From ndaisy@cobra.ordata.com  Fri Apr 21 01:16:50 1995
Received: from ordata.com  for ndaisy@cobra.ordata.com
	by www.ccl.net (8.6.10/930601.1506) id BAA27499; Fri, 21 Apr 1995 01:07:33 -0400
Received: by ordata.com (Smail3.1.28.1 #2)
	id m0s2AtW-0002fyC; Thu, 20 Apr 95 22:04 PDT
Date: Thu, 20 Apr 1995 22:04:41 -0700 (PDT)
From: Nick K Daisy <ndaisy@cobra.ordata.com>
To: "J.P. Northrop" <jpnort@mail.wm.edu>
cc: chemistry@ccl.net
Subject: Re: CCL:virus alert (fwd)
In-Reply-To: <Pine.3.89.9504202038.B42066-0100000@gopher.cc.wm.edu>
Message-ID: <Pine.SUN.3.90.950420215933.1101A-100000@cobra.ordata.com>
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII



All antivirus programs must read the virus code to detect the virus. 
There is no harm in reading virus code, ascii or binary, to the system 
with the exception of "mail bombs" which activate undesirable screen 
attributes - though no permanent damage is done. The virus must be 
'executable' to cause damage to the system. Read all the virus code you like.

NKD



From bouyer@ext.jussieu.fr  Fri Apr 21 03:46:53 1995
Received: from shiva.jussieu.fr  for bouyer@ext.jussieu.fr
	by www.ccl.net (8.6.10/930601.1506) id DAA28901; Fri, 21 Apr 1995 03:45:13 -0400
Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129])
          by shiva.jussieu.fr (8.6.10/jtpda-5.1) with ESMTP id JAA08166
          for <chemistry@ccl.net>; Fri, 21 Apr 1995 09:45:04 +0200
Received: from [134.157.11.12] by idf.ext.jussieu.fr
	  (8.6.10/jtpda-4.0) with SMTP; Fri, 21 Apr 1995 09:45:01 +0200
X-Sender: bouyer@idf.ext.jussieu.fr
Message-Id: <v01510101abbd14bb556c@[134.157.11.12]>
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 21 Apr 1995 08:55:42 +0100
To: chemistry@ccl.net
From: bouyer@ext.jussieu.fr (Frederic BOUYER)
Subject: Differences between MNDO and AM1


Hi Netters,
Would someone please provide me some informations (or a brief description,
differences) about MNDO and AM1 hamiltonians of MOPAC (v.6)?

Thank you in advance.

Frederic Bouyer
Lab. Electrochimie, ENSCP, Paris
bouyer@ext.jussieu.fr
http://alcyone.enscp.jussieu.fr/



From friedric@TechFak.Uni-Bielefeld.DE  Fri Apr 21 04:01:53 1995
Received: from techfac.TechFak.Uni-Bielefeld.DE  for friedric@TechFak.Uni-Bielefeld.DE
	by www.ccl.net (8.6.10/930601.1506) id DAA28934; Fri, 21 Apr 1995 03:48:26 -0400
Received: from puccini.TechFak.Uni-Bielefeld.DE
	by techfac.TechFak.Uni-Bielefeld.DE id AA24114; Fri, 21 Apr 1995 09:47:37 +0200
Received: by puccini.TechFak.Uni-Bielefeld.DE (5.65/tp.29.08.90)
	id AA00974; Fri, 21 Apr 1995 09:47:36 +0200
Message-Id: <9504210747.AA00974@puccini.TechFak.Uni-Bielefeld.DE>
Subject: molecular surfaces
To: chemistry@ccl.net
Date: Fri, 21 Apr 1995 09:47:36 +0200 (MET DST)
From: Friedrich Ackermann <friedric@TechFak.Uni-Bielefeld.DE>
X-Mailer: ELM [version 2.4 PL23]
Mime-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Length: 4040      



Dear Netters!
=============

I would like to invitate all those of you, that are working on
the fields of protein-protein-docking, molecular surfaces,
energy evaluation, electrostatic interactions in proteins etc.
to a little comparison of some results. Especially I would like
to compare the shape (geometry) of   m o l e c u l a r 
a c c e s s i b l e   s u r f a c e s   (MS) with each other. In 
addition, values of the electrostatic potential on the MS should 
be compared.
It is   n o t   intended to decide about the correctness of
underlying theoretical models, but rather to give all participants
a hint, how their results compare empirically with those of others.

