From h9290218@hkusub.hku.hk  Tue Apr 11 04:58:46 1995
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From: h9290218@hkusub.hku.hk (Danny Yau)
Message-Id: <9504110853.AA09683@hkusua.hku.hk>
Subject: order parameter of bcc lattice
To: chemistry@ccl.net
Date: Tue, 11 Apr 1995 16:53:07 +0800 (HKT)
Cc: h9290218@hkusub.hku.hk (Danny Yau)
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Dear Netters:

	I would like to calculate the order parameter of
	body-centre-cubic lattice(bcc). Is it the same calculation as
	face-centre-cubic lattice from Allen's Text book? What is the reciprocal
 lattice vector of bcc? For fcc the vector is (2*N)^(1/3)*pi/L. I got the vector
        of bcc is (4*N)^(1/3)*pi/L, but I cannot get unity in a bcc
	perfect lattice.

	I am very appreciated if anyone could provide any idea for the
	above subject.

Best wishes,	
-- 
Danny Yau                       email: h9290218@hkuxa.hku.hk   
Department of chemistry,           or  h9290218@hkusub.hku.hk
The university of Hong Kong.		

From heelisp@delta.newi.ac.uk  Tue Apr 11 05:58:50 1995
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From: <heelisp@delta.newi.ac.uk>
Date: Tue, 11 Apr 1995 10:44:57 +0100
Message-Id: <95041110445687@delta.newi.ac.uk>
To: CHEMISTRY@ccl.net
Subject: PDB files, residue solvent exposure 
X-VMS-To: SMTP%"CHEMISTRY@ccl.net"  


Dear CCL chemists,
Does anyone know of a program that can analyse a Brookhaven PDB file and
determine the degree of exposure of a particular residue to the surrounding
solvent and/or measure the effective dielectric constant of its environment.

I will summarise for the net if I receive useful replies.

Paul Heelis
Heelisp@newi.ac.uk

North East Wales Institute
UK

From darryl@om3.ch.umist.ac.uk  Tue Apr 11 08:13:48 1995
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Date: Tue, 11 Apr 1995 13:23:20 +0100 (BST)
From: Darryl Ellson <darryl@om3.ch.umist.ac.uk>
Sender: Darryl Ellson <darryl@om3.ch.umist.ac.uk>
Reply-To: Darryl Ellson <darryl@om3.ch.umist.ac.uk>
Subject: Thanks
To: chemistry@ccl.net
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In response to my query about hyperfine coupling, I'd like to thank the 
following for their useful input.

	Subhas Chakravorty
	James W. Gauld
	Fernando Villa.
	Frederick Bennett
	Jim Snyder
	Waegner Thomas
	Ernest Davidson.

	And most notably the following two people for their help.

	Lief Eriksson
	Abby Parril


I will forward a summary of my responses shortly.

Again, many thanks to all who contacted me.

	
			Darryl A. Ellson


    |_o_|
  []=(_)=[]	Hill 1 : Schumacher 0


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Darryl A. Ellson - Dept. Chemistry, UMIST, Manchester. M60 1QD
              Molecular Simulation & Design Laboratory
	    Tel: 061-236-3311 x4476    Fax: 061-236-7677
                E-mail: darryl@trigger.ch.umist.ac.uk

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~






From darryl@om3.ch.umist.ac.uk  Tue Apr 11 08:43:49 1995
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Date: Tue, 11 Apr 1995 13:46:56 +0100 (BST)
From: Darryl Ellson <darryl@om3.ch.umist.ac.uk>
Sender: Darryl Ellson <darryl@om3.ch.umist.ac.uk>
Reply-To: Darryl Ellson <darryl@om3.ch.umist.ac.uk>
Subject: Vincenzo Barone
To: chemistry@ccl.net
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I'm sorry to take up valuable bandwidth with such a request, but I need 
to contact Vincenzo Barone of Universita Federico II, Napoli Italy. If 
anyone has a contact number or e-mail I would greately appreciate it.
Also if anyone has e-mail adresses of his collaborators on J.Chem.Phys 
102 (1) 1995 pp384-393,--- Carlo Adamo or Alsessandro Fortunelli, they 
would be much appreciated.


