From chemistry-request@server.ccl.net  Mon Mar 27 01:28:37 2000
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Date: Mon, 27 Mar 2000 16:19:43 +1000
To: CHEMISTRY@ccl.net
From: Tien Luu <Tien_Luu@science.uow.edu.au>
Subject: Pharmacophores/CoMFA/QSAR

Hello All,

There is a lot of information about pharmacophore, CoMFA and QSAR
techniques in the general literature, mainly outlining what they are and
how they've been used in a particular case.  But would anybody know of any
recent articles or books that directly compare/critique these methods?  I
am looking for an unbiased and vigorous (and maybe even vicious)
comparison/criticism.

Thanks in advance



Tien T. T. Luu

     Department of Chemistry, University of Wollongong
     Northfields Ave Wollongong, Australia  2522
     Phone : (02) 42214334
     Fax : (02) 42214287
     Email : Tien_Luu@science.uow.edu.au		



From chemistry-request@server.ccl.net  Mon Mar 27 06:25:44 2000
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From: "Jan Dillen" <jlmd@maties.sun.ac.za>
To: <chemistry@ccl.net>
Subject: Huckel MO for C60
Date: Mon, 27 Mar 2000 13:24:58 +0200
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Hi,

Has anyone ever worked out how the secular
determinant and energy levels in the Huckel
approximation look for the C60 fullerene?

I am just curious how they look in terms of 
alpha + x*beta.

jd


From chemistry-request@server.ccl.net  Mon Mar 27 06:44:36 2000
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Dear Colleague,

You are cordially invited to participate in the "Electronic Structure:
Prediction and Applications" conference that will be held at San
Sebastian (Donostia, in Basque language) from October 4 - 6, 2000.

The Conference intends to bring together a broad audience of active
researches ranging from condensed matter physicists to laboratory
oriented organic chemists, going through the plethora of physical
chemists, chemical physicists, computational/theoretical chemists and
physicists, etc. You can realize that it is intended to be very
ambitious. We will do our best to fulfill these expectations. The list
of the topics covered is.

  1. Femtosecond dynamics
  2. Dielectric Response
  3. DFT, including TDDFT
  4. Change and Reactivity
  5. Molecular Dynamics, Quantum Molecular Dynamics and Quantum Monte
     Carlo
  6. QM/MM, Biochemical applications
  7. Clusters
  8. Transition Metal Chemistry, including Metallofullerenes
  9. Solvent effects and water

The list of invited speakers that have already confirmed their
participation includes.


  1. R. Saykally, Berkeley, USA
  2. P.B. Armentrout, Salt Lake City, USA
  3. R. Needs, Cambridge, UK
  4. J. Inglesfield, Cardiff, UK
  5. A. Eguliz, Oak Ridge National Lab., USA
  6. L.A. Eriksson, Upssala, Sweden
  7. R.J. Boyd, Dalhosie, Halifax, Canada
  8. F. Martin, Madrid, Spain
  9. U. Roethlisberger, ETH, Zurich, Switzerland
 10. T. Clark, Erlagen, Germany
 11. K. Hermansson, Upssala, Sweden
 12. X. Lopez, Oxford, UK
 13. M. Robb, London, UK
 14. P. Siegbahn, Stockholm, Sweden
 15. M. Yañez, Madrid, Spain
 16. S. Shaik, Jerusalem, Israel
 17. J.A. Alonso, Valladolid, Spain
 18. M. Sodupe, Barcelona, Spain
 19. R.W. Godby, Cambridge, UK
 20. J. Sabin, Gainsville, Florida, USA
 21. R. Amos, Cambridge, UK
 22. S. Alvarez, Barcelona, Spain

The Conference will be held at "Miramar Jauregia", a Palace by the sea.
All sessions will be held at the same room. Due to the space limitations
the organizing committee has set a maximum number of participants of 120
persons. Hence we urge you to complete an early preregistration at the
following web site: http://www.sc.ehu.es/espa .