My background:
==============
I am working on the problem of protein-protein-docking. The main
idea of our project is to integrate geometrical and chemical
surface features in the evalutation of complementarity in an
easy and fast manner. To this end I am developing a class library
(C++) to calculate and manipulate protein features and features
of the molecular surfaces. One of this features is the electrostatic 
potential on the surface. Now, the question arises: Am I computing
the right values? 

The comparison:
===============
Assume you can calculate the MS of a protein and possibly the 
electrostatic potential on it, i.e. you should be able to write down
a file similar to this:

x1 y1 z1 e1
x2 y2 z2 e2
x3 y3 z3 e3
x4 y4 z4 e4
...
xN yN zN eN

Hereby, xi, yi, zi, and ei are floats. xi, yi, and zi are the 
coordinates (in Aengstroem, given in the coordinate system of the 
PDB - entry) of a surface point and ei is the
electrostatic potential that you computed at this particular
surface point. Since we compare only relative values, it is not
important in which unit ei is given.
Your MS will be sampled in a 3D grid (isotropic lattice constants 
0.5, 0.8, and 1.2 Aengstroem will be used) and by counting hits and
missing voxels we will compare the shape (geometry) of the
different MSs. In a similar way we will compare by correlation on
the grid the values for the electrostatic potential on the MS.

You want to make one of the party?
==================================
Then please send me a note (friedric@techfak.uni-bielefeld.de)
(Name, institution, type of program you use, additional hints for
the comparison, references).
First all participants will be informed about the IDs of the others
and will receive a detailed description of the procedures used for 
comparison.
Then the PDB-IDs of some proteins I suggest to use for comparison 
and a description of possible file formats will be sent.
Afterwords you will calculate the MS and eventually the potential 
on it and you will send it to me. The comparisons will be performed, 
and the results will be posted to all participants as a set of upper
triangular matrices, containing cross correlations and similar values
of every MS with each other.
In addition the results will be compiled to a technical report, that 
will be made electronically available on our ftp server.

Schedule:
=========
5.5.1995	Deadline for note on intended participation.
10.5.1995	Posting of PDB-Ids and format descriptions.
		(Meanwhile eventually changes in procedure of 
		comparisons, depending on hints of participants.)
24.5.1995	Deadline for submission of MS
31.5.1995	Posting of results

I would be glad to here from you!
Friedrich Ackermann

THIS NOTE WAS POSTED BY ME ORIGINALLY TO THE FOLLOWING NEWSGROUPS:
bionet.biology.computational
bionet.molbio.proteins
bionet.software
bionet.announce
PLEASE FORWARD IT TO POSSIBLY INTERESTED PERSONS, THAT DON'T READ
THESE NEWSGROUPS!
PLEASE INFORM ME ABOUT OTHER NEWSGROUPS, INTO WHICH I SHOULD POST
THIS NOTE!

IN ADDITION IT WAS POSTED TO
chemistry@ccl.net (hint from Max Vasquez)

-------------------------------------------
Friedrich Ackermann
Applied Computer Science
Bielefeld University
P.O. 100131
D-33501 Bielefeld
Phone: +49 521 106 2938
Fax: +49 521 106 2992
email: friedric@techfak.uni-bielefeld.de
-------------------------------------------


