Subject: Re:Semi-empirical programs for teaching

From: [email-masked] (Jack Martin Miller)
Date: Fri, 26 Jan 1996 10:23:13 -0400

Below is a summary of responses I received in answer to my request for
advice on free or low cost semi-empirical programs for teaching purposes so
that students might have copies for their own computers. Information is in
the order recieved. My thanks, and that of my colleagues to all
respondents. One of my coleagues has ended up using MOPAC, another GAMES,
and several SPARTAN (currently on SGI, but the Mac version is awaited).

1.I don't know if this is what you are looking for, but we are about to
release MacSpartan for the PowerMac platforms.  Currently, you can acquire
information from our WEB site at http://www.wavefun.com.

MacSpartan is due to be released during the first quarter of 1996.
MacSpartan includes:

1. A Graphical User Interface, much like Spartan for UNIX systems, that
includes BUILDERS for:

A. Organic Molecules
B. Polypeptides
C. Transition States

2. Calculations using the following methodologies:

A. Molecular Mechanics (SYBYL)
B. Semi-Empirical (AM1)
C. Ab Initio Hartree-Fock (3-21G and 6-31G* basis sets)

3. Displays:

A. Structure
B. Molecular Orbitals, electron densities, electrostatic potentials C. Animation

MacSpartan will run on all PowerMac platforms with 16MB of RAM, preferably
with a 66MHZ processor or faster. All appropriate screens are supported,
but the minimum for practical use is 13" and ideal is 16"/17" or greater.
Obviously, the faster the machine, the better the performance--and your
8500 will more than do the job.

And...the academic price for MacSpartan is only $299!

If you have any further questions or are interested in acquiring
MacSpartan, please get in touch with me at the address below.

Thanks for your interest.

Jim Parisi
Marketing/Sales Coordinator

2. MNDO source code is available from the QCPE at Indiana University.  Also, it
is not semi-empirical, but I have a nice little version of an ordinary
Huckel (that is, pi systems only; energies in units of beta) program,
including parameters for heteroatoms, and an instruction manual.  I'd be
happy to make it available, free of course, on my ftp site.

Professor Ray Fort, Jr.             Voice:   (207)-581-1180
Department of Chemistry             FAX:     (207)-581-1191
University of Maine                 E-mail:  [email-masked]
Orono ME 04469                               [email-masked]

3. I have two Macintosh HMO programs:

1) HMO written by Harry Haddon and John Farrell at Franklin and Marshall
College in Lancaster, PA. It is quite old now: 1985 version. I don not know
if it has been updated. A so-so program.

2) HMO written by Allan Wissner, Oncology and Immunology Section, Medical
Research Division, American Cyanamide Co., Lederle Labs, Pearl River, NY
10965. This program would be nicely suited to Chemistry seniors. It
displays the MOs graphically, which can be copied and included in text,
etc. It also has an implementation of the "omega" technique. This one was
*free* at the time!!!

I searched the net for HMO (got many Health Management Orgs. hits) and
Huckel + HMO and got no hits. Apparently these programs are not supported
on the net.

Hope this helps! GN

Gary Newton
Professor of Chemistry
University of Georgia
Chemistry Department
Athens, GA 30602  USA

Phone 706-542-1969
Fax 706-542-9454

email [email-masked]

4. Inquire about MOBY:  there is an advert for MOBY 1.5 on p A27 of
J Chem Ed, 1994 Feb (Springer Verlag, Electronic Media Dept, 175 Fifth Ave,
New York, NY 10010, Tel (212)460-1653.
Errol Lewars,  Trent University
====

5. Jack, MOPAC for DOS is very good. The only thing I'm not happy about is it
doesn't have a graphical interface to create Input with. You have to literally
type in the numbers describing the geometry in order to create an Input, whihc
is very prone to error. I've never done this. Fortunately my advisor spent ca.
$1000 buying CAChe package including MOPAC and its Editor. The latter is a
chemistry-informed drawing program. I can use it to create a correct MOPAC
Input for any platform including DOS.

I have a feeling that somewhere on the Internet there's a program we can use in
place of my CAChe Editor. Somebosy suggested SYBIL but the free version can
only accept 10 (?) atoms which is too small for me. If you get a response about
such a program, please let me know. Thank you.

