII scripts as source files. It seems like a tool just waiting to be
used for scientific visualization.




From toukie@zui.unizh.ch Wed Feb  8 08:30:36 1995
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Message-Id: <9502081330.AA18177@rzurs10.unizh.ch>
Subject: Info needed re molec. dimensl. parameters
To: chemistry@ccl.net
Date: Wed, 8 Feb 1995 14:30:23 +0100 (MET)
Status: R



Dear Colleagues;

     I am interested in learning about the molecular dimensional parameters
known as "solvent accessible surface", "solvent inaccessible volume", "hard
volume", and "packing".  If anyone can recommend review or articles in which
these molecular dimensional parameters are clearly defined and discussed, I
would be grateful if you could share your information with me.  I am also in-
terested in learning the difference between van der Waals surfaces and solvent
accessible surfaces [e.g., Int. J. Quant. Chem. 44: 203-218 (1992].

     In some molecular dimensional calculations I have seen, use is made of a
"probe radius".  Exactly what does the "probe radius" refer to, and how does one
go about selecting a value for the probe radius?

     Finally, for some calculations I would like to perform, I need to know the
van der Waals radii of atoms in different types of molecules.  For instance, I
am given to understand that the van der Waals radius of carbon in benzene is
1.9924 A, whereas the van der Waals radius of hydrogen in benzene is 1.3582 A.
Can anyone recommend a published source containing a table of van der Waals
radii for atoms in different types of molecules?

     Thanks in advance to all responders.


Sincerely,

(Dr.) S. Shapiro
Institut fuer orale Mikrobiologie und allgemeine Immunologie
Zentrum fuer Zahn-, Mund-, und Kieferheilkunde der Universitaet Zuerich
Plattenstrasse 11
Postfach
CH-8028 Zuerich 7, Switzerland

Internet: toukie@zui.unizh.ch
FAX-nr: ( ... + 1) 261'56'83


From aiba@ir.phys.chem.ethz.ch Wed Feb  8 09:34:22 1995
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	by www.ccl.net (8.6.9/930601.1506) id JAA03935; Wed, 8 Feb 1995 09:34:17 -0500
Date: Wed, 8 Feb 1995 15:23:27 +0200
Message-Id: <95020815232682@ir.phys.chem.ethz.ch>
From: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich)
To: chemistry@ccl.net
Subject: ???: ftp-able 2e-electron code
X-VMS-To: SMTP%"chemistry@ccl.net"
X-VMS-Cc: AIBA
Status: R



Dear Netters,

can anyone advice me 
whether there are ftp-able
programmes, in FORTRAN,
which evaluate 2e-4center-integrals
provided the geometry is given ?

[or even commercial programmes]

The need is to manipulate these
integrals in a code which takes them
as input. So, there must be a possibility
to control evaluation and the form of the output.
The form in which g92 outputs the integrals
is, very unfortunately, not suitable for
our purposes.

Ideally, I look for a program
which could be taken as a subroutine
and told what particular 2e-4center-integral
to evaluate (not all at each run!).

Thanks for your responses.
It will be my pleasure to put them 
together and post in the net
afterwards.

Ayaz Bakasov.


From polowin@hyper.hyper.com  Wed Feb  8 17:38:04 1995
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Date: Wed, 8 Feb 95 17:30:56 -0500
From: polowin@hyper.hyper.com (Joel Polowin)
Message-Id: <9502082230.AA21267@hyper.hyper.com.hyper.com>
To: chemistry@ccl.net
Subject: Re: CCL:Extended Huckel Calculations


> Date: Wed, 8 Feb 1995 14:01:53 -0600 (CST)
> From: Laura Walsh <lwalsh@aries.scs.uiuc.edu>
> Subject: CCL:Extended Huckel Calculations
> 
> What programs are there for an SGI which would do Extended Huckel MO 
> calculations?

HyperChem has a semi-empirical module that runs on an SGI; it will
perform EHMO calculations (among others) and returns its results to
a networked PC front-end.

Regards,
Joel

------------
Joel Polowin, Ph.D.   Manager, Scientific Support
Email to: polowin@hyper.com 

Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
Info requests to: info@hyper.com    Support questions to: support@hyper.com
Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com


From pat@mercury.aichem.arizona.edu  Wed Feb  8 18:37:59 1995
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Date: Wed, 8 Feb 1995 16:25:25 -0700 (MST)
From: Pat Walters <pat@mercury.aichem.arizona.edu>
Subject: Re: CCL:POVRAY file ?
To: CCL Computational Chemistry <chemistry@ccl.net>
In-Reply-To: <9502081541.ZM16264@bch48.bch.ncsu.edu>
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Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII


On Wed, 8 Feb 1995, Michael R Rothwell wrote:

> I would also be interested in a PDB (or other format) - to - POVRAY converter.
> POVRAY is a cheap (free) fast raytracer available on almost any platform. It
> uses ASCII scripts as source files. It seems like a tool just waiting to be
> used for scientific visualization.

