From chemistry-request@server.ccl.net Thu Dec 13 00:15:00 2001
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From: "Dillen J, Prof" <JLMD@sun.ac.za>
To: "'chemistry@ccl.net'" <chemistry@ccl.net>
Subject: RE: Gaussian revised GUI
Date: Thu, 13 Dec 2001 07:13:55 +0200
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> Who's willing to pay Gaussian, Inc. to rewrite their code ...

Considering the long computational times involved in running
a QM job, any good GUI will have to offer the alternative
of running a calculation in the background. This implies that
all the button clicks and check boxes are somehow translated 
into commands/keywords and written to a file. If the original 
keyword syntax works, I see no reason why it should be redesigned 
and/or rewritten. Besides, a GUI that offers scripting will 
have to fall back to the old keyword driven operation.

> It would not surprise me if doing the GUI (or API) is harder 
> work than getting the algebra of the QM code "right", too.

In contrast to the writing of QM code which is done after "it works",
designing a GUI is a never-ending operation. See Microsoft: every
version of Word looks different. Obviously, part of these changes
are done to keep the interest in their development tools high,
but a lot of the changes are intended to improve ease of use.
In a sence, Microsoft has an easy job because they only support
Windows. Designing a GUI that will work for all the platforms
currently supported by Gaussian will not be an easy task.

Jan Dillen

From chemistry-request@server.ccl.net Thu Dec 13 05:05:06 2001
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From: Szilveszter Juhos <szilva@ribotargets.com>
To: William Wei <william@phm.utoronto.ca>
cc: CCLer <chemistry@ccl.net>
Subject: Re: CCL:Gaussian run error--util.so
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On Wed, 12 Dec 2001, William Wei wrote:

> on the supercomputer, it gave me the following message:
> 6554108:./g98: rld: Fatal Error: Cannot Successfully map soname
> 'util.so' under any of the filenames
> /usr/lib64/util.so:/usr/lib64/internal/util.so:/lib64/util.so:/opt/lib64/util.so:

Seems like a IRIX machine for me, but wuld be helpful to write the
operating system you are using. Anyway try 'man rld' or any man pages
about the runtime linker, you should add the path where libutil.so lives
to the LD_LIBRARY_PATH . The problem is that the runtime linker can not
load the actual dynamic library because it is not in its search path.


Szilva


From chemistry-request@server.ccl.net Thu Dec 13 07:30:34 2001
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From: "JinhyukLee" <mack@statchem.snu.ac.kr>
To: "ccl ccl" <chemistry@ccl.net>
Subject: Installing CHARMM with GAMESS
Date: Thu, 13 Dec 2001 21:29:17 +0900
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Hi Cclers

I have CHARMM ver 27b3 and the latest GAMESS downloaded before a few day. As the info file(gamess.doc) explains, I installed CHARMM with GAMESS.  I realized that this job was difficult. However, I had a sucess to install this without errors. I tested QM/MM with gmstst.inp (c25test case). I had a  error as follows.

.
.
 INPUT CARD>ATOM HB3  HA      0.09  !     |                                                  
 INPUT CARD>GROUP                   !                                                        
 INPUT CARD>ATOM C    C       0.51                                                           
    1000000 WORDS OF MEMORY AVAILABLE 
 **** ERROR, NO  $DATA   GROUP WAS FOUND      <-------- THIS
 EXECUTION OF GAMESS TERMINATED ABNORMALLY AT Thu Dec 13 14:14:46 2001 
 STEP CPU TIME =     0.21 TOTAL CPU TIME =        0.2 (    0.0 MIN) 
 TOTAL WALL CLOCK TIME=        0.0 SECONDS, CPU UTILIZATION IS 100.00% 
                     0 WORDS OF DYNAMIC MEMORY USED 
 IF YOU WANT A CORE FILE, SET COREFL=.TRUE. IN $SYSTEM. 
.
. 

I think the interface between CHARMM and GAMESS has a problem in my compiled CHARMM (CHARMM was compiled wrong). Is there anyone who succeed in compile CHARMM with GAMESS? I also think that installing CHARMM with GAMESS is dependent on their versions. 

Have a nice day. 

Sincerely,

JinhyukLee

P.S. (To men who send me the mail on QCMD)  I have not  received any information on QCMD so far. 

From chemistry-request@server.ccl.net Thu Dec 13 06:16:34 2001
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Subject: Re: CCL:somewhat obscure chemistry quote
References: <200112121757.JAA349457@socrates.cgl.ucsf.edu>
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I think the quote you are looking for is the following statement by the
French philosopher A. Comte (1838):
  Every attempt to employ mathematical methods in the study of chemical
questions must be considered profoundly irrational. If mathematical
analysis should ever hold a promiment place in chemistry  - an
aberration
which is happily impossible - it would occasion a rapid and widespread
degradation
of that science.

All the best,
    Trond SAUE
-- 
Trond SAUE                                (DIRAC:
http://dirac.chem.sdu.dk/)
Laboratoire de Chimie Quantique et Modélisation Moléculaire
Université Louis Pasteur ; 4, rue Blaise Pascal ; F-67000 STRASBOURG
tél: 03 90 24 13 01   fax: 03 90 24 15 89   email:
saue@quantix.u-strasbg.fr


From chemistry-request@server.ccl.net Thu Dec 13 08:07:22 2001
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To: "Dr. N. SUKUMAR" <nagams@rpi.edu>
CC: P.Boulet@qmul.ac.uk, chemistry@ccl.net
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I agree with what was said below by Dr. Sakumar.  Some current users of Gaussian
may remember G70 where the run was directed by a set of integers punched in
multiple 48I1 fields on route cards, or the like.  Users of current Gaussian may
not be aware of how things have progressed.  Resisting the temptation of
throwing the baby out with the bathwater should be easy.

