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Date: Thu, 22 Feb 1996 09:00:12 +0100 (NFT)
From: Zilberman Silviu <silviu@chemib5.tau.ac.il>
To: computational chemistry <chemistry@ccl.net>
Subject: Mathematical softwares for Unix - Summery
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Hi Netters,

Here is a summery of responses I got for my question.
My original mail was:

>>Hello netters,
>>I was looking but I couldn't find any unix mathematical software that is as 
>>comfortable and easy to use as MatCad.
>>Does anybody knows about a version of MatCad for unix, or similar 
>>softwares, that allows the presentation of graphics and calculations 
>>on the same screen?
>>I'll summerize the answers.
>>
>>        Silviu Zilberman


The answers I got are as follows:

####################################################

Date: Wed, 7 Feb 1996 17:05:44 +0100 (MET)
From: Serge Pachkovsky <ps@ocisgi7.unizh.ch>
To: Zilberman Silviu <silviu@chemib5.tau.ac.il>
Subject: Re: CCL:MatCad for unix (x11) ?


> I was looking but I couldn't find any unix mathematical software that is as 
> comfortable and easy to use as MatCad.

MatLab, as well as Mathematica and Maple are available on several
unices. All three are supported on Sun, IBM RS/6k and SGI machines.
Quite likely, other *nix dialects are also supported at least by
some of the vendors. 

Wolfram Research (vendor of Mathematica, which happens to be my
personal favorite) is accessible electronically at http://www.wri.com
(or sales@wri.com, if you'd like to order Mathematica right away ;-).

Be prepaired for a stiff price, though...

Regards,

/Serge.P

####################################################

Date: Wed, 7 Feb 96 17:32:27 GMT
From: Dave Cosgrove <cosgrove@zeneca-ph.co.uk>
To: silviu@chemib5.tau.ac.il
Subject: Re: CCL:MatCad for unix (x11) ?



Dear Silviu,
          I have recently installed octave which I got from the
/pub/gnu directory at prep.ai.mit.edu.  It seems to be pretty good and
claims to be able to use MathCad scripts.  

Dave


***     ---  __o       __o       __o       ***
***  ------  \<,       \<,       \<,       ***
*** ----- ( )/ ( )  ( )/ ( )  ( )/ ( )     ***

####################################################

Subject: Unix mathematical software

     Silviu,
     
     I believe Maple, Mathematica, and Macsyma all have unix versions.  I 
     think the MathCAD symbolic calculation engine is from Maple.
     
     Tom Huff

####################################################

Date: Wed, 7 Feb 1996 12:38:22 -0500 (EST)
From: Joseph Landman <landman@motown.detroit.sgi.com>
To: Zilberman Silviu <silviu@chemib5.tau.ac.il>
Subject: Re: CCL:MatCad for unix (x11) ?

Shalom Silviu:

In a nutshell, Mathematica, Maple, and Macsyma let you do precisely that.

Joe

####################################################

Date: Wed, 7 Feb 1996 19:37:11 +0200 (EET)
From: Jussi Eloranta <eloranta@voimax.voima.jkl.fi>
To: Zilberman Silviu <silviu@chemib5.tau.ac.il>
Subject: Re: CCL:MatCad for unix (x11) ?

Mathematica, Maple and Macsyma run on Unix. There is also a free package
(similar to Macsyma) available called maxima. Maxima compiles at least
on Linux machines.

I think that Mathematica is the easiest one to use from these.

Jussi

####################################################

Date: Wed, 7 Feb 1996 18:27:42 GMT
From: "Gregg B. Wells" <wells@athens.dental.upenn.edu>
To: silviu@chemib5.tau.ac.il
Subject: MatCad or other


Silviu, you may want to look at Maple as mathematical software for a 
UNIX computer.  You can get more information about Maple from
the company's web site at http://www.maplesoft.com.

Gregg Wells
Department of Pathology
University of Pennsylvania
Philadelphia, Pennsylvania
USA
email:  wells@athens.dental.upenn.edu

####################################################

Date: Thu, 8 Feb 1996 08:23:12 +0200 (GMT+0200)
From: Craig Taverner <craig@hobbes.gh.wits.ac.za>
To: Zilberman Silviu <silviu@chemib5.tau.ac.il>
Subject: Re: CCL:MatCad for unix (x11) ?

