From sunger@crl.com  Thu Nov 17 02:27:12 1994
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Date: Wed, 16 Nov 1994 23:05:18 -0800 (PST)
From: Stefan Unger <sunger@crl.com>
To: Mrigank <mrigank@imtech.ernet.in>
Cc: chemistry@ccl.net
Subject: Re: CCL:Protein Structure/COnformational Analysis ?
In-Reply-To: <9411151909.AA14660@doe.ernet.in>
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> 
>   I am looking for the programs/algorithms/references regarding protein
>   structure analysis. I mean the analysis of various conformational
>   features by which we can compare two proteins, Can comment on
>   flexibility/accesibility or get  other topological/geometrical feauters.

Protein Expert (for MAC with math coprocessor) can do some nice analysis
of protein structure, including comparisons of structures digested into
a database of sequence, distance and angle relationships.  You can search 
for motifs.  Volume comparisons of proteins is also quite complete. A 
demo is available at www.camsci.com
Or, email a request to me and I can email the demo to you.
I hope this helps.

From mutz@ifp.mat.ethz.ch  Thu Nov 17 04:27:14 1994
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To: chemistry@ccl.net
Subject: Software for archiving literature
Date: Thu, 17 Nov 94 10:09:07 +0100



Dear collegues

I am looking for a public domain package for
archiving and organizing literature reference 
data on a IBM RS6k (or any UNIX platform). A pretty
X11 
user interface would be nice, but even a collection
of clever awk scripts would do. Thanks for your help

Marcel.

------------------------------------------------------------------------------
Marcel Utz                                              phone:  +41 1 632 5672 
Institute of Polymers                                     fax:  +41 1 632 1096
ETH-Zurich CNB E 98.2
CH-8092 Zurich, Switzerland                  email: Marcel.Utz@ifp.mat.ethz.ch
------------------------------------------------------------------------------

From toukie@zui.unizh.ch  Thu Nov 17 04:29:56 1994
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	id AA14729; Thu, 17 Nov 94 10:01:46 +0100
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Date: Thu, 17 Nov 1994 09:55:47 +0100 (MET)
From: "Hr Dr. S. Shapiro" <toukie@zui.unizh.ch>
Sender: toukie@zui.unizh.ch
Reply-To: toukie@zui.unizh.ch
Message-Id: <35748.toukie@zui.unizh.ch>
To: chemistry@ccl.net
Subject: Three questions


Dear Colleagues:

     I have three questions, as follows:

     (i) Does anyone know substituent pi constants (used for calculating
partition coefficients) for the isobutyl {-CH2CH(CH3)2} and/or sec-butyl
{-CH(CH3)CH2CH3} groups?  If so, kindly advise me of the values and the
reference(s) in which these experimental values can be found.  I would like
to use these pi-values to estimate the partition coefficients of some
phenolic derivatives.

    (ii) With respect to the Hammett substituent constants (sigma)m and
(sigma)p, is it legitimate to assume that the sigma constant for an ortho-
substituted derivative, "(sigma)o" will be (approximately) the same as the
(sigma)p value?  Why or why not?  Any published references specifically ad-
dressing this question would be most sincerely appreciated.

     My third question is NOT a computational chemistry one, but whilst I
have your attention I tought that I might as well ask it:

   (iii) Does anyone know of any commercial source anywhere of reagent-grade
o-, m-, and/or p-isobutylphenol and any types of o-, m-, and/or p-pentyl-
and/or hexylphenols?  If so, kindly send details.


     I thank all responders in advance for kindly sharing their experience
(and data) with me.


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, Switzerland

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

From vaxinf@chclu.chemie.uni-konstanz.de  Thu Nov 17 06:27:16 1994
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Date: Thu, 17 Nov 1994 11:33:27 CET
From: Eberhard Heuser-Hofmann <vaxinf@chclu.chemie.uni-konstanz.de>
To: chemistry@ccl.net
CC: vaxinf@chclu.chemie.uni-konstanz.de
Message-ID: <00987997.814A3073.17279@chclu.chemie.uni-konstanz.de>
Subject: need aimpac-input data


Hi,

I've generated the aimpac-programs successfully after 
some modifactions ("uninitialized variables").