Yong
[email-masked]

6. Hi,
   I am not sure if this is what you are looking for but the price is
right. My group produces the GAMESS ab initio package which includes
several semi-emperical wavefunctions (AM1, PM3...). It runs on most
workstations and on PowerMacs. If you are interested you can check out
our WWW page at http://www.msg.ameslab.gov/   or send an email to
Mike Schmidt at [email-masked] to request a copy. There is no
charge, but we do require that you sign a simple license agreement.

Brett
--

7.    I think Mopac95 is a good choice. It is easy to get
the source code on the Internet. In addition, there are
few freeware of drawing molecules and those data format
could be converted by "babel"(also freeware).

xxx   name withheld on request.

8.   Spartan is coming out with desktop computer versions which, although
not cheap, probably cost about the same as many textbooks students are
accustomed to paying for.  I would appreciate receiving a summary of
responses to this question.

__________________________________________________________

                      Abby Parrill
                  Chemistry Department
      Artificial Intelligence in Chemistry Laboratory
                The University of Arizona
             [email-masked]

__________________________________________________________

9.
Hello,
        Contact Serena Software Co in Bloomington, INDIANA
They have made semi-empirical package MOPAC available
for PC/Mac. Price very nominal.
Ramesh

10. MacSpartan (PowerMac version) could do the job. It includes quantum
mechanics (ab initio and semiempirical) and molecular mechanics methods.
Its high-end graphics provides great visual teaching tools
for organic chemistry. It prices at $299 (US & Canada academics).
Along with it, Wavefunction also offers publications related to your
purpose - teaching in organic chemistry:

(1) Educational CD-ROM: "Visualization of chemical structures and reactions",
    (facusing on organic chemistry), by Tom Hehre, Lonnie Burke,
    Wayne Huang, Warren Hehre, 1995.

(2) Self-guided Tutorial: "A MacSpartan Tutorial", Wavefunction, 1996.

(3) Experiment book: "A Laboratory Book of Computational Organic Chemistry"
    by Warren Hehre, Wayne Huang & Alan Shusterman, 1996.

For more information, check http://www.wavefun.com/MacSpartan.html

--Wayne

11. and Ralph Puchta's summary of responses to his similar question.

>Dear CCL-Users!
>
>1. Does anyone know free semiempirical calculation program, that are not
>     versions of ampac and mopac.
>2. Which was the last free version of ampac?
>3. Are there any free forcefield calculating programs?
>4. On which ftp-server can I find these programs?
>
>Thank you very much for your help
>
>Ralph Puchta

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

Here is my summary - and many thanks to all that wrote to me and helped.

>1. Does anyone know free semiempirical calculation program, that are not
>   versions of ampac and mopac.

There is a program called VAMP, that should be free up to VAMP 4.5.

>2. Which was the last free version of ampac?

All the MOPAC programs with single digit extensions, e.g. MOPAC 5, MOPAC 6,
MOPAC 7, are public domain, and are `free'.

Jimmy Stewart

[email-masked] (Dr. James Stewart)

>4. On which ftp-server can I find these programs?

You can find free versions of MOPAC6 & MOPAC7 for DOS, LINUX and sources
at www.ccl.net. Look in the webpage of CCL.
I couldn't compile MOPAC7 for the SGI.

Dr.Edgardo Garcia
Cristol Chem & Biochem
University of Colorado at Boulder

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++++End

A word to VAMP: I know it, as we use the newest version, that you have to
buy, on our
workstations in the university. If you can handle MOPAC5 to MOPAC7 you can
handle VAMP
also very good. AMPAC is also as suitable, but in my oppinion the available
versions on
ftp are to old, MOPAC is much newer. MOPAC is now developed also for
buying, but if you
look in chemical newspapers, there are still a lot of articels, that were
calculated with
MOPAC6. I personal run MOPAC6 on my PC by using DOS and by using LINUX. I
have to point
out the version compiled for LINUX is faster. The general handling is the same.
The geometric input for the molecules and nearly all keywords are the same.
So MY PERSONAL hint for your problem "no money - good results" is use MOPAC.

A friend of mine used archie and gave me the following. here you can find
MOPAC and related
things.