MuPAD is the only one I know, but I think it puts the mathematics and the 
graphics on separate screens

Here are the www and ftp sites for MuPAD:

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

http://math-www.uni-paderborn.de/~cube/

math-ftp.uni-paderborn.de:/pub/MuPAD/doc/muphtml.tgz. 

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


"Never make anything simple and efficient when a way can be found to
 make it complex and wonderful."

Craig Taverner
Structural Chemistry, University of the Witwatersrand, South Africa
tel:   +27-11-716-2290                fax: +27-11-716-3826
email: craig@hobbes.gh.wits.ac.za
www:   http://www.gh.wits.ac.za/craig

####################################################

Date: Mon, 12 Feb 1996 09:26:50 +0100 (MET)
From: Carlo Nervi <nervi@chpc06.ch.unito.it>
To: Zilberman Silviu <silviu@chemib5.tau.ac.il>
Subject: Re: CCL:MatCad for unix (x11) ?

You can find a lot of Free and Commercial Scientific Software
(including Mathematica) under Linux on:

http://chpc06.ch.unito.it/linux/linux_prg.html

If you don't have Netscape 2.0, try:

http://chpc06.ch.unito.it/linux/linux_old.html

Hope this help,

        Carlo Nervi

----------------------------------------------------------------------------
Dr. Carlo Nervi
Dipartimento di Chimica Inorganica, Chimica Fisica e Chimica dei Materiali,
via P. Giuria 7, 10125 Torino, ITALY
phone: (Italy)-11-6707508               |  e-mail: nervi@chpc06.ch.unito.it
fax:   (Italy)-11-6707855               |          nervi@silver.ch.unito.it
                         http://chpc06.ch.unito.it/
----------------------------------------------------------------------------

####################################################

Thanks again for all the answers.

Silviu.

****************************************************
*  Silviu Zilberman                                *
*  Tel - Aviv University                           *
*  Faculty of Exact Sciences, Chemistry department *
*  Israel                                          *
*                                                  *
*  E-mail: silviu@chemib5.tau.ac.il                *
****************************************************


From wallenborn@phys.chem.ethz.ch  Thu Feb 22 08:48:48 1996
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Subject: [S] Summary: MOPAC POLAR problems
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Thanks to all who responded.


My original message was


----begin included message----
Hi there,

I'm trying to calculate molecular polarizabilities of medium sized
organic molecules with MOPAC 93. Typically an input deck would look
like that:

am1 polar
foo
bar
H   0.00000  0   0.00000  0   2.48400 0
C   0.00000  0   0.00000  0   1.39800 0
[...]

This works as long as i restrict the calculation to ground states
even with keywords like CISD.

However as soon as i specify ROOT=n (even with n==1) or EXCITED
the calculation fails, giving NaNs for all of the polarizabilities,
for example with

am1 polar(e=0) cisd c.i.=4 root=1 singlet


In MOPAC 6 polarizabilities used to be available for all states
and methods.


Am i doing something wrong or just something i'm not supposed
to do anyway?

----end included message----


Basically the answer to my question was: I was doing something
i was not supposed to do anyway. Henry Kurtz pointed out that
TDHF as employed in MOPAC93 does not compute CI polarizabilities:
----begin quote----
Ernst,

    The polarizability and hyperpolarizability calculations in MOPAC96
are defaulted to be done using a TDHF (freq. dep.) method.  This does
not allow anything but RHF reference states (If anything else works
it's an accident.)  
    The older versions of mopac used a finite-field procedure to 
calculate polarizabilities.  This does not allow frequency dependent
calculations but does allow any type of reference state.
    If it wasn't done, it should be possible to have both methods 
available but that's up to Jimmy Stewart to work out.
    If you have any questions about these methods, let me know.  My
group
wrote the code that is in the MOPAC programs.

                  Henry
----end quote----

In the documentation of MOPAC7 it is mentioned that 
switching between the two methods should be possible. 
However the MOPAC7 source code made no provisions for
this, and the MOPAC93 documentation doesn't even mention 
it anymore. 

