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From: "Victor Anisimov" <victor@fqspl.com.pl>
To: <chemistry@ccl.net>
Subject: Re: CCL:MOPAC2000 and MOLZYME
Date: Fri, 6 Aug 1999 09:36:11 +0200
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Deepak Singh wrote:

>Does anyone have experience with the MOLZYME module of MOPAC2000.  We
>have been running it of a DELL XPS-T500 and it requires a LOT of memory
>for minimizing a 28 kDa protein.  Does anyone have a memory requirement
>for something like a SGI Octane?
>


SGI Octane does not bring special memory benefits for MOPAC2000 jobs comparing
with other hardware/software platforms. And the solution is to specify BFGS
keyword.

Single point calculation in MOPAC2000 (MOZYME) requires unbelievably small
memory
even for huge size proteins (5000 atoms - 500Mb) but gradient optimization needs
more
memory. Default optimization method is EF which is very memory consuming one.
Usually it
requires 10-20 times more memory than single point calculation. BFGS is 5 times
less
memory demanding one and usually it is the best for very large molecules in
MOPAC2000
(MOZYME).

Hope, it helps.
Victor.

=========================================================================
Victor Anisimov, PhD, Software Researcher - Computational Chemistry
FQS Poland, Palac Pugetow, ul. Starowislna 13-15, 31-038 Krakow, Poland
Email: victor@fqspl.com.pl  Tel.(+48 12) 429 4345  Fax(+48 12) 429 6124
=========================================================================



From chemistry-request@server.ccl.net  Fri Aug  6 10:40:32 1999
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From: Denys Bashtovyy <bashtovyy@yahoo.com>
Reply-To: basht@iname.com
Subject: [Announce] www.MolBio.org -- New Biology Portal
To: chemistry@ccl.net
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From: Alan Williams <Alan@MolBio.org>

Subject: [Announce] www.MolBio.org -- New Biology Portal

Date: 04 Aug 1999 16:13:21 GMT


There is a new web portal for all things related to molecular biology
and 
bioinformatics (including the related fields of cell biology,
biochemistry,
genetics, genomics, XXX). Currently www.MolBio.org provides a news 
service where the web community can post information related to 
molecular biology (et al.) and bioinformatics. In addition to the news
service, www.MolBio.org provides spam free discussion groups. 

Do you have information to share such as:
- Conference - Press Release
- Course - Protocol
- News Bite - Software
- Research Finding - Tip
- Database - Web Site
- FTP Site - Web Based Program/Tool
- Mailing List - Other
Related to the fields of:
- Biochemistry - Biotechnology/Biotech
- Cell Biology - Computational Biology
- Genetics - Genomics
- Molecular Biology - Other

Then please submit it to www.MolBio.org via the news form at
http://www.molbio.org/postnews.cgi. The more info you post, the
more useful www.MolBio.org will be. The information you post
doesn't need to originate from yourself -- it can be anything
you come across in searching the web, reading a journal, 
browsing bionet, etc... If in doubt, post it!

If you have any questions, comments, or requests -- feel free to 
contact me at Alan@MolBio.org.

Thanks,
Alan Williams
www.MolBio.org 

ps -- www.MolBio.org is loosly setup as a slashdot (www.slashdot.org) 
for biology.

Follow-ups have been directed to bionet.general

I seem to be having problems with UCR's news server, so my 
apologies if multiple posts show up.

************************************************************************

Alan Williams 
------------------------------------------------------------------------

University of California, Riverside "Where observation is concerned,
Dept. of Botany and Plant Sciences chance favors the prepared mind." 
Alan@MolBio.org -- Louis Pasteur
************************************************************************


_____________________________________________________________
Do You Yahoo!?
Free instant messaging and more at http://messenger.yahoo.com

From chemistry-request@server.ccl.net  Fri Aug  6 04:01:25 1999
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Date: Fri, 06 Aug 1999 09:54:07 +0200
From: Christoph Steinbeck <steinbeck@ice.mpg.de>
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Organization: Max-Planck-Institute of Chemical Ecology
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To: Laura Andersson <lauraa@bbcc.ctc.edu>, ccl <chemistry@www.ccl.net>
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I have never send a mail to you personally, nor are you in my address
book. 
If you received the JChemPaint announcement, then it is due to your
subscription of either the ChemInf mailing list
(CHMINF-L@LISTSERV.INDIANA.EDU) or the computational chemistry list
(chemistry@www.ccl.net)
Since no one gets subscribed to these academic, non-profit lists just by
doing nothing, you yourself must be responsible for being on the list.
You must also have received detailed instructions on how to unsubscribe
>from these lists in the first welcome message after you subscribed. 