Great progress has been made in providing stable codes for doing some basic
things with affordable ab initio methods, but I can't forget something that Mike
Zerner forwarded to me "There's nothing so semi-empirical as an ab initio
calculation," or a "lemma" that was attributed to a very prominent theoretical
chemist then an Carnegie-Mellon University, "Creativity is inversely related to
cycles available."  I find it amusing that the implication of the latter sent a
Cornell faculty member to Sweden to see the King, and that later the above
mentioned CMU professor also went....

Come on, people.. have a sense of humor..  We never had it so good..

John McKelvey

"Dr. N. SUKUMAR" wrote:

> On Wed, 12 Dec 2001 16:24:37 +0000 Pascal Boulet wrote:
>
> >  It's of course
> > easier
> > to click on a button rather than looking for command lines in the manual!
>
> >
>
> I may be part of a very rapidly dwindling paleozoic minority, but I
> actually find it easier and more intuitive to learn simple keywords (like
> HF/6-31G* or CISD) than to memorize arcane heiroglyphs (icons) for every
> single action in this world, as seems to be the fashion nowadays.
>
> >
> > Black-boxes are of course very user friendly, but in some cases it can
> > also lead to non-reproducible results.
> >
>
> ESPECIALLY when the source code is not made available for these
> "user-friendly" programs.
>
> Dr. N. Sukumar
> Rensselaer Department of Chemistry
>
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From chemistry-request@server.ccl.net Thu Dec 13 01:50:30 2001
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Date: Thu, 13 Dec 2001 01:54:59 -0500 (EST)
From: "Ha-Yeon Cheong" <hcheong@bowdoin.edu>
To: <chemistry@ccl.net>
cc: Ha-Yeon Cheong <hcheong@bowdoin.edu>,
   "Elizabeth A. Stemmler" <estemmle@bowdoin.edu>,
   Faraj Abu-Hasanayn <fabu@bowdoin.edu>
Subject: Gaussian Makefile Policy.
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Dear CCL community,

I just have a couple questions regarding this argument, if somebody would 
like to spend 2 minutes to write out the response.

1) Why bother have the source code available to the general user if 
your're not going to support 'any' variations on the makefile? NOT 
sourcecode, the makefile.
2) Is there a concern as to whether the other compilers, namely Intel 
Fortran Compilers and Absoft Fortran Compilers are not up to standard and 
prone to irregular mathematical errors? I think they'd have some very 
interesting things to say about such suggestions.
3) If as somebody mentioned, that support is something to be purchased 
> from Gaussian Inc. as a separate service, then isn't it unfair to suggest 
that nobody is allowed to help you out? Yes, there is the classic argument 
of if you can't do it, don't buy it. But rather on the contrary, because 
Gaussian98 is such a massive program, trying to figure out what went wrong 
is extremely difficult even for an experienced programmer.
4) Gaussian Inc. hasn't updated any of its specs yet. The BLAS library is 
optimized for the Pentium Pro (this library in itself hasn't been 
updated in a long time) and the recommended compiler is gcc 2.7~ up 
(regardless of the issue that gcc 2.95.3 has severe problems and that 
gcc 3.0~ gives rather slow performance). Wouldn't Gaussian and the whole 
Chemistry community benefit tremendously from a newly optimized and 
configured Makefile that uses the better ATLAS BLAS libraries and 
supposedly better performing Intel and Absoft compilers?

I don't mean to bash Gaussian. I've used Gaussian for most of my work and 
probably will continue to do so. It's as David Young puts it, "a 
monolithic" package.

But I cannot understand why Gaussian Inc. is so abjectly refusing to 
cooperate in any way. Technically speaking, Gaussian can only benefit 
> from the additional optimizations and work people do.

Yes, Gaussian Inc. gets the blame for faulty results people are getting 
> from tampered Source Code or changed Makefile. But they also get the 
recognition when it performs exceptionally or adequately. You cannot 
objectively say that Gaussian only gets the short end of the stick.

And if Gaussian Inc. truly says that they work with academic groups to 
improve their products, why isn't such things as this makefile changeover 
and additional optimizations from certain groups completely ignored or 
restricted? It seems to me that this would be the easiest thing that you 
can do to show the Chemistry and CCL community to show that you are 
indeed in this business to make money AND to satisfy customers.

I don't mean to add the fuel to the e-mail debate, but truth be told, 
there is gold mine here in store for Gaussian. And they don't even have to 
move a finger, and they're shoving it away because of past ghosts. It may 
be cheasy, but if you only consider things that can go wrong when 
programming software, you shouldn't sell it in the first place.

Yours,
Ha-Yeon Cheong

-- 
Ha-Yeon Cheong
Intern
Chemistry Department
Bowdoin College

Tel: 207-725-3840
Ext: 3840
Cell: 617-851-2825




From chemistry-request@server.ccl.net Thu Dec 13 03:11:29 2001
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From: Konrad Hinsen <hinsen@cnrs-orleans.fr>
To: chemistry@ccl.net
CC: Joe Leonard <jle@world.std.com>
Subject: Re: CCL:Gaussian revised GUI

Joe Leonard <jle@world.std.com> writes:

> I've been in this business a long time, and I've not seen terribly many
> cases where people wanted useability vs. feature improvements (either

That is partly due to filtering. Most scientific codes with a long
history are quite messy and complicated. Those who have taken the
effort to learn what needs be be learned want to profit from this
investment and use the tool as much as possible, and what they want
most of all is new features to make the tool more useful. Those who
weren't motivated enough to become experts are not users of the code
and become invisible to its developers.