The inscription will be carried out electronically by using the web page
that we have prepared to that end, and that can be found at the web site
of the conference. We would appreciate receiving your preregistration as
soon as possible, at the latest on May 15, 2000.

Accommodation is not expected to suppose any trouble for the
participants, who are refereed to the web site of the Conference for
more information about this point. As a matter of fact, we like to point
it out that a very decent room in a Hotel within a walking distance from
the Conference Palace, will cost approx. 8000 Ptas (50 Euro), including
breakfast. Please be advised that accommodation will be your sole
responsibility. Needless to say, that we will be happy to assist you
just in case that you want us to do so. Please get in touch with us at
the following e-mail address: espa@sq.ehu.es

San Sebastian is located in Northern Spain very close to the France
South border and it is surrounded by three airports. The closest is the
airport of San Sebastian, which is 10 Km East. The Biarritz airport  in
France, is also close to San Sebastian at approximately 40 Km North.
However, the major airport is at Bilbao, approximately at 100 Km West
for San Sebastian. Transportation from Bilbao airport to San Sebastian
is fluent by bus. They run from Bilbao downtown every 30 minutes. San
Sebastian can also be conveniently reached by car, and traffic in the
city is easy.

By early October, mild weather conditions should be expected. For more
information on this topic, please visit the following web site.
http://my.netscape.com/weather/home.tmpl?city=08029&units=metric

The International Journal of Quantum Chemistry has agreed to publish the
Proceedings of the Conference in a Special Issue. Manuscript submission
and handling procedures will be announced in the second circular.  We
will feel honored if you could consider to publish your contribution to
the Conference in that issue.

The organizing committee has set a tentative Inscription Fee of 30000
Ptas (180. Euro). For graduate students the Inscription Fee will 15000
Ptas (90. Euro). Further details will be given in the second circular.

Finally, may I ask you to distribute this message to all of your
colleagues that might be interested in the Conference. The organizing
committee is pleased to thank you in advance for you help in the
dissemination of this announcement.

Please do not hesitate to contact us if you need further information. We
look forward to your reply.

Ana Arrieta
Andres Arnau
Jesus Ugalde
(Local Organizing Committee)



















From chemistry-request@server.ccl.net  Mon Mar 27 11:17:30 2000
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From: "Golab, Joseph T" <golabjt@bp.com>
To: "'CHEMISTRY@ccl.net'" <CHEMISTRY@ccl.net>
Subject: Awards for Modeling
Date: Mon, 27 Mar 2000 10:16:31 -0600
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Dear List Members:

How many awards exist for modeling?

By "award", I mean scholarships, certificates, honorarium, organization
awards, etc.  By "modeling", I mean computational chemistry, molecular
modeling, simulation, computational engineering, computational fluid
dynamics, etc.

Is there a web based (or other) documentation for any of these awards, i.e.
what are the requirements for nomination, what is the award recognizing,
etc.?

I will summarize for the list.  Thank you. 

:Joe
golabjt@bp.com
+1 630 961-7878 (SOCON 231-7878)

From chemistry-request@server.ccl.net  Mon Mar 27 11:28:46 2000
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From: yu@wavefun.com
Date: Mon, 27 Mar 2000 08:36:26 -0800
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 >
In-Reply-To: "Alexander Shchepalov" <sasha@ichem.unn.runnet.ru>
        "CCL:NDDO for d-elements" (Mar 25,  5:14pm)
References: <008c01bf9664$775ec9e0$cbe4bec2@unn.runnet.ru>
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To: "Alexander Shchepalov" <sasha@ichem.unn.runnet.ru>
Subject: Re: CCL:NDDO for d-elements
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On Mar 25,  5:14pm, Alexander Shchepalov wrote:
> Subject: CCL:NDDO for d-elements
>
> Dear CCL's,
>
> I'm looking for semi-empirical software for calculations molecules with
> d-elements in NDDO aproximation.
>
> Alexander Shchepalov
>
> University of Nizhnii Novgorod, Russia

All of three main stream semi-empirical methods, MNDO, AM1 and PM3, are based
on NDDO approximation. SPARTAN series, developed by Wavefunction, supports
d-function modules MNDOD and PM3(TM).