		
			Many Thanks.


    |_o_|
  []=(_)=[]     

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Darryl A. Ellson - Dept. Chemistry, UMIST, Manchester. M60 1QD
              Molecular Simulation & Design Laboratory
	    Tel: 061-236-3311 x4476    Fax: 061-236-7677
                E-mail: darryl@trigger.ch.umist.ac.uk

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~






From h9290218@hkusub.hku.hk  Tue Apr 11 08:58:51 1995
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From: h9290218@hkusub.hku.hk (Danny Yau)
Message-Id: <9504111238.AA13603@hkusua.hku.hk>
Subject: fcc lattice of binary hard sphere mixture
To: chemistry@ccl.net
Date: Tue, 11 Apr 1995 20:38:35 +0800 (HKT)
Cc: h9290218@hkusub.hku.hk (Danny Yau)
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Dear Netters:

	I would like to investigate the liquid-solid transition state of
binary hard sphere mixture by using order parameter in Monte-Carlo
simulation. I need a perfect fcc lattice of binary hard sphere mixture
for my starting configuration. In Allen's text book, it only provide the
fcc perfect lattice in pure component. It work ok in binary mixture if
the reduced density is low(e.g. 0.2). But overlap is occured when
reduced density is getting high such as 0.9. That what I need in the
phase transition density of binary mixture. Would anyone has that kind
of program to create the perfect face-centre-cubic lattice of binary
mixture(i.e. two different size of the particles,such as NaCl, KCl) in high
density? Would you please send this program to me or give me any idea to
get them?

	Thank in advance for any responds.

Best wishes,
-- 
Danny Yau                       email: h9290218@hkuxa.hku.hk   
Department of chemistry,           or  h9290218@hkusub.hku.hk
The university of Hong Kong.		

From byw@novo.dk  Tue Apr 11 09:13:49 1995
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Date: Tue, 11 Apr 95 15:04:20 +0200
From: byw@novo.dk (Robert Bywater)
Message-Id: <9504111304.AA08779@bisse.novo.dk>
To: chemistry@ccl.net
Subject: molecular shape and surfaces



Seongbin Park asks :

>I am looking for references about measure for surface complementarity
>between two molecules, especially protein/protein (or protein/ligand)
>Could anyone kindly give me such information ?


Since others may also be interested in this, I am sending my reply to
him over the net. There are many methods for studying surface
shape and complementarity, but the one I favour is the method of
shape descriptors based on spherical harmonics. Here are some
key references to publications in this field.  

Leicester S.E., Finney J.L., and Bywater R.P., Description of
molecular surface shape using Fourier descriptors. J. Mol. Graph. (~1988~) 
{\bf 6} 104-108. 

Leicester S.E., Finney J.L. and Bywater R.P., A quantitative
representation of molecular surface shape  i) Theory and development of the
method. {\em J. Math. Chem.} (~1994~) {\bf 16} 315-341.

Leicester S.E., Finney J.L. and Bywater R.P., A quantitative
representation of molecular surface shape ii) Protein classification using
Fourier descriptors and classical scaling. {\em J. Math. Chem.} (~1994~) 
{\bf 16} 343-365.

Max N.L. \& Getzoff E.D., Spherical harmonic molecular surfaces.
IEEE Comput. Graphics Appl. (~1998~) {\bf 8} 42-50.

Duncan B.S. \& Olson A.J., Approximation and Characterization of Molecular
Surfaces {\em Biopolymers} (~1993~) {\bf 33} 219-229.


The `shape' method gives a purely geometric description of molecular
surface shape, but there is more in store - watch out for new developments
that will alow the inclusion of charge and `hydrophobicity' in the
determination of surface complentarity being developed by myself and
colleagues. More info on this in about 1/2 a year from now.



regards

Robert Bywater


  
                     ******************************
                     *                            *
                     *      Robert Bywater        *
                     *                            *
                     *  Biostructure Department   *
                     *      NOVO NORDISK A/S      *
                     *                            *
                     * DK-2880  BAGSVAERD Denmark *   
                     *                            *
                     *    email byw@novo.dk       *
                     *   fax :: +45 4442 1400     *
                     ******************************







From MOSES@cmchem.chem.cmu.edu  Tue Apr 11 09:58:50 1995
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Date: Tue, 11 Apr 1995 9:49:35 -0400 (EDT)
From: "D.J. Moses" <MOSES@cmchem.chem.cmu.edu>
To: chemistry@ccl.net
CC: MOSES@cmchem.chem.cmu.edu
Message-Id: <950411094935.20e01d29@cmchem.chem.cmu.edu>
Subject: G94 versions


>Anthony J. Dyson writes:
>
>I don't see VAX/VMS amongst the list of current or proposed platforms for 
>Gaussian94. Why is this so? We ourselves use the unix version, but the 
>fact that a VMS version is not promised has meant that our associates in 
>the Chemistry department are refusing to share the cost of the license 
>upgrade this time. Does anyone know why Gaussian seems to be moving off 
>VMS platforms?
>
>
 Gaussian, Inc. strives to make its software available on a wide range of
 platforms.  Our initial release of Gaussian 94 included those that we were
 able to validate at release time, and was not an indication that these
 are the only platforms we intend to support.