If someone sends me a the specifications and a few sample files I'd be glad
to add the POVRAY file format to Babel.  Then people could go from just
about anything to POVRAY.

Pat

_________________________________________________________________________
W. Patrick Walters                 pat@mercury.aichem.arizona.edu
Graduate Student       http://mercury.aichem.arizona.edu/pat.html
Laboratory for Artificial Intelligence in Chemistry    *
Dept of Chemistry                                    * * *  
University of Arizona, Tucson  AZ 85721              * * * 
Voice : 602-621-6334   FAX :  602-621-8407            ***
"At least it's a dry heat"                             * 
_______________________________________________________*__________________


From mf10119@sc.msc.edu  Wed Feb  8 18:54:22 1995
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From: <mf10119@sc.msc.edu>
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Date: Wed, 8 Feb 95 17:00:57 -0600
Message-Id: <9502082300.AA335600@sc.msc.edu>
To: chemistry@ccl.net
Subject: Non-Linear-Optics_and_MOPAC93


Hi netters.

   One year ago (more or less) I posted a question about a strange behaviour
in MOPAC 93 when it is requested to calculate frequency-dependent NLO proper-
ties. This code use the TDHF equations and it is the same method implemented in
HONDO package (Karna S.P., Dupuis M., J. Comp. Chem, vol.12,p.487,(1991)).

The method is able to calculate the frequency-dependent values up to the first
pole (i.e. the homo-lumo gap). If I'm investigating a Second Harmonic
Generation effect, it means that the fundamental perturbating frequency can't
go beyond half the gap; if I'm investigating a Third Harmonic Generation
effect, it can't go beyond 1/3 gap.
An example of such a calculation is shown in  Karna S.P., Prasad P.N, Dupuis
M,  J. Chem. Phys. 94  1171  (1991). Calculations were carried out with the
ab-initio code HONDO.

I've tried to run MOPAC93 with the same molecule (p-nitroaniline) and I still
got strange results. Strange means out-of-format numbers... 
The calculated homo-lumo gap is between 8.2 and 8.4 eV (it depends on the
semiempirical methods, AM1, MNDO or PM3), but i get a "resonance" at 1.7 eV
of fundamental frequency for a SHG effect and at 1.2 eV for a THG effect.
Karna, Prasad & Dupuis have been able to calculate with TDHF equations SHG
>from 0 to 1.786 eV and THG from 0 to 1.494 eV of fundamental frequency.
One year ago I had similar problems in calculating NLO dispersion for fullere-
nes. The value at w=0.65 eV for SHG in C70 was absolutely meaningless (i.e.
very different from zero).

I would like to know if anybody else have faced (or is fighting with) the same
problem AND/OR if you are aware of referencies, people using MOPAC93-TDHF to
get frequency-dependent non-linear tensors AND/OR whatever you guess could help
me.

I will post a summary if I receive some answers. 

Many thanks.

Marianna



++++++++++++++++++++++++++++++
      MARIANNA  FANTI
PhD Student
Dept. of Chemistry
207 Pleasant street  S.E
University of Minnesota
Minneapolis, MN 55414
Minnesota, USA

e-mail: mf10119@sc.msc.edu 
+++++++++++++++++++++++++++++

From mf12101@sc.msc.edu  Wed Feb  8 20:38:02 1995
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From: <mf12101@sc.msc.edu>
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	id AA03387; Wed, 8 Feb 95 19:15:39 -0600
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	id AA379608; Wed, 8 Feb 95 19:15:39 -0600
Message-Id: <9502090115.AA379608@sc.msc.edu>
Subject: polyrate
To: CHEMISTRY@ccl.net
Date: Wed, 8 Feb 95 19:15:38 CST
X-Mailer: ELM [version 2.3 PL11]


With respect to:

>I am trying to model the chemical reactions of some polyatomic
>gases on the polysilicon surface. Firstly, I want to calculate the reaction
>constants of those reactions and I found that the QCPE program "Polyrate"
>would fit this purpose. Is there any other possibilities?
>And does anybody know the contact point(fax or e-mail) of Donald G. Truhlar
>who is one of authors of "Polyrate"?
>Any suggestions shall be greatly appreciated.
>Bye.
>
>Jai K. Shin

We (Rozeanne Steckler, Wei-Ping Hu, Ivan Rossi, and myself) have just 
completed POLYRATE 6.5, and we are finishing a few small details on the 
documentation.  We also expect to have MORATE 6.5 done very soon.

I do not recommend using older versions.  Versions 6.5 have a new form for
the keyword input, which I hope will be stable over a reasonable period of
time.  However, the input differs from previous input so new users will want to
start with 6.5 rather than start with an older version and then convert.

I am preparing a mailing describing the new versions and explaining the 
licensing, distribution, etc.  I plan to send the mailing out by postal
mail (i.e., the kind that uses stamps and envelopes) before the end of 
the month.

The new versions of both codes will be distributed by San Diego Supercomputer 
Center, by QCPE, and through the Computer Physics Communication Program 
Library.  Further details will be available soon in my mailing and also in the
May issue of QCPE Bulletin.