Jianguo Yu

-- 
+-----------------------+------------------+-------------------------+
|Jianguo Yu, Ph.D.      |  ______________  | E-Mail: yu@wavefun.com  |
|Computational Chemist  |  \  _________ /  | Phone:  (949)955-2120   |
|Wavefunction Inc.      |   \ \\\\\\\\/    | Fax:    (949)955-2118   |
|18401 Von Karman       |    \ \\\\\/      | "The doctrines observe  |
|Suite 370              |     \ \\/        |  nature"                |
|Irvine, CA 92612       |      \/          |   Lao-tzu (604-531 B.C.)| 
+----------------------http://www.wavefun.com------------------------+

From chemistry-request@server.ccl.net  Mon Mar 27 12:22:28 2000
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From: "Students of Dr. S.R. Gadre" <tcg@chem.unipune.ernet.in>
To: chemistry@ccl.net
Subject: stepit.c ?
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Hi all!


    Can anybody tell me where I can get C code for stepit ( not the one
converted using f2c).

Thanks in advance

Kamalakar Jadhav


From chemistry-request@server.ccl.net  Mon Mar 27 12:48:32 2000
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Date: Mon, 27 Mar 2000 14:45:42 -0300
From: Alfredo Mayall Simas <ams@npd.ufpe.br>
Subject: NDDO - for d elements:  Sparkles
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On Mar 25,  5:14pm, Alexander Shchepalov wrote:
Subject: CCL:NDDO for d-elements

Dear CCL's,

I'm looking for semi-empirical software for calculations molecules with
d-elements in NDDO aproximation.

Alexander Shchepalov

University of Nizhnii Novgorod, Russia

-----------------------------------------------------
Dear Alexander,

Please consider using our Sparkle model which is a simple and very cost
effective way of determining the geometries of metal complexes.
Our model was introduced in 1994 ("Sparkle model for the quantum chemical
AM1 calculation of europium complexes", Chem. Phys. Lett., 227(3) 349-353,
1994) for the purpose of obtaining geometries of lanthanide complexes. At
the time we observed it could also be used to determine the geometries of d
element complexes as well. Since then it has been used for determining not
only geometries, but also electronic spectra, for the design of luminescent
complexes, etc.
Cundari and Saunders have also extended it to other elements.
More recently, Puchta and Hommes showed that it could be used for gallium
and lead complexes as well [J. Mol. Model. 6(2) 126-132, 2000].
The title of their paper is suggestive:
"Exploring {2}-metallacryptands and {2}-metallacryptates with quantum
chemical methods - When (not only) computer chemists' dreams come true"

Alfredo Mayall Simas
DQF/CCEN
Universidade Federal de Pernambuco
Recife, PE, Brazil


From chemistry-request@server.ccl.net  Mon Mar 27 13:06:00 2000
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To: Lin Kui <linkui@bic.nus.edu.sg>, "chemistry@ccl.net" <chemistry@ccl.net>
Subject: Re: CCL:why autogrid3 can't run on my DEC alpha?
References: <38DECE1F.43C42527@bic.nus.edu.sg>
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Hi Lin Kui,

we get the same error message, but already while running autodock3.
Therefore I would like to ask you to send me your makefile.

I would then let you know of any differences between your and our
makefile.

Yours 
	Edgar

--
Edgar Luttmann                           

University of Paderborn, Germany        
Department of organic chemistry         
                                        office: J6.302
Warburger Str. 100                      phone:  (+49) 5251 60-2498
33098 Paderborn                         eMail:  edgar@upb.de

From chemistry-request@server.ccl.net  Mon Mar 27 10:21:34 2000
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From: "Teodorico Ramalho" <teo@epq.ime.eb.br>
To: <CHEMISTRY@ccl.net>
Subject: Cadmium complex
Date: Mon, 27 Mar 2000 12:25:08 -0300


Dear CCL:

    Which programs (commercial or not) are available for the calculation
of the cadmium complexes. I used semi-empirical pm3(tm), in PC Spartan
Pro. But it is distorce the tetraedric geometry. There is 60 atoms in my
complex. Can I use DFT ?  Which basic sets I can use. 