 For current and reliable information regarding Gaussian, it is always best
 to contact contact us directly.  We will be happy to answer any questions
 that you may have.

 Yours Sincerely,
 David Moses

 Phone: 412-279-6700
   Fax: 412-279-2118
 email: info@gaussian.com
 -----

 

From PA13808%UTKVM1.BITNET@phem3.acs.ohio-state.edu  Tue Apr 11 11:43:58 1995
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 11 Apr 1995 11:39:36 EDT
Date: 11 Apr 95   11:06 LCL
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    A number of researchers have reported problems with ab initio
  calculations such as unrealistic charges, large changes on changing the
  method( Basis set or inclusion of correlation by diff methods, lack of
  convergence etc). It is POSSIBLE that these problems all have a
  common source, namely the existence of low lying virtual orbitals.
  This canlead to a different order in the eigenvalues from one iteration
  to another   and since most programs use the aufbau principle to
  fill up the MOs the type of MOS occupied can change during the
  calculation.This can be common in systems containing metal atoms
  wwith unfilled D orbitals or when 3D and 4S have similar energies. In
  the case of molecules with lowlying unoccupied MOs such as nitro
  compounds a small basis set can give an incorrect ground state
  at the HF level and then of course will also give nonsense on going to
   MP2 level. One needs to look at the occupied MOs from iteration to
   iteration to see if a) the correct MOs are occupied and b) whether
   there is a switch between occ and unocc MOs between diff calculations.
    If there is you have to remedy the situation by freezing the occupati
     ion numbers or use some shift parameter to separate the energies
   of the occupied MOs from the unocupied ones. This used to be
   explained in earlier Gaussian manuals eg G90 so I assume there
   is something on it in the later versions.
                                John E. Bloor(UTK TENN)



From thomas_w@btm2x2.mat.uni-bayreuth.de  Tue Apr 11 11:58:52 1995
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Date: Tue, 11 Apr 95 16:18:31 +0200
From: thomas_w@btm2x2.mat.uni-bayreuth.de (Thomas Wieland)
Message-Id: <9504111418.AA24478@btm2x2.mat.uni-bayreuth.de>
To: chemistry@ccl.net
Subject: New release of the structure generator MOLGEN



MOLGEN - automatic structure elucidation in chemistry

The program system MOLGEN is devoted to the computation of all
structural formulae (= connectivity isomers) that correspond to a prescribed
brutto formula together with optional further conditions (e.g. prescribed and
forbidden substructures). MOLGEN provides an efficient, portable and
inexpensive tool for molecular structure elucidation in science and
education.
The system consists of several components:
 - A generator for all connectivity isomers
 - A graphical molecule editor and 2D-display
 - A display for 3D-placements using an energy optimization MM2, and 
 - A generator for all configurational isomers as well as their spatial
   realizations.

Pursuing advanced programming techniques, MOLGEN is available on different
computing platforms: IBM OS/2, MS WINDOWS and SUN Motif versions are 
available now. Ask for APPLE, IBM-RS6000 and DEC ALPHA AXP versions, as well. 
A native DOS version is also available.

For any further information and free demo versions, take a look at
http://btm2xd.mat.uni-bayreuth.de/molgen 
or write to: molgen@btm2x2.mat.uni-bayreuth.de.


Thomas Wieland               +---------------+
Dipl. Math.                  |+----    +----+|
Lehrstuhl II f. Mathematik   |\    \   |    ||
Universitaet Bayreuth        | \    \  |    ||
                             |  \    \ |    ||
95440 Bayreuth               |   \    \\    ||
Germany                      |    \    \\   ||
Tel. +49 (921) 553386        |     \     \\ ||
Fax  +49 (921) 553385        |      \-------||
                             +---------------+

From bennett@ubaclu.unibas.ch  Tue Apr 11 12:14:40 1995
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          Tue, 11 Apr 1995 18:00:58 +0200
Date: Tue, 11 Apr 1995 17:05:16 +0100
From: bennett@ubaclu.unibas.ch (Frederick Bennett)
Subject: G94 Accurate Methods ?
To: chemistry@ccl.net
Message-id: <v01510100abb055332c48@[131.152.105.87]>
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Hello everyone,
               like everyone else I have received some announcements
regarding the release of G94. I also received a very nice brochure today in
the mail that I had requested for further information. Unfortunately it
didn't provide any substantial details on my query.