> for their support money, or whatever).  Rewriting and validating code's
> a SIGNIFICANT undertaking, and not one to be taken on whim.  I've

True in principle, although developing big packages now is a lot less
painful than it was twenty years ago, due to improved development
tools. Unfortunately, scientists are largely ignoring them.

Moreover, user interfaces can be improved without necessarily
rewriting the code. Interfacing with a modern scripting language can
make an enormous difference in usability for a comparatively small
investment.

Finally, a good user interface isn't necessarily a graphical one, nor
a simple one. A good user interface is one that lets users express
their computations in terms of concepts that they are familiar with
and without arbitrary complexities (such as inconsistent syntax).
Meaningful error reporting is another important issue.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
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From chemistry-request@server.ccl.net Thu Dec 13 02:52:05 2001
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Date: Thu, 13 Dec 2001 10:02:05 +0200 (EET)
From: Ulrike Salzner <salzner@fen.Bilkent.EDU.TR>
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To: David Konerding <dek@cgl.ucsf.edu>
cc: chemistry@ccl.net
Subject: Re: CCL:somewhat obscure chemistry quote 
In-Reply-To: <200112121843.KAA353819@socrates.cgl.ucsf.edu>
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Dear David,
the quote "we can compute anything" is from Enrico Clementi, Proceedings
of the Robert A. welch Foundation Conference on Chemical Research. XXI
Theoretical Chemistry. Robert A. Welch Foundation, Houston, 1973, p. 117.

Clementi et al. published an article in Chem. Rev. 1991, 91, p. 679 where
it was shown that Hylleraas CI calculations for H3 would take 3500 CPU
years on a IBM ES/3090-J/VF computer. 

Best regards,
Uli Salzner 

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

Dr. Ulrike Salzner
Associate Professor
Department of Chemistry		Tel.: (312) 290-2122
Bilkent University		Fax.: (312) 266-5097
06533 Bilkent, Ankara 		e-mail: salzner@fen.bilkent.edu.tr
Turkey

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

On Wed, 12 Dec 2001, David Konerding wrote:

> David Konerding writes:
> >
> >I'm looking for the source of a somewhat obscure chemistry quote I once
> >came across but cannot find definitevly.  I think it was written by a 19th
> >century chemist who thought that math/computation in chemistry was wholly
> >inappropriate.  Does this ring a bell for anybody?
> 
> Excellent, I have already received three messages that gave the quote.
> This will make a great quote for my thesis, which of course, is about
> using mathematics in chemistry :-)
> 
> Now, here's a harder one.  I also once came across a pair of quotes, about
> the use of math in chemistry, where the first said somethign like
> "We can compute anything" and the response was more or less "True, but
> it will take a very long time".  Given that my simulations each took over
> 3 months to run (10ns of duplex RNA in a box of water using 4 cpus and AMBER6)
> I thought this would also be appropriate.
> 
> Dave
> 
> 
> -= This is automatically added to each message by mailing script =-
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> 
> 
> 
> 
> 
> 



From chemistry-request@server.ccl.net Thu Dec 13 04:37:50 2001
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Hello,

>
>After reading all of the posts on Gaussian and the failings (or lack
>thereof) of Gaussian Inc., I decided to do a search of Chemical Abstracts
>>... a very simple one.
>
>I searched:
>
>Gaussian		29922 citations
>ADF			 1111 citations
>MOPAC			  596 citations
>Jaguar			  378 citations
>Spartan		  215 citations
>GAMESS			  117 citations
>AMPAC			   73 citations
>AIMPRO			   17 citations
>
>I chose these as each of these is a computational chemistry (or Physics)
>program that I have used or am currently using (or hope to use).  Of
>course, I was unsurprised that Gaussian got so many citations, but I was
>surprised at the overwhelming majority toward Gaussian 


For my part, I am surprised that a Gaussian's user (or any
other ab initio package) is not surprised by this result/ratio.
AFAIK, Gaussian term don't only designate a quantum program.

Regards,
EGW.


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From chemistry-request@server.ccl.net Thu Dec 13 09:22:16 2001
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Subject: Re: CCL:QSAR - somewhat obscure chemistry quote
In-Reply-To: <5.1.0.14.2.20011212103735.02820120@sparky2.sd.accelrys.com
 >
References: <5.1.0.14.2.20011212102031.027d3790@sparky2.sd.accelrys.com >
 <200112121757.JAA349457@socrates.cgl.ucsf.edu>
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"; format=flowed

At 10:39 AM 12/12/01 -0800, Osman F. Guner wrote:
>My all time favorite quote is actually from Niels Bohr, I think:
>
>"Prediction is very difficult... especially about the future."
>

Has not this quote been attributed to Yogi Berra as well?