From Patrick.Bultinck@rug.ac.be  Fri Apr 21 05:46:54 1995
Received: from mserv.rug.ac.be  for Patrick.Bultinck@rug.ac.be
	by www.ccl.net (8.6.10/930601.1506) id FAA29709; Fri, 21 Apr 1995 05:31:42 -0400
Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA04653
  (5.67b/IDA-1.5 for <chemistry@ccl.net>); Fri, 21 Apr 1995 11:30:23 +0200
Received: by allserv.rug.ac.be (5.x/SMI-SVR4)
	id AA04030; Fri, 21 Apr 1995 11:31:24 +0200
Date: Fri, 21 Apr 1995 11:31:24 +0200 (MET DST)
From: Patrick Bultinck <Patrick.Bultinck@rug.ac.be>
To: "comp. chem. list" <chemistry@ccl.net>
Subject: GAMESS and xlf3.0* on RS6k
Message-Id: <Pine.SOL.3.91.950421112949.3011C-100000@allserv.rug.ac.be>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII



Dear,

My compilation of GAMESS v. 59 on RS6k and xlf3.01 works, but examples 
show very significant differences depending on the compiler used. I have 
looked up the compilation scripts in detail and tried to alter the comp. 
flags, but e.g. in exam01 I find lower energies (not too much lower 
though) in a smaller number of iterations. For exam06 however I get a ton 
of errors of files being opened already but with another status, and 
results differing significantly from the ones given in the example.

Do you know of someone having succeeded in compiling GAMESS with xlf3.0.* ?
Or do you have some useful advice ?

Thank you very much,

Patrick


From mmadrid@gardel.psc.edu  Fri Apr 21 10:31:58 1995
Received: from gardel.psc.edu  for mmadrid@gardel.psc.edu
	by www.ccl.net (8.6.10/930601.1506) id KAA03520; Fri, 21 Apr 1995 10:27:43 -0400
Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO)
	for chemistry@ccl.net id AA15043; Fri, 21 Apr 95 10:27:40 -0400
From: "Marcela Madrid" <mmadrid@gardel.psc.edu>
Message-Id: <9504211027.ZM15041@gardel.psc.edu>
Date: Fri, 21 Apr 1995 10:27:31 -0400
X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail)
To: chemistry@ccl.net
Subject: CCL: SEQUENCE ANALYSIS WORKSHOP
Content-Type: text/plain; charset=us-ascii
Mime-Version: 1.0



                   NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS
                       WORKSHOP FOR BIOMEDICAL RESEARCHERS
                              Pittsburgh, Pennsylvania
                              June 4-9, 1995



Pittsburgh Supercomputing Center (PSC) is again offering a five-day workshop on
"Nucleic Acid and Protein Sequence Analysis," June 4-9, 1995.  It is
funded by a grant from the National Center for Human Genome Research of
the National Institutes of Health.

The workshop will familiarize biomedical researchers
in applying supercomputing resources to
problems of concern in macromolecular sequence analysis.  Emphasis will be
on alignment of and pattern extraction from multiple sequences.
Participants will gain practical experience on PSC's Cray C-90 and T3D in
(1) comparing and aligning sequences, (2) identifying informative patterns
in a set of sequences; and (3) using extracted informative patterns to
identify related sequences.  Researchers will also learn several approaches
to database searching and  multiple sequence alignment, how to use profile
analysis effectively, and how to identify patterns in their sequences.
Participants are encouraged to bring sequence analysis problems from their
current research.  Extensive documentation will be given at the outset on
the PSC computing environment as well as on the specific programs
to be employed in the workshop.  No prior supercomputing experience is
required.

Workshop leaders are Dr. Gary Churchill, Cornell University, Dr. Michael
Gribskov, San Diego Supercomputing Center, and Dr. Hugh Nicholas, PSC.

A limited number of grants to cover travel and hotel accommodations are
available for U.S. academic participants.  ALL PARTICIPANTS ARE REQUIRED
TO PAY A $135 REGISTRATION FEE, IN ADVANCE, UPON ACCEPTANCE INTO THE WORKSHOP.

DEADLINE FOR SUBMITTING APPLICATIONS IS FRIDAY, APRIL 21, 1995.
Enrollment is lmited to 20 participants.