Now I would be thankful to get some input-data to test 
the whole stuff. 

thanks

Eberhard Heuser-Hofmann
Univ.Konstanz
Germany

From herbert.homeier@rchs1.chemie.uni-regensburg.de  Thu Nov 17 07:27:16 1994
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Date: Thu, 17 Nov 94 13:03:26 +0100
From: Herbert Homeier (t4720) <Herbert.Homeier@chemie.uni-regensburg.de>
Message-Id: <9411171203.AA18618@rchs1.chemie.uni-regensburg.de>
To: eccc@hackberry.chem.niu.edu
Subject: Re: 80: Multimedia Chemistry / MIME types for symbolic computations
Cc: rzepa@ic.ac.uk, monagan@inf.ethz.ch, CHEMISTRY@ccl.net,
        maple-list@daisy.uwaterloo.ca, maple@daisy.uwaterloo.ca
Reply-To: na.hhomeier@na-net.ornl.gov



Dr. Henry Rzepa writes with respect to ECCC (see below), Paper 80:
> I was very impressed with the breadth of coverage and the quality of this
> teaching tool.
> 
> I wonder if in teaching Quantum mechanics and other mathematically orientated
> subjects, the authors have considered serving up "live" Mathematica notebooks
> as well as images, movies etc. I believe that the MIME type of
> application/x-mathematica is being formalised. This enables readers to
> participate in the maths actively, but of course does presuppose that they
> have Mathematica installed on their system.  Such "hyperactive"
> maths is in use in our course, as well as "hyperactive" programs in the
> computing
> course. I believe that the inclusion of semantic content as well as "passive"
> bitmaps is essential in such courses.
> 
> Try http://www.ch.ic.ac.uk/hyperactive/diff.ma for an example. Configure
> your WWW "helper" types to correspond to the above MIME type.
> 
> Dr Henry Rzepa, Department of Chemistry, Imperial College, LONDON SW7 2AY;
> rzepa@ic.ac.uk via Eudora 2.1.1, Tel  (44) 171 594 5774 or 594 5809.
> Fax: (44) 171 594 5804. World-Wide-Web URL:
> http://www.ch.ic.ac.uk/rzepa.html        
> 

In my opinion, the use of symbolic computational tools like Mathematica is very
promising, for teaching and as well for research, in all sciences. 

However, I would like to have
available  support on WWW for other very powerful symbolic algebra packages like Maple.
(see http://129.97.140.58/) This package is of growing importance, especially in Europe.
It also has worksheets. A very positive aspect of Maple is that it has an active 
Maple Users Group.

A MIME type for Maple would definitely be helpful.

Best regards

Herbert
--------------------------------------------------------------
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
--------------------------------------------------------------

What is ECCC? See http://rchs1.uni-regensburg.de/ECCC/ECCC.html

From tolja@maya.geo.uu.se  Thu Nov 17 08:27:18 1994
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Date: Thu, 17 Nov 94 14:01:57 +0100
From: tolja@maya.geo.uu.se (Anatoli Belonoshko)
Message-Id: <9411171301.AA06526@maya.geo.uu.se.geo>
To: CHEMISTRY@ccl.net
Subject: Nice animations: summary of responds
X-Charset: LATIN1
X-Char-Esc: 29



  Dear Colleague,

     The respond on my request for "nice animations"
of preferably of inorganic systems was not
overwhelming at all. Therefore, special thanks to
those who provided me with cyberspace coordinates.

     I have received three useful pointers. Two of them
I already knew. The third was for organic systems. As
a matter of fact I have not found what I expected. Still
it might be of some help to you.

     "Enclosed" please find three informative responds.

      Hope it helps. 