********************************************************
Anthony J. Duben
Professor and Chairman
Computer Science Dept., MS 5950
Southeast Missouri State University
1 University Plaza
Cape Girardeau MO 63701-4799
phone:  573-651-2194
fax:         573-651-2791
e-mail: ajduben@semovm.semo.edu
   or        c867buc@semovm.semo.edu

"Education: That which reveals to the wise, and conceals from the
stupid, the vast limits of their knowledge." - Mark Twain

"If we knew what it was we were doing, it would not be called
  research, would it?" -- Albert Einstein


From chemistry-request@server.ccl.net Thu Dec 13 11:52:23 2001
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Date: Thu, 13 Dec 2001 08:51:04 -0800
To: chemistry@ccl.net
From: Eric Scerri <scerri@chem.ucla.edu>
Subject: somewhat obscure chemistry quote
Content-Type: multipart/alternative; boundary="============_-1203860228==_ma============"

--============_-1203860228==_ma============
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

I think the quote you are looking for is the following statement by the
French philosopher A. Comte (1838):
   Every attempt to employ mathematical methods in the study of chemical
questions must be considered profoundly irrational. If mathematical
analysis should ever hold a promiment place in chemistry  - an
aberration
which is happily impossible - it would occasion a rapid and widespread
degradation
of that science.

All the best,
     Trond SAUE

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

Whereas the German philosopher, Kant, believed that chemistry was not 
a proper science because it was not sufficiently mathematical in his 
time!

regards,
eric scerri
-- 

Dr. Eric Scerri ,
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri@chem.ucla.edu
tel:  310 206 7443
fax:  310 206 2061
Web Page:    http://www.chem.ucla.edu/dept/Faculty/scerri/index.html

Editor  of  Foundations of Chemistry
http://www.wkap.nl/journalhome.htm/1386-4238

Also see International Society for the Philosophy of Chemistry
http://www.georgetown.edu/earleyj/ISPC.html
--============_-1203860228==_ma============
Content-Type: text/html; charset="us-ascii"

<!doctype html public "-//W3C//DTD W3 HTML//EN">
<html><head><style type="text/css"><!--
blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 }
 --></style><title>somewhat obscure chemistry
quote</title></head><body>
<div>I think the quote you are looking for is the following statement
by the<br>
French philosopher A. Comte (1838):<br>
&nbsp; Every attempt to employ mathematical methods in the study of
chemical<br>
questions must be considered profoundly irrational. If
mathematical<br>
analysis should ever hold a promiment place in chemistry&nbsp; -
an<br>
aberration<br>
which is happily impossible - it would occasion a rapid and
widespread<br>
degradation<br>
of that science.<br>
<br>
All the best,</div>
<div>&nbsp;&nbsp;&nbsp; Trond SAUE</div>
<div><br></div>
<div>--------------------</div>
<div><br></div>
<div>Whereas the German philosopher, Kant, believed that chemistry
was<b> not a proper science</b> because it was not sufficiently
mathematical in his time!</div>
<div><br></div>
<div>regards,</div>
<div>eric scerri</div>
<x-sigsep><pre>-- 
</pre></x-sigsep>
<div><br>
Dr. Eric Scerri ,<br>
UCLA,<br>
Department of Chemistry &amp; Biochemistry,<br>
607 Charles E. Young Drive East,<br>
Los Angeles,&nbsp; CA 90095-1569<br>
USA<br>
<br>
E-mail :&nbsp;&nbsp; scerri@chem.ucla.edu<br>
tel:&nbsp; 310 206 7443<br>
fax:&nbsp; 310 206 2061<br>
Web Page:&nbsp;&nbsp;&nbsp;
http://www.chem.ucla.edu/dept/Faculty/scerri/index.html<br>
<br>
Editor&nbsp; of&nbsp; Foundations of Chemistry<br>
http://www.wkap.nl/journalhome.htm/1386-4238<br>
<br>
Also see International Society for the Philosophy of Chemistry<br>
http://www.georgetown.edu/earleyj/ISPC.html</div>
</body>
</html>
--============_-1203860228==_ma============--

From chemistry-request@server.ccl.net Thu Dec 13 12:44:55 2001
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From: "Phillip Matz" <matz@wsunix.wsu.edu>
To: "Dillen J, Prof" <JLMD@sun.ac.za>, <chemistry@ccl.net>
Subject: RE: Gaussian revised GUI
Date: Thu, 13 Dec 2001 09:44:31 -0800
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Regarding the discussion if a GUI for Gaussian98, what about:

1) G98client available in Chem3D Ultra 5.0 and 6.0 from Cambridgesoft (works
with G98W)
2) Molden 3.7 from Gijs Schaftenaar at the Centre for Molecular and
Biomolecular Informatics (free, works with G98 in linux)
3) GaussView available from Gaussian, Inc.

I haven't used GaussView yet, but the G98W interface provided Chem3D is
pretty easy to use (can run gaussian jobs from Chem3D or by exporting the
G98 input job for you to run manually).  If the linux version is your flavor
of the decade then you can try the Molden 3.7 package which provides a GUI
to G98 as well (and is free to download and try).

Regards,

Phil Matz


-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On
Behalf Of Dillen J, Prof
Sent: Wednesday, December 12, 2001 9:14 PM
To: 'chemistry@ccl.net'
Subject: CCL:Gaussian revised GUI



> Who's willing to pay Gaussian, Inc. to rewrite their code ...

Considering the long computational times involved in running
a QM job, any good GUI will have to offer the alternative
of running a calculation in the background. This implies that
all the button clicks and check boxes are somehow translated
into commands/keywords and written to a file. If the original
keyword syntax works, I see no reason why it should be redesigned
and/or rewritten. Besides, a GUI that offers scripting will
have to fall back to the old keyword driven operation.

> It would not surprise me if doing the GUI (or API) is harder
> work than getting the algebra of the QM code "right", too.