Additional information about this workshop can be found in
http://pscinfo.psc.edu/biomed/workshops95.html



				      * * * * *



                     PITTSBURGH SUPERCOMPUTING CENTER
                     NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS
                     WORKSHOP FOR BIOMEDICAL RESEARCHERS
                               June 4-9, 1995

                               APPLICATION


Name:	       ________________________________________________________________

Affiliation:   ________________________________________________________________

Address:       ________________________________________________________________
	       (Business)
	       ________________________________________________________________

	       ________________________________________________________________
	       (Home)
	       ________________________________________________________________

Telephone:  ____________________________         ______________________________
	           (Business)				     (Home)

*Social Security Number:  _______-_____-_______	Citizenship:___________________

Electronic Mail Address:_______________________________________________________

Status: ___Graduate  ___Post-doctoral Fellow  ___Faculty  ___Other (specify)

In order to attend the workshop, will you need funds for travel?___ lodging?___

Please indicate specifically any special housing, transportation or dietary
arrangements you will need: __________________________________________

How did you learn about this workshop:_________________________________________

REQUIREMENTS:

Applicants must submit a completed application form and a cover letter.  The
letter should describe, in one or two paragraphs, the sequence analysis
problems encountered in your research, and how participating in the workshop
will enhance this research.  Please include a brief statement describing your
level of experience with computers.  Faculty members, staff and post-docs
should provide a curriculum vita.  Graduate students must have a letter
of recommendation from a faculty member. If you have requested travel funds,
please include the cost of roundtrip air fare from your home to Pittsburgh and
indicate the amount of travel funds you will need. ALL PARTICIPANTS WILL BE
REQUIRED TO PAY A $135 ADVANCE REGISTRATION FEE UPON ACCEPTANCE INTO THE
WORKSHOP.

Please return all application materials by APRIL 21, 1995 to:



          Biomedical Workshop Applications Committee
          Pittsburgh Supercomputing Center
          4400 Fifth Avenue, Suite 230C
          Pittsburgh, PA 15213

Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960.

*Disclosure of Social Security Number is voluntary.

PSC does not discriminate on the basis of race, color, religion, sex, age,
creed, national or ethnic origin, or handicap.
















From jacque@isadora.albany.edu  Fri Apr 21 11:31:59 1995
Received: from UACSC2.ALBANY.EDU  for jacque@isadora.albany.edu
	by www.ccl.net (8.6.10/930601.1506) id LAA04635; Fri, 21 Apr 1995 11:24:42 -0400
Received: from isadora.albany.edu by UACSC2.ALBANY.EDU (IBM VM SMTP V2R2)
   with TCP; Fri, 21 Apr 95 11:22:04 EDT
Received: by isadora.albany.edu (931110.SGI/930416.SGI)
	for @uacsc2.albany.edu:chemistry@ccl.net id AA14895; Fri, 21 Apr 95 11:22:16 -0400
From: jacque@isadora.albany.edu (Jacque Fetrow)
Message-Id: <9504211522.AA14895@isadora.albany.edu>
Subject: Albany Conference-Computational Biology
To: chemistry@ccl.net
Date: Fri, 21 Apr 95 11:22:15 EDT
X-Mailer: ELM [version 2.3 PL11]