      Best regards,

      Anatoly Belonoshko
      Uppsala University, Sweden
----------------------------------------------

From savary@sc2a.unige.ch Fri Oct 14 16:34:04 1994

Dear Anatoly,

You can have a look at our WWW server you can find a few animations, with
e.g. a ferrocene dynamics

see : http://scsg9.unige.ch/eng/toc.html

hope this helps


Francois Savary

----------------------------------------------------------------------------
Francois Savary
University of Geneva
Department of Physical Chemistry CHIFI Weber
30 quai Ernest-Ansermet
CH-1211 Geneva 4

Lab       : 112
Phone     : +4122 702 65 32
Fax       : +4122 702 65 18
e-mail    : savary@sc2a.unige.ch
HTML      : http://scsg9.unige.ch/tabmat.html  (in french)
          : http://scsg9.unige.ch/eng/toc.html (in english)
----------------------------------------------------------------------------


From GLASSER@AURUM.CHEM.WITS.AC.ZA Fri Oct 14 16:58:13 1994

For starting points on visualisation in chemistry,
try http://www.nih.gov/molecular_modeling/mmhome.html  and
http://scsg9.unige.ch/eng/toc.html for a start. 
There are now quite a few WWW sites accessible. 
Leslie Glasser
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
PLEASE NOTE: New E-mail address.  
   Old address: 009lgzs@witsvma.wits.ac.za should no longer be used.
======================================================================
(Prof.) Leslie Glasser                     Dept. of Chemistry    
E-mail: glasser@aurum.chem.wits.ac.za      Univ. of Witwatersrand     
Tel: Intl + 27 11 716-2070                 P. O. WITS 2050            
Fax: Intl + 27 11 339-7967                 South Africa               
====================================================================== 

From lars@sodium.mps.ohio-state.edu Sun Oct 23 23:54:37 1994


Dear Dr. Belonoshko,

you can find a small collection of animations of inorganic MD computer
simulations at the anonymous-ftp site chem-ftp.mps.ohio-state.edu, in the
directory /moviemol. At the same place you will find the molecular animation
program "moviemol" for MS-DOS, ibm risc/6000 and silicon graphics platforms.
Some more animations will probably be added to this site in the not-to-distant
future.

Best regards,
#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#
 Dr. Lars Ojamae                           Phone (614) 292-7806
 Dept of Chemistry, Ohio State University  Email lars@sodium.mps.ohio-state.edu
#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#


From gjt@ccl.net  Thu Nov 17 11:27:22 1994
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Date: Thu, 17 Nov 1994 10:25:29 -0700
To: chemistry@ccl.net
From: gjt@t12.lanl.gov.Greg.Tawa (Greg Tawa, 7-8765)
Subject: Matches


Dear people,
  This may not be a quantum chemistry question but:
  I need to know what kind of chemical reaction takes place when one strikes
  a match?  Also when were matches invented?
Thanx

Gregory J. Tawa
gjt@t12.lanl.gov




From oesterei@hrz.ba-freiberg.de  Thu Nov 17 11:32:33 1994
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From: Ralf Oestereich <oesterei@hrz.ba-freiberg.de>
Subject: SUMMARY: G92/GAMESS/SPARTAN
To: chemistry@ccl.net (Computer Chemistry List)
Date: Thu, 17 Nov 94 17:07:06 MEZ
Mailer: Elm [revision: 66.25]


Dear netters!

Thank you very much for all your answers concering my
questions with GAMESS/GAUSSIAN and SPARTAN.

You really helped us with your comments and ideas.
   
Because I received emails that showed general interest
I will summarize those for the whole cummunity.
If I, however, forgot someone
please mail me and I will correct this!

Again: I was impressed from your fast and extremly useful
help !!!

		R. Oestereich



From: peeter@chem.ut.ee (Peeter Burk)
	
> 
> And further: Does anyone have some experiences in combining
> GAMESS with SAPRTAN 3.0?
> 
	You should look at program babel somewhere at chemistry.ccl.net,
it should be able to take spartan output and generate from it gamess
(or gaussian or ...) input file.


---> This was infect a really great help! Whenever you need a programm to 
     convert different file formats into eachother try BALBES!
     (archie will find it!)



From: <peon@medchem.dfh.dk>:


        Spartan can create the input for you directly.  It is NOT true that
you must use internals, the keyword COORD=CARTESIAN allows normal cartesian
input (and is automatically introduced by Spartan).
        If you have Gaussian and Spartan on the same machine, everything is
simple, you just submit things from Spartan 3.1 directly.
        If Gaussian is on another machine without the ability to run
Spartan, it's a little more complicated.  I have created some simple Unix
scripts for utilizing the Spartan setup and sending it directly to another
machine running Gaussian.  There is no need for daemons or anything on the
remote machine.  If you want, I can send you the scripts.
        With any of these methods, you can view the output in Spartan easily.