Host www.ccl.net    (128.146.36.48)
Last updated 03:47  5 Aug 1995

    Location: /pub/chemistry/documents
      DIRECTORY    drwxr-xr-x     512 bytes  00:00 22 May 1994  mopac_doc

    Location: /pub/chemistry/documents/mopac_doc
      FILE    -rw-r--r--  521604 bytes  23:00  6 Oct 1992  mopac6.doc
      FILE    -rw-r--r--  494856 bytes  00:00 16 Nov 1992  mopac6.ps

    Location: /pub/chemistry/software/DEC-ALPHA
      DIRECTORY    drwxr-xr-x     512 bytes  00:00  1 Dec 1994  mopac6

    Location: /pub/chemistry/software/MS-DOS/mopac_for_dos
      DIRECTORY    drwxr-xr-x     512 bytes  10:51 17 Feb 1995  mopac6

    Location: /pub/chemistry/software/OS-2
      DIRECTORY    drwxr-xr-x     512 bytes  00:00  1 Dec 1994  mopac6

    Location: /pub/chemistry/software/LINUX
      DIRECTORY    drwxr-xr-x     52 bytes  14:34 27 Jun 1995  mopac7

    Location: /pub/chemistry/software/MS-DOS/mopac_for_dos
      DIRECTORY    drwxr-xr-x     512 bytes  16:53 16 Mar 1995  mopac7

    Location: /pub/chemistry/software/LINUX/mopac7/older_version_do_not_take
      FILE    -rw-r--r--     618 bytes  00:00 18 Aug 1994  mopac

Host ftp.uni-koeln.de    (134.95.100.202)
Last updated 05:16  3 Aug 1995

    Location: /usenet/comp.archives/bionet/chemistry
      DIRECTORY    drwxrwxr-x    2048 bytes  22:00 22 Apr 1993  mpac

Host www.ccl.net    (128.146.36.48)
Last updated 03:47  5 Aug 1995

    Location: /pub/chemistry/software/LINUX/mopac7/older_version_do_not_take
      FILE    -rw-r--r--  811586 bytes  00:00 19 Aug 1994  mopac7.Z

    Location: /pub/chemistry/software/MS-DOS
      DIRECTORY    drwxr-xr-x     512 bytes  10:51 17 Feb 1995  mopac_for_dos

    Location: /pub/chemistry/software/MS-DOS/mopac_for_dos/mopac6
      FILE    -rw-r--r--  627791 bytes  00:00 22 Dec 1993  mopac.exe.Z
      FILE    -rw-r----  471300 bytes  00:00 22 Dec 1993  mopacdos.zip

    Location: /pub/chemistry/software/MS-DOS/mopac_for_dos/mopac7
      FILE    -rw-r--r--  585910 bytes  16:45 16 Mar 1995  mopac7b.zip

    Location:
/pub/chemistry/software/MS-DOS/mopac_for_dos/mopac7/old-version.95.02.17
      FILE    -rw-r--r--  389585 bytes  11:03 17 Feb 1995  mopac7b.zip

    Location: /pub/chemistry/software/MS-DOS/mopac_for_dos/mopac7
      FILE    -rw-r--r--  540413 bytes  16:46 16 Mar 1995  mopac7s.zip

    Location:
/pubchemistry/software/MS-DOS/mopac_for_dos/mopac7/old-version.95.02.17
      FILE    -rw-r--r--  359562 bytes  11:03 17 Feb 1995  mopac7s.zip

    Location:
/pub/chemistry/software/MS-DOS/mopac_for_dos/mopac7/junk-do-not-look-here
      FILE    -r-xr-xr-x 3541222 bytes  11:04 10 Mar 1995  mopac7.dos.big
      FILE    -r-xr-xr-x 1725514 bytes  11:04 10 Mar 1995  mopac7.dos.sml

    Location: /pub/chemistry/software/OS-2/mopac6
      FILE    -rw-r--r--  491975 bytes  00:00  1 Dec 1994  os2mopac.zip

    Location: /pub/chemistry/software/SOURCES/FORTRAN
      DIRECTORY    drwxr-xr-x     512 bytes  00:00 22 May 1994  mopac6_sources
      DIRECTORY    drwxr-xr-x     512 bytes  12:18  5 Jul 1995  mopac7_sources