If you would like to receive the mailing when it is ready, please send me your 
name and mailing address, and I will send you a personal copy when everything
is ready.

Background:

     POLYRATE (version 4.0.1 is described in Ref. 1) is a computer program 
for calculating unimolecular and bimolecular chemical reaction rates of 
polyatomic species (and also of atoms and diatoms as special cases) from 
analytic potential energy functions or electronic structure input data.  
Rate constants are calculated by variational transition state theory (Ref. 2), 
and tunneling contributions may be estimated by semiclassical small-curvature 
and large-curvature tunneling approximations.  Rate constants may be calculated
for canonical or microcanonical ensembles and for reactions in the gas phase or
solid state or at gas-solid interfaces.  In addition, rates may be calculated 
for adiabatic and diabatic reactions in which one or more of the vibrational 
modes is restricted to the ground state or to the first excited state, while 
the translational, rotational, and remaining vibrational modes are treated 
thermally.  The program may also be used to find stationary geometries of 
reactants, products, and transition states and to calculate reaction paths, 
Arrhenius parameters, and equilibrium constants.

MORATE is an interface of POLYRATE with MOPAC-version 5.05mn.  The 
latter is a very portable version of MOPAC developed and enhanced at the 
University of Minnesota.  Whereas POLYRATE obtains the required energy, 
gradient, and hessian data for its dynamics calculations from analytic 
potential energy surfaces or electronic structure data in input files, MORATE 
calculates all energies, gradients, and hessians "on the fly" by 
carrying out MINDO/3, MNDO, AM1, PM3, or NDDO-SRP calculations as 
required.  This makes it particularly convenient for studying organic 
reactions (or Si chemistry).  The interested reader is referred to a 
published paper describing an earlier version (4.5) of MORATE (Ref. 3) and 
two prototype application papers (Refs. 4 and 5):

1.  D.-h. Lu, T. N. Truong, V. S. Melissas, G. C. Lynch, Y.-P. Liu, B. 
C. Garrett, R. Steckler, A. D. Isaacson, S. N. Rai, G. C. Hancock, J. G. 
Lauderdale, T. Joseph, and D. G. Truhlar, Computer Physics 
Communications 71 (1992) 235.

2.  D. G. Truhlar, A. D. Isaacson, and B. C. Garrett, in: Theory of 
Chemical Reaction Dynamics, Vol. 4, ed. M. Baer (CRC Press, Boca Raton, 
FL, 1985) pp. 65-137.

3.  T. N. Truong, D.-h. Lu, G. C. Lynch, Y.-P. Liu, V. S. Melissas, J. 
J. P. Stewart, R. Steckler, B. C. Garrett, A. D. Isaacson, A. Gonzalez-
Lafont, S. N. Rai, G. C. Hancock, T. Joseph, and D. G. Truhlar, Computer 
Physics Communications 75 (1993) 143.

4.  Y.-P. Liu, G. C. Lynch, T. N. Truong, D.-h. Lu, D. G. Truhlar, and 
B. C. Garrett, J. Amer. Chem. Soc. 115 (1993) 2408.

5.  Y.-P. Liu, D.-h. Lu, A. Gonzalez-Lafont, D. G. Truhlar, and B. C. 
Garrett, J. Amer. Chem. Soc. 115 (1993) 7806.

POLYRATE is written in portable FORTRAN 77 with the INCLUDE and DO WHILE
extensions.  It is tested on Cray, IBM, Silicon Graphics, and Sun computers.

Don Truhlar
truhlar@t1.chem.umn.edu

From excellon.COM!dennis@excellon.com  Wed Feb  8 22:38:03 1995
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	id AA15799; Wed, 8 Feb 1995 19:16:33 +0800
Date: Wed, 8 Feb 1995 19:16:33 +0800
From: dennis@excellon.com (Dennis Pumphrey)
Message-Id: <9502090316.AA15799@magic.excellon.COM>
To: chemistry@ccl.net
Subject: wire debonding
X-Sun-Charset: US-ASCII
Content-Length: 1161


Hi:

My name is Dennis Pumphrey, and I have been involved in some problems
with laser diodes with which we are seeing higher than expected failure rates.

The predominant failure mode seems to be debonding of the gold wires
connecting the semiconductor devices inside of the diode "can".

This laser diode is a commercial device (mf'd by Sharp), used in a
commercial machining application seeing G forces in excess of 20 Gs.

I'm afraid that my background is software development, so I'm pretty ignorant
about the actual mechanics of the device and bonding. However, I'm the one
with the computer and the access to the net, so I thought I'd give it a
shot...

I located your name by browsing recent traffic on the net and thought it
would be worthwhile to seek your advice.

Could you please let me know of experts or other resources that my company
could use or contact?

You can respond to me at dennis@excellon.com or to really talk to the one that
knows the details, you could call Larry Niles, VP of operations at
1-310-534-6710.

DO NOT REPLY TO THIS E-MAIL ADDRESS - IT WON'T WORK.

Any direction you can provide would be GRATEFULLY received.

- Thanks!