        Per-Ola Norrby


From: Maitre Ph <Philippe.Maitre@cth.u-psud.fr>

Hi,
I have some experience switching between gamess and gaussian92.
First of all, 1) yes it is possible and easy to use cartesian coordinates
with gaussian92, 2) if you are used to gamess, there is an option
(FRIEND=GAUSSIAN in the namelist CONTRL) which generates an input for
gaussian92, 3) we have a simple fortran codes to convert MOs from one
program to the other.

PS : The FRIEND keyword might not be available in an old Gamess version.



From: "Joe Leonard" <jle@toyota.wavefun.com>

	It should be straightforward to connect GAMESS to Spartan, as long as
GAMESS writes an archive file with the basis set specification, molecular
orbital coefficients and the like.  The Spartan archive is a readable file, and
I can send a brief description of its contents if you would like.

	Spartan, however, does not support internal coordinates.  We use the
new(er) Cartesian optimization capabilities of G92 - does GAMESS use cartesian
coord?

	If you are interested in seeing graphics from GAMESS calculations, if
GAMESS writes grid files, I can also email a description of the external
gridfile format supported by Spartan's graphics module...



From: Pat Walters <pat@mercury.aichem.arizona.edu>
Our program Babel will interconvert files from SPARTAN, GAUSSIAN,
and GAMESS (as well as alot of other programs).  I'm attaching more
information below.  If you have any questions please let me know.

Pat
_______________________________________________________*__________________
BABEL is a program designed to interconvert a number of file formats
currently used in molecular modeling.  The program is available for
Unix (AIX, Ultrix, Sun-OS, Convex, SGI, Cray, Linux), MS-DOS, and on 
Macs running at least System 7.0.

Babel will read the following file types :

Alchemy                  AMBER PREP               Ball and Stick           
Biosym .CAR              Boogie                   Cacao Cartesian          
Cambridge CADPAC*        CHARMm*                  Chem3D Cartesian 1       
Chem3D Cartesian 2       CSD CSSR                 CSD FDAT*                
CSD GSTAT                Free Form Fractional     GAMESS Output*           
Gaussian Z-Matrix        Gaussian Output*         Hyperchem HIN*           
Mac Molecule             Macromodel               Micro World              
MM2 Input                MM2 Ouput                MM3*                     
MMADS*                   MDL MOLfile*             MOLIN*                   
Mopac Cartesian          Mopac Internal           Mopac Output             
PDB                      ShelX                    Sybyl Mol*               
Sybyl Mol2*              XYZ                      

Babel will write the following file types :

Alchemy                  Ball and Stick           Cacao Cartesian          
CAChe MolStruct*         Chem3D Cartesian 1       Chem3D Cartesian 2       
ChemDraw Conn. Table*    CSD CSSR*                Gamess Input*             
Gaussian Cartesian*      Gaussian Z-matrix        Hyperchem HIN*            
IDATM                    Mac Molecule             Macromodel               
Micro World              MM2 Input*               MM2 Ouput                
MM3*                     MMADS*                   MDL Molfile*              
Mopac Cartesian          Mopac Internal           PDB                      
Report                   Sybyl Mol*               Sybyl Mol2*               
XYZ                      

Babel is capable of assigning hybridization, bond order, and connectivity 
when these elements are not present in the input file.

NOTE:  The file formats indicated with * are not currently supported in the
Mac version.  We're currently working on a Mac update which will include all
these formats, and few other new goodies.  This update should be ready in a
couple of weeks.

INSTALLATION OVERVIEW
Babel is availiable via anonymous ftp from 
joplin.biosci.arizona.edu in pub/Babel


Any questions regarding BABEL should be directed to 
babel@mercury.aichem.arizona.edu



From: FOX@cmchem.chem.cmu.edu


  Doug Fox from Gaussian, Inc. here.  I will include a sample Gaussian
input at the end of my message but in general I think you will find that
the Gaussian input is easier and more flexible than the GAMESS input and
SPARTAN will simplify that further.

  1) Gaussian could always do single points with cartesian coordinates but
     Gaussian 92 allowed optimizations with either internals, cartesians
     or a mixture of both.