 G94 has automated some "high accuracy methods" such as G1, G2 and G2(MP2)
all of which I am aware of. What I am not fimilar with is the complete
basis set methods (CBS) called CBS-4, CBS-q. CBS-Q and CBS-APNO. I presume
it has something to do with the work that Dunning and the rest of the
people at pnl have been working on, but does anyone have any futher details
on these methods in particular. A reference would be excellent.

Ciao

Fred


======================================================
Papernet Address :  Frederick R. Bennett
                    Institute for Physical Chemistry
                    Klingelbergstrasse 80
                    CH-4056 Basel
                    Switzerland

Mouthnet Address :  [41]-(61)-267-3821

Internet Address :  bennett@ubaclu.unibas.ch

======================================================




From srheller@nalusda.gov  Tue Apr 11 15:13:54 1995
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	by www.ccl.net (8.6.10/930601.1506) id PAA21117; Tue, 11 Apr 1995 15:01:16 -0400
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Date: Tue, 11 Apr 1995 14:58:21 -0400 (EDT)
From: "Stephen R. Heller" <srheller@origin.nalusda.gov>
To: jcicshelp <chemed-l@uwf.cc.uwf.edu>, chemistry@ccl.net,
        chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu
Subject: Sftware for Review
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Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII


11 April, 1995

Subject:  Computer Software for Review

     As the Software Review Editor for the ACS Journal of
Chemical Information and Computer Science (JCICS) I often get
software for review in the journal.   I have 4 new software
products. All four run under Windows!! I am looking for people
who are willing to review these software/databases products.  In
return for the review which is published in JCICS you get to keep
the software or database.  The review should be completed in 1-3
months.  The length of the review is 4-10 double spaced typed
pages.  Sample reviews can be found in most of the recent issues
of JCICS.

     Please try to give me some (short) reason to choose you over
another person. DO NOT SAY YOU WILL REVIEW ANYTHING I HAVE
AVAILABLE.  Messages with such replies are trashed!

     I have tried this approach for about the past four years and
it is working reasonably well. (REMINDER: For those who haven't
finished your reviews of software sent months and months ago,
this last sentence does not apply to you!)  As a result, I am
continuing this new method to find reviewers using this e-
mail/user group system.  I reserve the right to abandon this if
it is a problem, or inappropriate.  I will not notify people if I
have found a reviewer.  If you don't hear from me within a few
days I have chosen someone else to review the particular package.

     As I get many, many, (too many) replies to this message,
please do not respond after 13 April 1995 (Thursday), as I am
sure the software will be gone by then.

     I can be reached on Internet (SRHELLER@NALUSDA.GOV).

     PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX
NUMBER!!!  (I send the software by Federal Express.)  Without
this information I WILL NOT consider your request.


     Steve Heller


The packages I now have are:



1. ChemWindow, Version 3.1 from SoftShell.  This is a structure
drawing program which runs under Windows.

2. Lab Glassware collection, Version 1.0 from SoftShell.  This
requires ChemWindow 3.1 or later.

3. SciLogP from SciVision.  One needs either HyperChem 3.0 or 4.0
and Excel 4.0 or 5.0 to run this program. The program calculates
logP values.  The reviewer will have to contact SciVision to get
the unlocking code for the program.

4. SCAN from Minitab Statistical Software.  This is a Windows
based program for chemometric analysis.  This is a data analysis
program, with three main features: preprocessing, data
exploration, and modeling.


Steve Heller, USDA, ARS, Plant Genome Program
Bldg. 005, Room 337
Beltsville, MD 20705-2350
E-Mail: srheller@nalusda.gov
Phone: 301-504-6055  FAX:  301-504-6231


From SEGALEMB%BRUSPVM.BITNET@phem3.acs.ohio-state.edu  Tue Apr 11 16:43:55 1995
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Date: Tue, 11 Apr 95 17:33:28 BD2
From: Sergio Emanuel Galembeck
 <SEGALEMB%BRUSPVM.BITNET@phem3.acs.ohio-state.edu>
Subject: Q: AMBER parametrization?
To: Computational Chemistry List <chemistry@ccl.net>
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Content-transfer-encoding: 7BIT


Dear All,

     I am looking for references (or hints) about ab initio or semiempirical
parametrization of a molecule and its interactions with water using AMBER
force field.