Sincerely, 

Christoph Steinbeck

--
Dr. Christoph Steinbeck (http://www.ice.mpg.de/~stein)
MPI of Chemical Ecology, Tatzendpromenade 1a, 07745 Jena, Germany
Tel: +49(0)3641 643644 - Mobile: +49(0)177 8236510 - Fax: +49(0)3641
643665

What is man but that lofty spirit - that sense of enterprise. 
... Kirk, "I, Mudd," stardate 4513.3..




Laura Andersson wrote:
> 
> Please remove me from your mailings.
> 
> Laura Andersson, Ph.D.
> Big Bend Community College
> 7662 Chanute Street
> Moses Lake, WA 98837
> 
> 509-762-6268
> email: lauraa@bbcc.ctc.edu
> 
> -----Original Message-----
> From:   Christoph Steinbeck (by way of FLGRABOWSKA@vassar.edu (Flora
> Grabowska)) [mailto:steinbeck@ICE.MPG.DE]
> Sent:   Tuesday, August 03, 1999 12:48 PM
> To:     flgrabowska@vassar.edu
> Subject:        ANNOUNCE: JChemPaint 0.4
> 
> I'd like to announce the release of JChemPaint v0.4
> 
> JChemPaint is a Java program for drawing 2D chemical structures like
> those found in most chemistry textbooks. Its GUI is based on the Swing
> tool kit. The program is developed as an Open Source
> Project and released under GNU General Public License. The code should
> be considered pre-alpha quality, but there are enough features
> implemented to get an idea about where the program development
> is heading.
> 
> JChemPaint development is coordinated by Christoph Steinbeck and his
> Chemical Information group (http://www.ice.mpg.de/departments/ChemInf)
> at the Max Planck Instiutute of Chemical Ecology
> (http://www.ice.mpg.de).
> 
> Version 0.4 now features one-click condensation of rings using
> predefined templates.
> 
> The program currently supports:
> 
> 1. A subset of the regular drawing features of commercial programs, as
> there are
>     - drawing of single, double and triple bonds (no stereo descriptors
> yet).
>     - deletion of bonds and atoms
>     - one-click drawing of ring templates (3-8)
>     - one-click attachment of rings to an atom or a bond (spiro
> attachment and ring condensation).
> 2. Loading and saving of structures as MDL Molfiles and in Chemical
> Markup Language (CML).
> 3. Automated Structure Layout, aka Structure Diagram Generation.
> 
> More information as well as a download option can be found on
> http://www.ice.mpg.de/~stein/projects/JChemPaint/
> 
> People a sought to join the development of JChemPaint.
> 
> JChemPaint is associated with the OpenScience project
> (www.openscience.org) and the 3D molecular viewer JMol
> (http://www.openscience.org/jmol/), both initiated by Dan Gezelter at
> Columbia University (http://www.chem.columbia.edu/~gezelter/).
> 
> I'd be happy to get some feedback from people who have downloaded the
> program and got it up and running.
> 
> Cheers,
> 
> Chris
> 
> --
> Dr. Christoph Steinbeck (http://www.ice.mpg.de/~stein)
> MPI of Chemical Ecology, Tatzendpromenade 1a, 07745 Jena, Germany
> Tel: +49(0)3641 643644 - Mobile: +49(0)177 8236510 - Fax: +49(0)3641
> 643665
> 
> What is man but that lofty spirit - that sense of enterprise.
> ... Kirk, "I, Mudd," stardate 4513.3..
> 
> bcc: chemo
From chemistry-request@server.ccl.net  Fri Aug  6 04:48:34 1999
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A colleague, who subscribes, received this missive a couple of days ago.
It would be a shame to see what is close to a venerable institution vanish.

INDIANA UNIVERSTTY

July 1,1999

DEPARTMENT OF CHEMISTRY

Dear QCPE Member:                        .  .      . 

It is with mixed feelings that I must inform you that Richard Counts, who
has been the Director of the Quantum Chemistry Program Exchange (QCPE) for
nearly 25 years, will retire on July 31, 1999.