So all CI polarizabilities have to be done in MOPAC6.



BTW, the bug reported in (Stewart, CCL:13-DEC-1994) is still
there. I got MOPAC93 from QCPE four weeks ago, and had to
patch i. (Thanks to Steve Bowlus for giving me this information.)





-- 
-ernst wallenborn.

i'm not a bug.
i'm an undocumented feature.

From wallenborn@phys.chem.ethz.ch  Thu Feb 22 09:04:23 1996
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Hi there,


another problem i have with MOPAC (both 6.0 and 93.00) is:

Seemingly the way to do a CIS/D/T calculation without the
use of the CIS/D/T keywords (which are only available in MOPAC93)
is:

am1 GEO-OK 1SCF POLAR &
C.I.=(4,2) SINGLET ROOT=1  MICROS=27
NAPHTALENE.DAT CISD 
C   0.00000 1  0.00000 1  0.00000 1
C   2.80302 1  0.00000 1  0.00000 1
C   2.10703 1  1.23867 1  0.00000 1
C   0.69729 1  1.23804 1  0.00014 1
C   0.69404 1 -1.17964 1  0.00020 1
C   2.10888 1 -1.17944 1  0.00030 1
C   0.00329 1  2.47858 1 -0.00051 1
H  -1.09571 1  0.00871 1  0.00027 1
H   0.16306 1 -2.13719 1  0.00017 1
H   2.63994 1 -2.13695 1  0.00039 1
H   3.89787 1  2.46987 1 -0.00138 1
H   3.89877 1  0.00797 1  0.00004 1
C   0.69398 1  3.65960 1 -0.00154 1
H  -1.09260 1  2.46977 1 -0.00017 1
H   0.16219 1  4.61658 1 -0.00193 1
C   2.10894 1  3.65856 1 -0.00237 1
H   2.64064 1  4.61573 1 -0.00360 1
C   2.80216 1  2.47849 1 -0.00131 1


MICROS
11001100
01101100
01011100
11000110
11000101
[rest cut off]
 
 

This works well in both versions (apart from the POLAR)
and produces energies  identical to MOPAC93 with the
CISD keyword.

The number of microstates necessary to produce a given
state of course grows fast. 
C.I.(8,4) CISD for a singlet state has 361 microstates,
(8,4) CISDT should have 1545 (i wrote a program to generate
MICROS and checked its correctness on smaller active space
CIs by comparing it with the MOPAC93 MECI output. I feel
pretty sure that the program works although there is 
no guarantee, as usual).

And here comes the problem: The maximum number of microstates
is given by NMECI in SIZES (NMECI**2 actually). The MOPAC93
documentation indicates that setting NMECI to 39 is sufficient 
for (8,4) CISDT (section 8.5, page 137), stating that MICROS=1513
in this case (not 1545 as i think). Now 39**2 is 1521, so
including 1545 microstates requires at least NMECI=40.
I tried this (setting NMECI in SIZES to 40, recompiling,
then running the above .dat file with MICROS=1545 and the 
required microstates) with both MOPAC6 and MOPAC93, and failed.

In MOPAC6 the calculation would run for about 30 minutes, 
calculate the energy corretly, then say


1******************** FINITE-FIELD POLARIZABILITIES *************

    THE F-F METHOD IS PERFORMED USING BOTH AN ENERGY
    AND DIPOLE MOMENT EXPANSION.  THESE RESULTS ARE
    LISTED BELOW AS "E4" AND "DIP", RESPECTIVELY.
 ITERATION  1 PLS=-0.627E+00 0.116E+02 ENERGY   
   99.7604317 DELTAE   -0.2395683


                EIGENVECTORS AND EIGENVALUES ON ITERATION  1

dump the EIGENVECTORS and then crash. Just crash. The funny 
thing is, it ALWAYS dumps the EIGENVECTORS, even without 
the VECTORS keyword! Hence PRTVEC is set to .TRUE. during the
run. 

I suspect that the memory allocated for this variable is getting
overwritten by some array. I was meditating over the
source code for a while but couldn't find the bug (if it
is one).