In contrast to the writing of QM code which is done after "it works",
designing a GUI is a never-ending operation. See Microsoft: every
version of Word looks different. Obviously, part of these changes
are done to keep the interest in their development tools high,
but a lot of the changes are intended to improve ease of use.
In a sence, Microsoft has an easy job because they only support
Windows. Designing a GUI that will work for all the platforms
currently supported by Gaussian will not be an easy task.

Jan Dillen

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Date: Thu, 13 Dec 2001 15:05:34 -0500 (EST)
From: Jay Ho <jayho@zopyros.ccqc.uga.edu>
To: chemistry@ccl.net
Subject: reading output and drawing program
In-Reply-To: <5.1.0.14.0.20011213082717.044c3d60@semovm.semo.edu>
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	Hello,


	Does anyone know any program that can read atomic charges from
gaussian output, then atomatically put it into chemdraw program (into
figure) ???



thanks,


jay.




____________________________________________________
Chaeho Pak                                                               
Center for Computational Quantum Chemistry
University of Georgia
Athens, GA 30602-2556                
Phone: (706) 542-7738        
Fax: (706) 542-0406                
E-mail: jayho@ccqc.uga.edu                                                 
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----------------------------------------------------

"One thought driven home is better than three left on base."

James Liter      



From chemistry-request@server.ccl.net Thu Dec 13 09:33:46 2001
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Could some kind soul e-mail me off-list with the workaround
to get g98 to compile with the intel fortran compiler?
Ironically, I am trying to compile on a dual athlon!
It would be very much appreciated and of course kept confidential.
Thanks in advance.
	Dave

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

Dr. David W. Price MA CChem MRSC      Tel: +44 (0)118 9875123  extn
7415
Department of Chemistry,              Fax: +44 (0)118 9316331
University of Reading,                mailto:d.w.price@reading.ac.uk
Whiteknights, 
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RG6 6AD 
U.K.
 
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From chemistry-request@server.ccl.net Thu Dec 13 15:10:40 2001
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Subject: Re: CCL:Gaussian revised GUI
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WebMO is another excellent computational chemistry GUI.  It is available 
for free at
                    www.webmo.net

WebMO is an entirely web-based interface to popular computational chemistry 
programs.  In addition to Gaussian, it supports MOPAC and GAMESS.

You can conveniently try out the WebMO Working Demo from the above website 
without actually having to install it on your system!  The above website 
also has a good amount of linux and computational chemistry general support 
material .

Some specific follow-ups to previous comments are:

At 03:22 PM 12/12/01, Joe Leonard wrote:
>FWIW, I've not seen anybody redoing MOPAC's GUI, or any other dusty-deck 
>codes.

WebMO is a modern GUI for MOPAC.

At 09:13 PM 12/12/01, Prof J Dillen wrote:
>Designing a GUI that will work for all the platforms currently supported 
>by Gaussian will not be an easy task.

Since WebMO is web-based, it overcomes the platform-dependence of the 
underlying computational chemistry code.  All the user needs is a 
web-browser on his/her desktop computer, irrespective of the platform 
actually running the computational chemistry code.

Also, although the most common method of installing WebMO is on a computer 
that has both the computational chemistry engine and a web-server, WebMO 
supports accessing computational chemistry code on other machines.  Thus 
one instance of WebMO can serve to integrate multiple codes running on 
multiple platforms.

At 09:44 AM 12/13/01, Phillip Matz wrote:
>Regarding the discussion if a GUI for Gaussian98, what about:
>1) G98client available in Chem3D Ultra 5.0 and 6.0 from Cambridgesoft (works
>with G98W)
>2) Molden 3.7 from Gijs Schaftenaar at the Centre for Molecular and
>Biomolecular Informatics (free, works with G98 in linux)
>3) GaussView available from Gaussian, Inc.

4) WebMO 3.1 from www.webmo.net (free, works with any unix flavor, e.g., 
linux, IRIX, AIX, etc.)

Will Polik
polik@hope.edu
Professor of Chemistry
Hope College






From chemistry-request@server.ccl.net Thu Dec 13 12:08:38 2001
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Date: Thu, 13 Dec 2001 12:07:12 -0500
From: "Shobe, Dave" <dshobe@sud-chemieinc.com>
Subject: RE: Gaussian and search strategies
To: "'CCL'" <chemistry@ccl.net>,
   "'engel@netcourrier.com'" <engel@netcourrier.com>,
   "'rwz7001@humboldt.edu'" <rwz7001@humboldt.edu>
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A "normal" Chemical Abstracts search is probably not best here, since the
program is probably mentioned in the computational details section, but not
necessarily in the title or abstract.  And you have the problem implied
below that "Gaussian" can also refer to a curve or probability distribution,
as well as to the program.  "Jaguar" and "Spartan" (and probably "ADF") have
this problem to some extent, although the additional meanings won't be as
likely to occur in the chemical literature.

However, you could do a citation search looking for the mandatory citation
that Gaussian and some other program licenses require be included whenever
computational results from the program are published.  

--David Shobe
Süd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  dshobe@sud-chemieinc.com

Don't bother flaming me: I'm behind a firewall.



-----Original Message-----
From: engel@netcourrier.com [mailto:engel@netcourrier.com]
Sent: Thursday, December 13, 2001 4:37 AM
To: rwz7001@humboldt.edu
Cc: CHEMISTRY@ccl.net
Subject: CCL:Gaussian



Hello,

>
>After reading all of the posts on Gaussian and the failings (or lack
>thereof) of Gaussian Inc., I decided to do a search of Chemical Abstracts
>>... a very simple one.
>
>I searched:
>
>Gaussian		29922 citations
>ADF			 1111 citations
>MOPAC			  596 citations
>Jaguar			  378 citations
>Spartan		  215 citations
>GAMESS			  117 citations
>AMPAC			   73 citations
>AIMPRO			   17 citations
>
>I chose these as each of these is a computational chemistry (or Physics)
>program that I have used or am currently using (or hope to use).  Of
>course, I was unsurprised that Gaussian got so many citations, but I was
>surprised at the overwhelming majority toward Gaussian 


For my part, I am surprised that a Gaussian's user (or any
other ab initio package) is not surprised by this result/ratio.
AFAIK, Gaussian term don't only designate a quantum program.