Since Richard has been the driving force behind QCPE for so many years, his
departure will necessitate a number of changes in the operation of this
service. I am evaluating several options related to the future management
and operation of QCPE. We hope to be able to provide you with services
somewhat similar to those previously available, but possibly in a webbased
Internet environment. I welcome your suggestions and thoughts on what you,
as a customer, consider appropriate and desirable. Information on changes
or temporary suspension of services will be available to customers on the
QCPE Web site at qcpe5.chem.indiana.edu

Richard has requested that there be no formal acknowledgement of his
retirement, but I'm sure that he would appreciate hearing from you as he
makes this transition.

Gary M. Hieftje

Distinguished Professor and Chairman

/jr

  CHAIRMAN'S OFFICE

Chemistry Building C125 
800 E. KirkwoodAve. 
Bloomington, Indiana 474054001

8128556239 
Fax: 8128565050 Internet:
cemchair@indiana.edu




__________________________________________________________________
Stephen P. Molnar, Ph.D.						Life is a fuzzy set
Foundation for Chemistry						Stochastic and multivariant
http://web.jadeinc.com/FoundationChem
From chemistry-request@server.ccl.net  Fri Aug  6 12:14:16 1999
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Subject: Beautify geometry: clarification
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Based on the responses, I need to clarify my earlier posting on beautifying
geometry.

I'm working on a rule-based clean geometry for coordinates in 3D.
It's a tricky problem to generalize for ring systems.

I was hoping to tap the collective experience of the CCL for pointers to 
work done by others which I could study.

All of my responses thus far pointed to a very interesting sounding chapter
by Harold  Helson (see below), which I will examine.

>
>if you are interested in 2D coordinates, there is an excellent
>article in the recent volume of Reviews in Computational
>Chemistry by Harold E. Helson: "Structure Diagram Generation", pp
>313-398.
>
>Markus
>




From chemistry-request@server.ccl.net  Fri Aug  6 12:24:54 1999
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Date: Fri, 6 Aug 1999 11:31:22 +36000
From: Richard Wood <dmpc@hugh.chem.uic.edu>
To: computational chemistry list <chemistry@ccl.net>
Subject: A software question
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Hi all
   Since just about everyone else does it, I will join the bunch :).  I 
am wondering if anyone can point me to a program that will calculate, 
given the coordinates of a molecule, both the dipole (D) and rotational 
(R) strengths.  I would also like a program that would accept the output 
of this program and is able to simulate vibrational absorption and CD 
spectra.

Thanks,
R.

From chemistry-request@server.ccl.net  Fri Aug  6 13:33:10 1999
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Subject: MOPAC2000 SEMINAR: Applications and New Developments
To: chemistry@ccl.net
Date: Fri, 6 Aug 1999 10:26:07 -0700 (PDT)
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SEMINAR: Applications and New Developments of MOPAC2000 for the
Experimental Chemist

DATES & VENUES:  
September 13-17, 1999
     - 13th: Washington, D.C. 9:00AM - 12:00PM
     - 14th: Newark, DE       1:00PM - 4:00PM
     - 15th: Philadelphia, PA 1:00PM - 4:00PM
     - 16th: Parsippany, NJ   1:00PM - 4:00PM
     - 17th: Boston, MA       1:00PM - 4:00PM

October 4-8, 1999 (Tentative)
     - 4th: Chicago, IL       1:00PM - 4:00PM
     - 5th: Houston, TX       1:00PM - 4:00PM
     - 6th: San Diego, CA     1:00PM - 4:00PM
     - 7th: Palo Alto, CA     1:00PM - 4:00PM
     - 8th: Seattle, WA       9:00AM - 12:00PM

Registration Deadlines: East - September 3; West - September 24

WHO SHOULD ATTEND: Research and development chemists and managers in
the following areas of chemistry: organic, inorganic, polymer, bio,
solid state, spectroscopy, computational, and educational.