Any ideas?


Besides: Of course i tried

am1 GEO-OK 1SCF  C.I.=(8,4) CISDT
FOOBAR
NAPHTALENE.DAT
C   0.00000 1  0.00000 1  0.00000 1
[snip]

in MOPAC93. The result was a

  TOO MANY CONFIGURATIONS REQUESTED

crash with NMECI=39 (supporting my claim that the number of
microstates is not 1513 but rather >1521) and a crash similar
to the one described above when NMECI is bigger than 39.

So the problem is there in both MOPAC6 and MOPAC93.

Help?




-- 
-ernst wallenborn.

i'm not a bug.
i'm an undocumented feature.

From jsb2@camsci.com  Thu Feb 22 13:48:50 1996
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From: <jsb2@camsci.com>
Date: Thu, 22 Feb 96 13:28:05 EST
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	id AA02409; Thu, 22 Feb 96 13:28:05 EST
Message-Id: <9602221828.AA02409@camsci.com>
To: CHEMISTRY@www.ccl.net
Subject: Beta testers wanted: CS Chem3D with MOPAC



In the next few months we will be starting testing of CS Chem3D 3.5 with 
MOPAC, for Macintosh (68K and PowerPC) and Windows (3.1, 95, and NT) 
computers.  

We will be testing a fully-functioning version of MOPAC 93, the "latest 
and greatest" version of MOPAC developed by Fujitsu and Dr. Jimmy 
Stewart with significant improvements and enhancements over the public 
domain MOPAC 6 and even over MOPAC 7.  This is an authorized release 
that we are producing in collaboration with Fujitsu and 
Dr. Stewart.  In combining MOPAC with Chem3D, we have been able to 
retain all of the powerful computational features of MOPAC while adding 
the ease-of-use features of Chem3D's graphical interface.  No more 
having to generate Z-matrixes and input files -- Chem3D handles all of 
that for you (although you can still run input files directly if you 
want).

There will also be a bunch of enhancements to Chem3D itself.

We have a limited number of openings for qualified beta testers for this 
new product.  If you are interested in testing, we'd love to hear from 
you, but we are particularly interested in people who match any of the 
following descriptions:

1)  Currently use MOPAC and would be able to verify that our results 
    match those produced by other versions (they should!)
2)  Have used MOPAC before and are familiar with its non-obvious
    features (MOPAC power-users)
3)  Have wanted to use MOPAC in the past, but have been put off by its
    interface or unavailability.
4)  ...or?

Anyone interested in participating in this test should complete an 
application form available at http://www.camsoft.com/betainfoform.html 
or by anonymous ftp from ftp.camsoft.com in /pub/support/BETA_README
Please read the important additional information at the top of the form, 
and only submit the application if you agree to the terms listed there.

Thanks a lot.  We hope to hear from you!

Jonathan Brecher
CambridgeSoft Corporation
jsb@camsoft.com


From nick@cherwell.com Thu Feb 22 06:09 EST 1996
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Date: Thu, 22 Feb 1996 11:06:57 +0000
To: chemistry@www.ccl.net
From: Nick Lynch <nick@cherwell.com>
Subject: gNMR



Cherwell Scientific are pleased to announce that gNMR for Windows is now
available.

Many thanks to the members of the CCL who beta-tested the Mac and Windows
version of gNMR.

gNMR is designed for chemists who perform NMR analysis and require immediate
results on their desktop computer. Single molecules, or mixtures of
molecules containing many different NMR-active nuclei, may be simulated and
analysed. Users can also 'cut and paste' chemical structures from most
popular drawing packages directly into gNMR for NMR simulation. gNMR
converts experimental spectra from many file formats. The wide range of
analysis techniques available do not require any programming expertise.

For a more detailed description, user comments and the opportunity to
download a demo please go to our home page:

http://www.cherwell.com/cherwell

Or e-mail csp@cherwell.com

Or write to:

Cherwell Scientific
Magdalen Centre
Oxford Science Park
Oxford
OX4 4GA
Tel +44 (0)1865 784800
Fax +44 (0)1865 784801


Users in North America are encouraged to contact SoftShell International at:

http://www.softshell.com/
e-mail info@softshell.com
+1 970-242-7502

If you have a chemistry program which you think should be commercially
published please e-mail me with the details. I will be happy to advise you.