    Location: /pub/chemistry/software/SOURCES/FORTRAN/mopac6_sources
      FILE    -rw-r--r-- 1104875 bytes  00:00 23 Feb 1994  mopac6.tar.Z
      FILE    -rw-r--r--  857080 bytes  00:00 19 Mar 1994  mopac6.zip

    Location: /pub/chemistry/software/SOURCES/FORTRAN/mopac7_sources
      FILE    -rw---r--  331505 bytes  00:00 26 Jan 1995  mopac7-man-300.ps.Z
      FILE    -rw-r--r-- 1487313 bytes  00:00 19 Aug 1994
mopac7-man-300.ps.Z.orig-does-not-work
      FILE    -rw-r--r--  378449 bytes  00:00 26 Jan 1995  mopac7-man-600.ps.Z

For AMPAC try www.ccl.net:

software/SOURCES/FORTRAN/mopac6_sources:
total 2529
-rw-r--r--  1 ccl        597133 Feb 23  1994 ampac21.tar.Z

If you are looking for a visualistion tool for your outputs try CASCADE V2.
This version is
in the moment only for DOS/OS/WINDOWS available, but we hope that up to
february we have
CASCADE V3 running, it should run with DOS/OS/WINDWS and X. And the most
interesting
it is copyrighted as GNU - that meens free for all! For more infos about
CASCADE, mail
me, as I am a member of the CASCADE Development Team. As we do not have the
chance
to test CASCADE V3 on a X for MACs, I do not know if it will run on MAC
too. Here is the
text I mailed to the CCL some weeks ago.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++start

Dear CCL users!

We proudly announce our program CASCADE:

Here the readme-file

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

C A S C A D E   V 2     (DOS/Win/OS2 VERSION)
==========================================================================
>> Cascade Aids Semi-empiric Calculators Access Displays Eventually :-) <<
==========================================================================
Cascade V2 is a shell which converts semi-empirical data (from programs
like MOPAC, AMPAC and VAMP) into several 3d graphic formats. It thus
enables the user to visualize the resulting molecule geometry. The supported
display programs are:
  3DV, Chemview, JMR, MOLWIN, MV, PC MODEL, PLUTON, POVRAY,
 RASWIN.
--------------------------------------------------------------------------
Andreas Dosche          ([email-masked])
Ralph Puchta            ([email-masked])
Michael Reichenb"acher  ([email-masked])
--------------------------------------------------------------------------
Please use the program install.exe to uncompress cascade.zip,
otherwise you have to set the environment variables CASCADE and AWKDIR
manually.
If you have used install.exe, you can use cascade.bat to start cascde.

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

You can get CASCADE via ftp:

ftp://www.ccl.net/pub/chemistry/software/MS-DOS/cascade

ftp://uni-stuttgart.de/pub/scivi/cascade

You have to get 3 files:

cascade2.rea -> the readme file (you have read in *)
cascade2.zip -> the program
install.exe  -> this part installs CASCADE in the right way on your PC

We hope that you will enjoy it.
If you find any bugs or have any problems, think something should be changed,
should be added or any thing else, feel free to contact us.

We wish all CCl users a merry Christmas and a happy new year 1996.

Andreas Dosche
Ralph Puchta
Michael Reichenb"acher

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++end

I think you know most of the supported programs and you know, that they are
free or not
to expensive, too.

If you want to combine the education in ab initio and semiempirical calculation,
you can use GAMESS, that can do both, as they included parts of MOPAC. But
I never tried
it myself, for more infos try:

Mike Schmidt via e-mail ([email-masked]).

As far as I know it runs on PC only via LINUX. About MAC I do not know anything.
I fear GAMESS will not be supported in CASCADE V3, as I had not the time to
get into GAMESS.

To run Linux you need a PC 386 or higher, for running MOPAC5 you need also
as 386
or hihger. I personal run my semie-empiric calculations at home on a 486 DX
2/66, and
in order to calculate e.g. C60 it lasts a night.

I hope this helped a little bit.

Many greetings

Ralph Puchta

[email-masked]

Jack Martin Miller
Professor of Chemistry
Adjunct Professor of Computer Science
Brock University,
St. Catharines, Ontario, Canada, L2S 3A1.

Phone (905) 688 5550, ext 3402
FAX   (905) 682 9020
e-mail [email-masked]
http://chemiris.labs.brocku.ca/staff/miller/miller.html