ABSTRACT: New tools that enable the chemist to calculate properties of
both small and large molecules (e.g. proteins, DNA, crystals,
polymers, etc.) in solution, on both UNIX and Windows-based personal
computers, are becoming available through recent advances (the
patented MOZYME technology) in quantum mechanics.  The seminar will
review a range of chemistry applications that can be addressed by
these new tools, including prediction of physical, chemical and
biological properties such as UV-visible & IR spectra, reaction
pathways, thermodynamics & kinetics, non-linear optics, water
solubility, vapor pressure, carcinogenicity, etc. Application of these
new tools to QSPR & QSAR will also be discussed.  Recent QM algorithm
developments and breakthroughs will be reviewed by guest speaker,
Dr. J. J. P. Stewart (creator of MOPAC) including MOZYME to optimize
giant molecules of up to 20,000 atoms on a Windows PC.

The seminars are sponsored by Schrodinger, Inc. and attendance is
free; however, space is limited.  Please register at our website
(http://www.schrodinger.com/mopac_tour.html) before the appropriate
registration deadline to ensure a space is reserved for you.  Exact
locations and directions will be sent to all registered attendees.  If
you have any questions or comments, please contact Dr. Shi-Yi Liu by
email at syl@schrodinger.com or by phone at +1 503 299-1150.
From chemistry-request@server.ccl.net  Thu Aug  5 16:56:13 1999
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Date: Thu, 05 Aug 1999 13:48:04 -0700
To: CHEMISTRY@ccl.net
From: "Jeffrey L. Nauss" <jnauss@msi.com>
Subject: Re: CCL:Re[2]: natural internal coordinates
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 du>
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At 10:31 PM 8/4/99 +0000, Mike wrote:
>Well, these coordinates have been used "since day 1" in polymer
>simulations ...
>
>More details can be found in any simulation text...

And please do not forget the work by Paul J. Flory and his group.

But I suspect, and not having looked at the JACS references yet I cannot be
certain, that these "natural" internal coordinates may be different.

--
Jeffrey L. Nauss, PhD		Phone: (858) 799-5555
Product Specialist, Simulations	Fax: (858) 458-0136
Molecular Simulations Inc.		E-mail: jnauss@msi.com
9685 Scranton Road
San Diego, CA 92121
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A colleague, who subscribes, received this missive a couple of days ago.
It would be a shame to see what is close to a venerable institution vanish.

INDIANA UNIVERSTTY

July 1,1999

DEPARTMENT OF CHEMISTRY

Dear QCPE Member:                        .  .      . 

It is with mixed feelings that I must inform you that Richard Counts, who
has been the Director of the Quantum Chemistry Program Exchange (QCPE) for
nearly 25 years, will retire on July 31, 1999.

Since Richard has been the driving force behind QCPE for so many years, his
departure will necessitate a number of changes in the operation of this
service. I am evaluating several options related to the future management
and operation of QCPE. We hope to be able to provide you with services
somewhat similar to those previously available, but possibly in a webbased
Internet environment. I welcome your suggestions and thoughts on what you,
as a customer, consider appropriate and desirable. Information on changes
or temporary suspension of services will be available to customers on the
QCPE Web site at qcpe5.chem.indiana.edu

Richard has requested that there be no formal acknowledgement of his
retirement, but I'm sure that he would appreciate hearing from you as he
makes this transition.

Gary M. Hieftje

Distinguished Professor and Chairman

/jr

  CHAIRMAN'S OFFICE

Chemistry Building C125 
800 E. KirkwoodAve. 
Bloomington, Indiana 474054001

 8128556239 
Fax: 8128565050 Internet:
cemchair@indiana.edu



__________________________________________________________________
Stephen P. Molnar, Ph.D.						Life is a fuzzy set
Foundation for Chemistry						Stochastic and multivariant
http://web.jadeinc.com/FoundationChem
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From: frisch@lorentzian.com (Mike Frisch)
Message-Id: <199908061941.PAA48403@holly.lorentzian.com>
Subject: TD-HF and TD-DFT oscillator strengths in Gaussian 98
To: chemistry@ccl.net
Date: Fri, 6 Aug 1999 15:41:44 -0400 (EDT)
Cc: jsl@virgil.ruc.dk, Kiet.Nguyen@ml.afrl.af.mil
In-Reply-To: <19990806120341.K141169@gershwin> from "Joe Ochterski" at Aug 6, 99 12:03:41 pm
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There has been some incorrect information about oscillator strengths in
Gaussian 98 posted here.  In fact, the oscillator strengths were originally
incorrect for TD-HF and TD-DFT but these have been fixed and are correct in
Revision A.7, which has been sent to all G98 licensees.  CIS oscillator
strengths were always correct.

Mike Frisch