    I would appreciate any comments and hints to this problem and will
summarize the answers if possible.

With best regards


Teodorico C. Ramalho
IME


From chemistry-request@server.ccl.net  Mon Mar 27 14:53:25 2000
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From: "Dimitris K. Agrafiotis" <dimitris@3dp.com>
To: <chemistry@ccl.net>
Subject: CWnd class for 3D molecule rendering
Date: Mon, 27 Mar 2000 14:55:30 -0500
Message-ID: <E12B9083E71CD311ACAD00105AA657DD202DF2@exchange.3dp.com>

Does anyone have a free MFC control (CWnd or ActiveX)
for simple 3D molecule rendering? Thanks in advance.

---
Dimitris K. Agrafiotis, PhD              | E-mail: dimitris@3dp.com
3-Dimensional Pharmaceuticals, Inc.      | Tel:    (610) 458-6045
665 Stockton Drive, Suite 104            | Fax:    (610) 458-8249
Exton, PA 19341
 



From chemistry-request@server.ccl.net  Mon Mar 27 18:00:15 2000
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From: "Dr. Daniel Glossman" <glossman@yakko.cimav.edu.mx>
To: "Computational Chemistry List" <CHEMISTRY@ccl.net>
Subject: convergence problems
Date: Mon, 27 Mar 2000 15:58:45 -0800

Dear netters:

I am trying to get the energy of a molecule using the CBS-Q method included
in G98. I've tried everything I found in the manuals and books, but it failed
to converge.
The molecule is a radical cation, positive 1,2,3-thiadiazole.
For if there is somebody (with spare time) willing to try it and help me, 

I am including the input:


%chk=23tcbsqp
#p CBS-Q Test

positive 1,2,3-thiadiazole - CBS-Q energy calculation

  1   2
 S
 N,1,R2
 C,1,R3,2,A3
 N,2,R4,1,A4,3,0.,0
 C,3,R5,1,A5,2,0.,0
 H,3,R6,1,A6,2,180.,0
 H,5,R7,3,A7,1,180.,0
      Variables:
 R2=1.67754496
 R3=1.72225201
 R4=1.19948006
 R5=1.35757068
 R6=1.075501
 R7=1.07151657
 A3=91.72935644
 A4=107.53925482
 A5=110.25406768
 A6=122.34970766
 A7=132.97856753

The input geometry comes from a geometry optimization at the HF/6-31(d'),
which is the first step in the CBS-Q energy calculation. The process fail
to converge during the 3rd step, that is, the MP2(full)/6-31G(d') geometry
optimization.

Any hints on how to solve this problem will be appreciated.

Thanks in advance. Best regards

                                                                        =
Dr. Daniel Glossman Mitnik



*************************************************************************=
***********
Dr. Daniel Glossman Mitnik
Centro de Investigaci=F3n en Materiales Avanzados (CIMAV)
Departamento de Pol=EDmeros                                              =
         Phone: (52) 1 4391151
Miguel de Cervantes 120                                                  =
          FAX: (52) 1 4391112
Complejo Industrial Chihuahua                                            =
        E-mail: glossman@mail.cimav.edu.mx
Chihuahua, Chih. 31109                                                   =
                      glossman@hotmail.com
Mexico
*************************************************************************=
***********

From chemistry-request@server.ccl.net  Mon Mar 27 19:41:27 2000
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Message-ID: <38E001A1.D8B1DEA6@bic.nus.edu.sg>
Date: Tue, 28 Mar 2000 08:49:37 +0800
From: Lin Kui <linkui@bic.nus.edu.sg>
Organization: BIC, NUS
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To: Edgar <edgar@uni-paderborn.de>
CC: "chemistry@ccl.net" <chemistry@ccl.net>
Subject: Re: CCL:why autogrid3 can't run on my DEC alpha?
References: <38DECE1F.43C42527@bic.nus.edu.sg> <38DFA4F2.3D711441@uni-paderborn.de>
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Hello, Edgar,

the attached file is the autogrid makefile I used to re-compile.