Regards,
EGW.


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Date: Thu, 13 Dec 2001 10:01:05 -0500 (EST)
From: William D Hobey <whobey@WPI.EDU>
To: chemistry@ccl.net
cc: stevejw@WPI.EDU
Subject: Re: CCL:somewhat obscure chemistry quote (fwd)
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I passed the quotes from Guner on to Steve Weininger, our local guru in
the history of chemistry. Here is his replies condensed from two emails.
						Wm. D. Hobey


Bill,

The author of the first quote (I'm not familiar with either) is Auguste
Comte (NOT Compte), a very famous philosopher and the founder of
positivism. There's been a lot written about Comte's views on science,
including his views on chemistry, although I don't know that literature
well at all, and writers who do have divergent ideas about what Comte
meant.

Quetelet was apparently an important mathematician; here's a URL with some
info:
http://www.mrs.umn.edu/~sungurea/introstat/history/w98/Quetelet.html

Steve

       ************************************************************
       Stephen J. Weininger		  Internet: stevejw@wpi.edu
       Professor of Chemistry		  Phone: (508) 831-5396
       WPI				  Fax:   (508) 831-5933
       Worcester, MA 01609-2280
       Director, WPI Bangkok Project Center
       ************************************************************



> ---------- Forwarded message ----------
> Date: Wed, 12 Dec 2001 10:29:45 -0800
> From: Osman F. Guner <osman@accelrys.com>
> To: David Konerding <dek@cgl.ucsf.edu>, chemistry@ccl.net
> Cc: qsar_society@accelrys.com
> Subject: CCL:somewhat obscure chemistry quote
>
>
> "Every attempt to employ mathematical methods in the study of chemical
> questions must be considered profoundly irrational and contrary to the
> spirit of chemistry.  If mathematical analysis should ever hold a prominent
> place in chemistry --an aberration which is happily almost impossible-- it
> would occasion a rapid and widespread degeneration of that science."
> A. Compte, 1798-1857
>
> There are some positive quotes from the same time period as well:
>
> "The more progress physical sciences make, the more they tend to enter the
> domain of mathematics, which is a kind of centre to which they all
> converge.  We may even judge the degree of perfection to which a science
> has arrived by the facility with which it may be submitted to calculation."
> A. Quetelet, 1796-1874
>
> Unfortunately, I have misplaced the actual references.  Hope this helps...Osman
>
> At 09:57 AM 12/12/2001, David Konerding wrote:
>
> >I'm looking for the source of a somewhat obscure chemistry quote I once
> >came across but cannot find definitevly.  I think it was written by a 19th
> >century chemist who thought that math/computation in chemistry was wholly
> >inappropriate.  Does this ring a bell for anybody?
> >
> >Thanks.
> >-----------------------------------------------------------------------------
> >David Konerding
> >Email: dek@cgl.ucsf.edu
> >WWW: http://www.cgl.ucsf.edu/home/dek
> >-----------------------------------------------------------------------------
> >
> >
>
> ---
> Osman F. Güner, Ph.D.
> Director,  Lead Identification & Optimization
> Accelrys Inc.   (858) 799-5341
> osman@accelrys.com        http://www.accelrys.com
>
>
>
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>
>
>
>
>




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Date: Thu, 13 Dec 2001 21:58:31 +0100 (CET)
From: David van der Spoel <spoel@xray.bmc.uu.se>
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To: chemistry@ccl.net
Subject: Re: CCL:g98 wishlist (was: Gaussian 98 makefile policy)
In-Reply-To: <200112122123.QAA05160@svega.gaussian.com>
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I would like to change the direction of the great Gaussian makefile
flamewar, and turn it into a wish list...

The fact is that building Gaussian is unneccarily complex (in my opinion).
If you have the slightest deviation in your system include files the
program does not compile. Moreover the progam compiles everything from
scratch all the time, making it very tedious to fix small things.

We should respect Gaussian if they basically refuse to support
unsupported hardware and/or compilers. But Gaussian should not (want to)
take responsibilty for the correctness of the calculations, this is the
responsibility of the user. That is why users need the source code of the
programs they are running. 

This is my wish list:
- easier compilation of Gaussian, making it easier to port to other
  hardware and or compilers, or different linear algebra libraries.
  When I say easier compilation I mean gnu autoconf (and while we're
  at it, throw out the messy fsplit operations, just plain source files
  and a Makefile).
- a comprehensive test system, so that users can verify their compilation

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel@xray.bmc.uu.se	spoel@gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From chemistry-request@server.ccl.net Thu Dec 13 19:12:29 2001
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Message-Id: <200112140012.QAA00599@canter-n-siegel.schrodinger.com>
Subject: Schrodinger Announces QSite 1.8
To: chemistry@ccl.net
Date: Thu, 13 Dec 2001 16:12:04 -0800 (PST)
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Schrodinger is pleased to announce the latest release of QSite, a mixed 
Quantum Mechanics/Molecular Mechanics (QM/MM) package specially tuned 
for studying reactive chemistry in large biological systems.  QSite allows 
highly accurate studies of protein-ligand interactions including 
hydrogen-bonding, proton-transfer, charge-transfer reactions, metal-ligand 
binding and metalloenzyme catalysis.