Nick Lynch

---                                                                       ---
     Nick Lynch  PhD                |  e-mail:  nick@cherwell.com
     Commissioning Editor           |  Phone:    +44 (0)1865 784812
     Cherwell Scientific Publishing |  Fax:      +44 (0)1865 784801
     Oxford OX4 4GA UK              |  http://www.cherwell.com/cherwell
---                                                                       ---



From owner-chemistry@ccl.net Wed Feb 21 10:18 EST 1996
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Date: Wed, 21 Feb 1996 18:11:25 
From: "Nekrasov Alex" <alne@ibch.siobc.ras.ru>
Organization: ibch
To: chemistry@ccl.net
Subject: research project




Dear Collegues:

	We would like to collaborate with you and submit a joint research 
proposal to U.S. Civilian Research and Development Foundation 
(WWW: http://www.internext.com/crdf).
We look forward to beginning the dialogue and then to expanding our research 
and business relations. If you are interested in cooperation in these mutual 
investigation we will greatly appreciate you kindly reply by FAX or E-mail. 
Please do not reply to the mailing list because we are not subscribed.

Dr. A. Wulfson, Ph.D.
Head of the Recombinant Proteins Group
FAX:  +7 (095) 330-7274
E-mail:  wan@ibch.siobc.ras.ru
_____________________________________________________________________________
General:  our research group of biotechnology of recombinant proteins deals 
with isolation, purification and production of biologically active human 
recombinant proteins such as cytokines and insulin. Recently we carried out 
the development of a technological scheme for the production of human 
TNF-alpha (wild-type as well as  mutants), Il-3 and IFN-gamma. Based upon 
strains designed at our Institute, we are developing at present the 
technological operation for production of insulin. Results of our 
investigation of TNF-alpha will be published in 
Russian Journal of Bioorganic  Chemistry N3, 1996 
(English edition is available)
"An Effective Method of Purification For Human Recombinant Tumor Necrosis 
Factor Alpha".
R.V. Tikhonov, S.A. Yakimov, V.G. Korobko, A.N. Wulfson
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 
Russian Academy of Sciences, 117871, Miklukho-Maklaya St. 16/10, 
Moscow, Russia.

During the progress of our research work we have faced some problems 
connected with preservation of biological activity of  rhIFN-gamma. 
That's only one reason why we have no opportunity to start the clinical 
trials of our product and make promotion of the medicines based on rhIFN-gamma 
for clinical applications. To solve this problem we are going to make 
experimental work to design more stable variants of  rhIFN-gamma in the 
following lines of investigation:

1. COMPUTER DESIGN OF PROTEINS
The computer modeling by the molecular dynamics method of protein spatial 
structure to determine potential mutation regions which allow formation of 
rhIFN-gamma dimer binding by S-S bonds.

2. GENETIC ENGINEERING
a) Preparation of  N-terminal deletion mutants lacking 7-10 residues. We 
suppose that such shortening will increase the stability of protein and 
facilitate its renaturation without lost of protein activity 
b). Preparation of mutant analogs of rhIFN-gamma in which the spatial 
structure would be stabilized by intermolecular S-S bonds.

3. STRUCTURAL ANALYSIS
Analysis  of  the protein dimer  spatial structure by  X-ray analysis  or  
NMR-spectroscopy.

4. BIOTECHNOLOGY
Isolation and purification of the recombinant protein, its renaturation and 
determination of reagents and buffer solutions in which the protein remains 
stable during long time periods and can be lyophilized with minimal lost of 
activity.

We hope that a combination of these approaches would give us the possibility 
to design stable substance of protein rhIFN-gamma for our further work.