Thanks a lot.

Yours

Kui Lin

--
Kui Lin

BIC-IMCB Bioinformatics Group
Institute of Molecular and Cell Biology
30 Medical Drive, Singapore 117609

e-mail: linkui@bic.nus.edu.sg phone: (+65) 874-3367



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 filename="Makefile"

# 
#  Makefile to build AutoGrid from Object files.
# 
#  (c) 1999, TSRI
#  Garrett M. Morris
# 

BIN = .

OBJS = main.o \
       check_size.o \
       setflags.o \
       timesys.o \
       timesyshms.o \
       printhms.o \
       prHMSfixed.o \
       printdate.o \
       strindex.o \
       banner.o \
       gpfparser.o

LNS = \
      main.ln \
      check_size.ln \
      setflags.ln \
      timesyshms.ln \
      timesys.ln \
      printhms.ln \
      prHMSfixed.ln \
      printdate.ln \
      banner.ln \
      gpfparser.ln \
      strindex.ln

LIB	= -lm

PROF	= #						no profiling
# PROF	= -p # for profilable code

DBUG	= #						no debugging
# DBUG	= -g # for dbx
# DBUG	= -DDEBUG #					turn on DEBUG code

# CFLAGS = $(PROF) $(DBUG) # Silicon Graphics
CFLAGS = -std -verbose $(PROF) $(DBUG) # DEC Alpha, Convex
# CFLAGS = -Aa -D_HPUX_SOURCE $(PROF) $(DBUG) #	Hewlett-Packard

# OPT	= -O3 -n32 -mips4 $(CFLAGS) # IRIX64 Silicon Graphics
# OPT	= -O3 -r4000 $(CFLAGS) # IRIX5 Silicon Graphics
OPT	= -O4 -ifo $(CFLAGS)	# DEC Alpha
# OPT	= -O2 -ur $(CFLAGS) # Convex
# OPT = -O2 $(CFLAGS) # Sun
# OPT	= -O +O3 +Obb2048 $(CFLAGS) # Hewlett-Packard
# OPT	= $(CFLAGS) #	-g debugging

# OPTLIM	= # Sun, Silicon Graphics Octane/IRIX6
OPTLIM = -Olimit 2048 # Hewlett-Packard, DEC Alpha
# OPTLIM = # Convex
# OPTLIM = # -g debugging

LINKOPT = $(OPT) # most compilers
# LINKOPT = -O2 -r4000 $(CFLAGS) # IRIX5 Silicon Graphics

LINT = lint # C code checking

LINTFLAGS = $(LIB) -lansi -c # DEC-Alpha # MA
# LINTFLAGS = -DHPPA -D_HPUX_SOURCE -Aa $(LIB) -c #	HP/Hewlett-Packard
# LINTFLAGS = -Aa $(LIB) -c #	HP/Hewlett-Packard Alt
# LINTFLAGS = $(LIB) -n -lansic #	Sun Sparc

autogrid3 : $(OBJS)
	echo $(BIN) on `date` using' >>> ' `hostname` ' <<<' >> LATEST_MAKE
	$(CC) $(LINKOPT) -o $@ $(OBJS) $(LIB)

convertmap : convertmap.o
	$(CC) $(OPT) -o $@ convertmap.o $(LIB)


lcheck :  $(LNS)
	$(LINT) -lansi $(LIB) $(LNS)