Hybrid QM/MM takes advantage of the best of both worlds - the accuracy of 
quantum mechanics and the efficiency of molecular mechanics.  In QSite, the 
molecular mechanics calculations are performed using the OPLS-AA force field, 
generally acknowledged to be the most reliable for treating medicinally 
relevant compounds and proteins.  The critical region is treated quantum 
mechanically using the highest-performance ab initio program, Jaguar.  
Additionally, QSite benefits from Jaguar's unique initial guess algorithm 
that ensures convergence to the correct electronic ground state for 
metal-containing systems.  QSite is able to perform full geometry 
optimizations and incorporate solvation effects using continuum dielectric 
methods.

Please visit http://www.schrodinger.com or contact info@schrodinger.com 
to learn more about QSite.


From chemistry-request@server.ccl.net Thu Dec 13 17:12:18 2001
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From: "Dr. Daniel Glossman-Mitnik" <daniel.glossman@cimav.edu.mx>
To: "Computational Chemistry List" <CHEMISTRY@ccl.net>
Subject: G98 compilation problems on LINUX
Date: Thu, 13 Dec 2001 15:10:30 -0800
Organization: CIMAV - LAQUICOM
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Dear netters:

I am trying to compile the g98 source code (rev A9) on a Pentium 3
800 running  Redhat 7.2. I have installed the Portland Group f77
compiler and I have put the blas-f2c.a and blas-opt.a files in
/usr/local/lib.
The compilation seems to run fine up to a point where it bombs. As I
have no previous experience I don´t know what the messages mean
and thus what action to follow.

I including the last lines of the bldg98.log file.  Any help would be
appreciated.

Thanks in advance. Best regards


                                                   Dr. Daniel
Glossman-Mitnik


....
set noglob
end
unset noglob
cd ..
rm -f -r temputil
fixlib util.a
endif
if ( 1 ) then
make -f bsd/g98.make JUNK1=JUNK exe
gau-cpp -I/root/g98 -I/root/g98s -DGAUSS_PAR -DGAUSS_THPAR  -DDEFMAXSHL=2000
0 -DDEFMAXATM=20000 -DDEFMAXNZ=20000 -DDEFNVDIM=257 -DDEFARCREC=1024 -DMERGE
_LOOPS -DUSE_ESSL -D_I386_ -DLITTLE_END -DUSING_F2C -DDEFMAXIOP=100 -DDEFMAX
CHR=1024 -DDEFLMAX=13 -DDEFN3MIN=10 -DDEFMAXHEV=2000 -DDEFCACHE=64 -DDEFMAXL
ECP=10 -DDEFMAXFUNIT=5 -DDEFMAXFFILE=10000 -DDEFMAXFPS=1300 -DDEFMAXINFO=200
 -DDEFMAXOP=120 -DDEFMAXTIT=100 -DDEFMAXRTE=4000 -DDEFMAXOV=500 -D_ALIGN_COR
E_ -DCA1_DGEMM -DCA2_DGEMM -DCAB_DGEMM -DLV_DSP -DO_BKSPEF -DDEFMXTS=1500 -D
DEFMXBAS=500 -DDEFMXOPT=50 -DDEFMXBOND=12 -DDEFMXSPH=250 -DDEFMXINV=1500
dummy.F dummy.f
pgf77    -O2 -tp p6  -Munroll -Mvect=cachesize:524288 -c dummy.f
NOTE: your evaluation license will expire in 13 days, 23.9 hours.
For a permanent license, please read the order acknowledgement
that you received.  Connect to https://www.pgroup.com/License with
the username and password in the order acknowledgement.

 Name: "Dr. Daniel Glossman-Mitnik"
 User: glossman
 Email: daniel.glossman@cimav.edu.mx
 Hostid: PGI=000103E0CCC6B0F71B198A
rm -f dummy.f dummy.c
ld -shared -o util.so dummy.o --whole-archive util.a \
  --no-whole-archive /usr/local/lib/blas-opt.a /usr/local/lib/blas-f2c.a
gau-fsplit -e ml0 bsd/main.F
ml0.F already exists, over-written
make -f bsd/g98.make OPTFLAG=' -O2 -tp p6  -Munroll -Mvect=cachesize:524288'
ml0.o
make[1]: Entering directory `/root/g98'
gau-cpp -I/root/g98 -I/root/g98s -DGAUSS_PAR -DGAUSS_THPAR  -DDEFMAXSHL=2000
0 -DDEFMAXATM=20000 -DDEFMAXNZ=20000 -DDEFNVDIM=257 -DDEFARCREC=1024 -DMERGE
_LOOPS -DUSE_ESSL -D_I386_ -DLITTLE_END -DUSING_F2C -DDEFMAXIOP=100 -DDEFMAX
CHR=1024 -DDEFLMAX=13 -DDEFN3MIN=10 -DDEFMAXHEV=2000 -DDEFCACHE=64 -DDEFMAXL
ECP=10 -DDEFMAXFUNIT=5 -DDEFMAXFFILE=10000 -DDEFMAXFPS=1300 -DDEFMAXINFO=200
 -DDEFMAXOP=120 -DDEFMAXTIT=100 -DDEFMAXRTE=4000 -DDEFMAXOV=500 -D_ALIGN_COR
E_ -DCA1_DGEMM -DCA2_DGEMM -DCAB_DGEMM -DLV_DSP -DO_BKSPEF -DDEFMXTS=1500 -D
DEFMXBAS=500 -DDEFMXOPT=50 -DDEFMXBOND=12 -DDEFMXSPH=250 -DDEFMXINV=1500
ml0.F ml0.f
pgf77   -O2 -tp p6  -Munroll -Mvect=cachesize:524288 -c ml0.f
NOTE: your evaluation license will expire in 13 days, 23.9 hours.
For a permanent license, please read the order acknowledgement
that you received.  Connect to https://www.pgroup.com/License with
the username and password in the order acknowledgement.