From polowin@hyper.hyper.com Wed Feb 21 13:11 EST 1996
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From: polowin@hyper.hyper.com (Joel Polowin)
Message-Id: <9602211822.AA18627@hyper.hyper.com>
To: dsmith@debye.dasgroup.com (Doug Smith), CHEMISTRY@www.ccl.net
Subject: Re:  CCL:problem running Hyperchem 4.5



> From: dsmith@debye.dasgroup.com (Doug Smith)
> Date: Tue, 20 Feb 1996 23:10:07 +0000
> 
> I have version 4.5 running on my Pentium, along with ChemPlus 1.5.  I have
> just changed from Windows 3.1 to Windows NT Workstation 3.51. Now Hyperchem
> does not find the hardware lock, and looks on the network for a network
> license (which doesn't exist). How can I quickly fix this problem?

For HyperChem to communicate with the hardware lock under Windows NT, it
is necessary to install an NT port driver.  That driver is available via
our WWW page (http://www.hyper.com ) under Support / FAQs, or from our
ftp site (ftp.hyper.com) in the support directory.  The file is rainport.exe,
and it is a self-extracting archive file that should be executed with the
'-d' option to restore the directory structure of the archive:

rainport -d

It contains README files that describe the installation procedure.  The
driver is, of course, also available by writing to support@hyper.com .

Joel

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

Hypercube Inc, 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
WWW: http://www.hyper.com/




From MAILER-DAEMON@www.ccl.net Wed Feb 21 08:46 EST 1996
Received: from gate.texaco.com  for MAILER-DAEMON@www.ccl.net
	by www.ccl.net (8.7.1/950822.1) id IAA08538; Wed, 21 Feb 1996 08:46:26 -0500 (EST)
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Message-Id: <MSBEA01.SUBRAPS.341827070096052FMSBEA01@PO>
Date: 21 Feb 1996 07:18:07 GMT
From: SUBRAPS@texaco.com
Subject: Dipole-Dipole Interaction in Dynamics
To: chemistry@www.ccl.net




----------------------------------------------------------------------
THIS MAIL MESSAGE IS FROM THE INTERNET AND MAY HAVE BEEN READ, COPIED,
OR MODIFIED BY USERS OTHER THAN INTENDED RECIPIENTS.
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Dear List Members,


   Is there a Molecular Dynamics Package which incorporates dipole-dipole
interaction in the electrostatic computation?.
I would appreciate any input in this regard.


  Thanks


 --Mani--

Dr. P. S. Subramanian
Fuels and Lubrication Division
Texaco Inc.
P. O. Box 509
Beacon, NY 12508
email: SUBRAPS@texaco.com
vmail: 914-838-7561







From wieland@btm2d1.mat.uni-bayreuth.de Thu Feb 22 03:17 EST 1996
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From: <wieland@btm2d1.mat.uni-bayreuth.de>
Message-Id: <9602220817.AA0204@btm2d1.mat.uni-bayreuth.de>
Date: Thu, 22 Feb 96 09:15:27 +0100
To: estiu@nahuel.biol.unlp.edu.ar, chemistry@www.ccl.net
Subject: Re: CCL:J. Computer-aided molecular design




ESCOM Science Publishers in collaboration with the Center for Molecular 
Design offers an experimental electronic version of the Journal of Computer-Aided 
Molecular Design.
Access to full text searchable files will be made available to subscribers of the 
printed journal.
	    http://wucmd.wustl.edu/jcamd/jcamd.html

If you have similar questions, it is a good idea to consult some of the
resource collections on the internet, like:
        http://www.rpi.edu/dept/chem/cheminfo/chemres.html

Best regards,

Thomas Wieland               +---------------+
Dipl. Math.                  |+----    +----+|   "Es irrt der Mensch,
Lehrstuhl II f. Mathematik   |\    \   |    ||      solang er strebt.
Universitaet Bayreuth        | \    \  |    ||    ...
                             |  \    \ |    ||    Doch nur wer immer strebend
95440 Bayreuth               |   \    \\    ||      sich bemueht, denn koennen
Germany                      |    \    \\   ||      wir erhoeren." 
Tel. +49 (921) 553386        |     \     \\ ||                      Goethe
Fax  +49 (921) 553385        |      \-------||
                             +---------------+
 **** Do you know MOLGEN? **** http://btm2xd.mat.uni-bayreuth.de/molgen ****