main.o : main.c autogrid.h autoglobal.h
	$(CC) $(OPT) $(OPTLIM) -c main.c

check_size.o : check_size.c autogrid.h
	$(CC) $(OPT) -c check_size.c

setflags.o : setflags.c autogrid.h
	$(CC) $(OPT) -c setflags.c

timesyshms.o : timesyshms.c autogrid.h
	$(CC) $(OPT) -c timesyshms.c

timesys.o : timesys.c autogrid.h
	$(CC) $(OPT) -c timesys.c

printhms.o : printhms.c autogrid.h
	$(CC) $(OPT) -c printhms.c

prHMSfixed.o : prHMSfixed.c autogrid.h
	$(CC) $(OPT) -c prHMSfixed.c

printdate.o : printdate.c autogrid.h
	$(CC) $(OPT) -c printdate.c

banner.o : banner.c autogrid.h
	$(CC) $(OPT) -c banner.c

gpfparser.o : gpfparser.c autogrid.h gpftoken.h
	$(CC) $(OPT) -c gpfparser.c

strindex.o : strindex.c autogrid.h
	$(CC) $(OPT) -c strindex.c

convertmap.o : convertmap.c
	$(CC) $(OPT) -c convertmap.c

# 
#  lcheck dependencies...
# 

main.ln : main.c autogrid.h autoglobal.h
	$(LINT) $(LINTFLAGS) $?

check_size.ln : check_size.c autogrid.h
	$(LINT) $(LINTFLAGS) $?

setflags.ln : setflags.c autogrid.h
	$(LINT) $(LINTFLAGS) $?

timesyshms.ln : timesyshms.c autogrid.h
	$(LINT) $(LINTFLAGS) $?

timesys.ln : timesys.c autogrid.h
	$(LINT) $(LINTFLAGS) $?

printhms.ln : printhms.c autogrid.h
	$(LINT) $(LINTFLAGS) $?

prHMSfixed.ln : prHMSfixed.c autogrid.h
	$(LINT) $(LINTFLAGS) $?

printdate.ln : printdate.c autogrid.h
	$(LINT) $(LINTFLAGS) $?

banner.ln : banner.c autogrid.h
	$(LINT) $(LINTFLAGS) $?

gpfparser.ln : gpfparser.c autogrid.h gpftoken.h
	$(LINT) $(LINTFLAGS) $?

strindex.ln : strindex.c autogrid.h
	$(LINT) $(LINTFLAGS) $?

# 
#  Remove objects, lint files, cores, etc.
# 
clean:
	/bin/rm -rf *.o *.s *.ln a.out core autogrid3 convertmap

# 
#  DEC Alpha
# 
openalpha :
	/bin/cp -f obj.alpha/*.o .
	/bin/cp -f obj.alpha/*.ln .

closealpha :
	/bin/mv -f *.o obj.alpha
	/bin/mv -f *.ln obj.alpha
# 
#  Convex
# 
openc2 :
	/bin/cp -f obj.c2/*.o .
	/bin/cp -f obj.c2/*.ln .

closec2 :
	/bin/mv -f *.o obj.c2
	/bin/mv -f *.ln obj.c2

# 
#  Hewlett-Packard Precision Architecture
# 
openhppa :
	/bin/cp -f obj.hppa/*.o .
	/bin/cp -f obj.hppa/*.ln .

closehppa :
	/bin/mv -f *.o obj.hppa
	/bin/mv -f *.ln obj.hppa

# 
#  Silicon Graphics
# 
opensgi4D :
	/bin/cp -f obj.sgi4D/*.o .
	/bin/cp -f obj.sgi4D/*.ln .

closesgi4D :
	/bin/mv -f *.o obj.sgi4D
	/bin/mv -f *.ln obj.sgi4D

# 
#  Sun
# 
opensun4 :
	/bin/cp -f obj.sun4/*.o .
	/bin/cp -f obj.sun4/*.ln .

closesun4 :
	/bin/mv -f *.o obj.sun4
	/bin/mv -f *.ln obj.sun4

# 
#  Architecture
# 
openxxx :
	/bin/cp -f obj.xxx/*.o .
	/bin/cp -f obj.xxx/*.ln .

closexxx :
	/bin/mv -f *.o obj.xxx
	/bin/mv -f *.ln obj.xxx

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