 Name: "Dr. Daniel Glossman-Mitnik"
 User: glossman
 Email: daniel.glossman@cimav.edu.mx
 Hostid: PGI=000103E0CCC6B0F71B198A
rm -f ml0.f ml0.c
make[1]: Leaving directory `/root/g98'
pgf77    -O2 -tp p6  -Munroll -Mvect=cachesize:524288 -o g98 ml0.o   util.so
ml0.o: In function `MAIN_':
ml0.o(.text+0x296): undefined reference to `gauabt_'
ml0.o(.text+0x330): undefined reference to `gauabt_'
ml0.o(.text+0x402): undefined reference to `gauabt_'
ml0.o(.text+0x4dc): undefined reference to `gauabt_'
ml0.o(.text+0x619): undefined reference to `gauabt_'
ml0.o(.text+0x63c): undefined reference to `fixinout_'
ml0.o(.text+0xe47): undefined reference to `ggeten_'
ml0.o(.text+0xea8): undefined reference to `getexen_'
ml0.o(.text+0x112c): undefined reference to `gsyst_'
util.so: undefined reference to `writwa_'
util.so: undefined reference to `closwa_'
util.so: undefined reference to `asynwa_'
util.so: undefined reference to `erfcx_'
util.so: undefined reference to `bkimov_'
util.so: undefined reference to `fixstdin_'
util.so: undefined reference to `gaufls_'
util.so: undefined reference to `fixenv_'
util.so: undefined reference to `ifalph_'
util.so: undefined reference to `ntrsiz_'
util.so: undefined reference to `guname_'
util.so: undefined reference to `openwa_'
util.so: undefined reference to `envfil_'
util.so: undefined reference to `ibkmov_'
util.so: undefined reference to `imove_'
util.so: undefined reference to `amove_'
util.so: undefined reference to `gfree_'
util.so: undefined reference to `gauexec_'
util.so: undefined reference to `readwa_'
util.so: undefined reference to `machin_'
util.so: undefined reference to `galloc_'
util.so: undefined reference to `ntrbks_'
util.so: undefined reference to `bkmove_'
util.so: undefined reference to `appfpd_'
util.so: undefined reference to `gfree1_'
util.so: undefined reference to `waitwa_'
util.so: undefined reference to `ntrext1_'
util.so: undefined reference to `intchr_'
util.so: undefined reference to `gferr_'
util.so: undefined reference to `getscm_'
util.so: undefined reference to `gsr48_'
util.so: undefined reference to `galloc1_'
util.so: undefined reference to `drand48_'
util.so: undefined reference to `appfp_'
make: *** [g98] Error 1
endif


**************************************************************************
Dr. Daniel Glossman-Mitnik
Centro de Investigacion en Materiales Avanzados (CIMAV)
LAQUICOM - Laboratorio de Química Computacional
Miguel de Cervantes 120  -  Complejo Industrial Chihuahua
Chihuahua, Chih. 31109   -   Mexico
Phone: (52) 614 4391151      FAX: (52) 614 4391112
E-mail: daniel.glossman@cimav.edu.mx
            glossman@hotmail.com
            dglossman@yahoo.com
**************************************************************************




From chemistry-request@server.ccl.net Thu Dec 13 17:00:34 2001
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Date: Thu, 13 Dec 2001 14:00:10 -0800 (PST)
From: Fred Salsbury <salsb@scripps.edu>
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> 
> However, you could do a citation search looking for the mandatory citation
> that Gaussian and some other program licenses require be included whenever
> computational results from the program are published.  

Just for kicks I did this on the web of science using the "cited work"
option. Added up the citations and found suprisingly few  citations, which
suggest that many people fail to include the citation as required, or else
the citation indexes don't do a good job of treating citations for 
programs.

Gaussian 237
GAMESS 62
Spartan 49
MOPAC 44
Q-Chem 26
ADF 21
jaguar 11
AMPAC 10

cheers
Fred Salsbury


> >After reading all of the posts on Gaussian and the failings (or lack
> >thereof) of Gaussian Inc., I decided to do a search of Chemical Abstracts
> >>... a very simple one.
> >
> >I searched:
> >
> >Gaussian		29922 citations
> >ADF			 1111 citations
> >MOPAC			  596 citations
> >Jaguar			  378 citations
> >Spartan		  215 citations
> >GAMESS			  117 citations
> >AMPAC			   73 citations
> >AIMPRO			   17 citations
> >
> >I chose these as each of these is a computational chemistry (or Physics)
> >program that I have used or am currently using (or hope to use).  Of
> >course, I was unsurprised that Gaussian got so many citations, but I was
> >surprised at the overwhelming majority toward Gaussian 
> 
> 
> For my part, I am surprised that a Gaussian's user (or any
> other ab initio package) is not surprised by this result/ratio.
> AFAIK, Gaussian term don't only designate a quantum program.
> 
> Regards,
> EGW.
> 
> 
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