         Thanks

            Sergio

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
               Sergio Emanuel Galembeck
               Assistant Professor in Theoretical Chemistry
               Departamento de Quimica
               Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto
               Universidade de Sao Paulo
               Av. dos Bandeirantes, 3900
     14040-901 Ribeirao Preto-SP
               Brazil

E-mail: SEGALEMB@BRUSPVM.BITNET
        segalemb@fox.cce.usp.br

fax: 0055-16-633-8151                 voice: 0055-16-633-3255 x  519
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

From Karl.F.Moschner@urlus.sprint.com  Tue Apr 11 17:13:57 1995
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From: Karl.F.Moschner@urlus.sprint.com
Message-ID:  <"Tue Apr 11 16:51:40 199500*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS>
To: chemistry@ccl.net, bennett@ubaclu.unibas.ch
Subject:  G94 Methods - Refs.


Since I came across you're note while installing Gaussian 94, I thought I'd 
take a moment to look up the references you, and I, are interested in.  
With apologies to "et. al.":

J. A. Pople, et. al., "Gaussian-1 theory: A general procedure for 
prediction of molecular energies," J. Chem. Phys. 90, 5622 (1989).

L. A. Curtiss, et. al., "Gaussian-1 theory of molecular energies for 
second-row compounds," J. Chem. Phys. 93, 2537 (1990).

L. A. Curtiss, et. al., "Gaussian-2 theory for molecular energies for 
first- and second-row compounds," J. Chem. Phys. 94, 7221 (1991).

M. R. Nyden and G. A. Petersson, "Complete basis set correlation energies. 
I. The asymptotic convergence of pair natural orbital expansions," J. Chem. 
Phys. 75, 1843 (1981).

G. A. Petersson, et. al., "A complete basis set model chemistry. I. The 
total energies of closed-shell atoms and hydrides of the first-row atoms," 
J. Chem. Phys. 89, 2193 (1988)

G. A. Petersson and M. A. Al-Lahman, " A complete basis set model 
chemistry. II. Open-shell systems and the total energies of the first-row 
atoms," J. Chem. Phys. 94, 6081 (1991).

G. A. Petersson, et. al., "A complete basis set model chemistry. III. The 
complete basis set-quadratic configuration interaction family of methods," 
J. Chem. Phys. 94, 6091 (1991)

J. A. Montgomery, et. al., "A complete basis set model chemistry. IV. An 
improved atomic pair natural orbital method," J. Chem. Phys. 101, 5900 
(1994).

J. W. Ochterski, et. al., "A complete basis set model chemistry. V. An 
extension to six or more heavy atoms," in preparation (1995).

You might consider getting a copy of the "Gaussian 94 User's Reference", 
$50, info@gaussian.com.  It's a useful reference with 289 citations on the 
various methods and a much improved explanation of features, keywords, and 
job setup options and procedures.

By the way, a poster a member of T. Wipke's group presented at the ACS 
Anaheim meeting suggested that UHF/3-21G(*) may provide results of 
comparable quality to G1 and G2 at significantly lower "cost".  I believe 
that a paper has been accepted for publication in the near future.

Good reading! Karl
 _______________________________________________________________________
/                                                                       \ 
| The opions are those of the author and not Unilever Research U. S.    |
|                                                                       |
| Karl F. Moschner, Ph. D.                                              | 
|                                                                       | 
| Unilever Research U. S.      e-mail: Karl.F.Moschner@urlus.sprint.com | 
| 45 River Road                Phone:  (201) 943-7100 x2629             | 
| Edgewater, NJ 07020          FAX:    (201) 943-5653                   | 
\_______________________________________________________________________/



From desimone@ics.enet.dec.com  Tue Apr 11 22:14:02 1995
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Date: Tue, 11 Apr 95 18:46:51 PDT
From: BILL DESIMONE DTN 223-6722 PERFORMANCE WS PRODUCT MKTG  11-Apr-1995 2125 <desimone@ics.enet.dec.com>
To: mail11:;@ccl.net (@foo.dirfoo)
Apparently-To: distribution:;@ccl.net (see end of body)
Subject: Change of address (note) (B. Desimone)



	I have moved to a new Digital facility.  My new contact info
is:

	e-mail   desimone@ics.enet.dec.com
	phone    508-493-6722

I have taken on a new position as Digital's Base Prodcut Marketing
Manager for Performance Workstations (mid to high end workstations).  My 
prior position was Digital's Market Segment Mngr. for computational 
chemisty.  In the future, the computation chemistry marketing
activity will be driven out of a combination other groups.  
This change does not reflect in Digital's lessening its commitment to this 
market segment.

>From a product view, computational chemistry is an important area for
Digital's Performance Workstations.  I expect to apply my computational 
chemsitry experience to future Digital workstation designs.  

I hope to continue to be in contact with you and welcome any mid to high 
end workstation product design inputs.

	Thanx,

		Bill


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