  2) The options selection in Gaussian92 is keyword driven with the optoin
     of overriding any of the defaults.  The vast majority of input data
     fields are free-format reducing input errors due to placing data in
     the wrong place on a line.

  3) The SPARTAN interface is based on an ongoing commitment to make Gaussian
     interact with a wide variety of graphical interfaces.  We maintain
     a dialog with a number of developers and as new features are added tp
     Gaussian we work to make the data available in a format for facile display.
  I am including a example from our test suite showing input with mixed
cartesian/internal coordinates.  It does an optimization calculating the
nuclear second derivative at the first point, with the STO-3G basis and the
restricted Hartee-Fock hamiltonian.  Data saved in the checkpoint file, named
in the first line can be passed to later jobs, i.e. structures, wavefunctions
and second derivatives to initialize optimization bigger basis set or a
different model.



This Technical data is licensed by the United States of America.  Use
of this Technical data contrary to U.S. law or in the design, development
production, stockpiling, or use of chemical or biological weapons is
prohibited.





From sunger@crl.com  Thu Nov 17 13:27:21 1994
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Date: Thu, 17 Nov 1994 09:39:47 -0800 (PST)
From: Stefan Unger <sunger@crl.com>
To: Anatoli Belonoshko <tolja@maya.geo.uu.se>
Cc: CHEMISTRY@ccl.net
Subject: Re: CCL:Nice animations: summary of responds
In-Reply-To: <9411171301.AA06526@maya.geo.uu.se.geo>
Message-Id: <Pine.SUN.3.91.941117093706.4643D-100000@crl2.crl.com>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII


>   Dear Colleague,
> 
>      The respond on my request for "nice animations"
> of preferably of inorganic systems was not
> overwhelming at all. Therefore, special thanks to
> those who provided me with cyberspace coordinates.
> 
>      I have received three useful pointers. Two of them
> I already knew. The third was for organic systems. As
> a matter of fact I have not found what I expected. Still
> it might be of some help to you.

An "animation" of Fe binding site in ferredoxin (from Protein Expert 
"wobble" mode for stereo viewing) is available at
www.camsci.com
I hope you find this useful.

From hinsenk@ERE.UMontreal.CA  Thu Nov 17 17:27:22 1994
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	id AA19503; Thu, 17 Nov 94 17:18:03 -0500
Date: Thu, 17 Nov 94 17:18:03 -0500
From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad)
Message-Id: <9411172218.AA19503@cyclone.ERE.UMontreal.CA>
To: CHEMISTRY@ccl.net
In-Reply-To: <9411171203.AA18618@rchs1.chemie.uni-regensburg.de> (Herbert.Homeier@chemie.uni-regensburg.de)
Subject: Re: CCL:80: Multimedia Chemistry / MIME types for symbolic computations



   However, I would like to have
   available  support on WWW for other very powerful symbolic algebra packages like Maple.
   (see http://129.97.140.58/) This package is of growing importance, especially in Europe.
   It also has worksheets. A very positive aspect of Maple is that it has an active 
   Maple Users Group.


Another package worth mentioning (because it is still relatively
unknown) is MuPAD, developed at the University of Paderborn in
Germany. It is not yet as complete as Mathematica or Maple,
but it does have all the basic features of symbolic algebra
packages. Its syntax resembles Maple's (intentionally), but
is much cleaner in some areas, e.g. matrix computations.
Being based on an object-oriented kernel, it is easier to extend
than some other programs. And not the least of its advantages
is that it is free for academic users. There are versions for
many Unix machines (including Linux) plus a Mac version; others
are in preparation. Look at ftp.uni-paderborn.de for more
information.

And let's not forget to mention GNU-Calc, which is of course
much less powerful than "real" symbolic algebra packages,
but so much more convenient that I still use it more
than anything else.

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Konrad Hinsen                     | E-Mail: hinsenk@ere.umontreal.ca
Departement de Chimie             | Tel.: +1-514-343-6111 ext. 3953
Universite de Montreal            | Fax:  +1-514-343-7586
C.P. 6128, succ. A                | Deutsch/Esperanto/English/Nederlands/
Montreal (QC) H3C 3J7             | Francais (phase experimentale)
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