> 3rd Albany Conference on Computational Biology
> "Phylogenetic & Structural Relationships Among Proteins"
> 
> September 28-October 1, 1995 
> 
> Rensselaerville Conference Center, Rensselaerville, NY
> 
> 
> This interdisciplinary meeting will be the third in our series of Albany
> Conferences on Computational Biology, and will be held September 28 -
> October 1, 1995 in Rensselaerville near Albany, New York.  Like the two
> predecessors ("Converging Approaches in Computational Biology" in 1990
> and "Patterns of Biological Organization" in 1992), the aim of this
> conference is to explore the computational tools and approaches being
> developed in diverse fields within biology, with emphasis this year on
> phylogeny as apparent in relationships on the molecular level. 
> 
> The conference will be designed to provide an environment for a frank and
> informal exchange among scientists and mathematicians that is not normally
> possible within the constraints of topical, single-discipline meetings.  The
> theme of the conference, "Phylogenetic and Structural Relationships Among
> Proteins", will be developed in five sessions: 3-D Structural Relationships
> Among Proteins, Sequence-Structure Interface, Data Bases, and
> Phylogenetic Methods and Protein Trees (I,II).  Leading specialists in the
> various disciplines have been invited, with the degree of involvement in
> novel computational approaches as one of the most important criteria of
> selection.  Speakers will include:
> 
>        Steven Benner: ETH, Zurich, Switzerland
>        Stephen Bryant: NIH, Computational Biology Branch                   
>        Cyrus Chothia: MRC, Cambridge, England
>        G. Brian Golding: McMaster University, Hamilton, Ontario
>        David Hillis: University of Texas, Austin, TX
>        Charles Lawrence: Wadsworth Center, Albany, NY
>        Peter Munson: NIH, Analytical Biostatistics Section 
>        Caro-Beth Stewart: University at Albany
>        Arlin Stoltzfus: Dalhousie Univ, Halifax, Nova Scotia
>        Joel Sussman: Brookhaven National Lab, Protein Data Bank
>        David Swofford: Smithsonian Institution, Washington, DC
>        Shoshana Wodak:  Univ Libre de Bruxelles Brussels, Belgium
> 
> For further details, see the WWW document 
> http://www.cs.albany.edu/albany_conference95
> 
> 
> Registration information also can be obtained by directly contacting the
> conference coordinator:
> 
> Carole A. Keith
> Center for Molecular Genetics & 1995 Albany Conference
> BIO 126 
> University at Albany
> 1400 Washington Avenue        Phone: 518/442-4327 
> Albany, NY 12222 USA          FAX: 518/442-4354 
>                               Email: carole@cnsibm.albany.edu
> 
> Information about the meeting sessions and format can be obtained from
> the following members of the organizing committee:
> 
> Joachim Frank (co-chair), Wadsworth Center
> 518-474-7002
> joachim@orkney.ph.albany.edu
> 
> Carmen Mannella (co-chair), Wadsworth Center
> 518-474-2462
> carmen@orkney.ph.albany.edu
> 
> Jacquelyn Fetrow
> 518-442-4389
> jacque@isadora.albany.edu
> 
> Charles Lawrence, Wadsworth Center
> 518-473-3382
> lawrence@wadsworth.ph.albany.edu
> 
> Caro-Beth Stewart, University at Albany
> 518-442-4342
> cs812@csc.albany.edu



From alper@moldyn.com  Fri Apr 21 16:32:03 1995
Received: from netcomsv.netcom.com  for alper@moldyn.com
	by www.ccl.net (8.6.10/930601.1506) id QAA09622; Fri, 21 Apr 1995 16:29:17 -0400
Received: from moldyn.com by netcomsv.netcom.com with UUCP (8.6.9/SMI-4.1)
	id NAA08953; Fri, 21 Apr 1995 13:22:07 -0700
Received: by bart.moldyn.com (931110.SGI/921111.SGI.AUTO)
	for netcomsv!ccl.net!chemistry id AA12826; Fri, 21 Apr 95 12:20:23 -0400
From: moldyn.com!alper@moldyn.com (Howard Alper)
Message-Id: <9504211620.AA12826@bart.moldyn.com>
Subject: phosphate solvation energies
To: chemistry@ccl.net
Date: Fri, 21 Apr 1995 12:20:18 -0500 (EDT)
Reply-To: moldyn.com!alper@moldyn.com
X-Mailer: ELM [version 2.4 PL22]
Mime-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Length: 1252      



  Dr. Zhou,

  I was involved in lipid simulation research.  In particular, the group
I was in performed simulations of hydrated DMPC lipid monolayers and bilayers.
Among other quantities that we calculated was the solvation of the phosphate
and choline portion of the lipid headgroups.  The results are highly dependent
on the potential/force cutoffs used, since phosphate is charged, but using
cutoffs of effectively 30angstroms we obtained a solvation energy of -83.49
kcal/mole.  Computational requirements prevented using larger cutoffs, but the
infinite-cutoff result is most likely near the value quoted above.  One must
also keep in mind that the phosphate group is not isolated, but is part of the
lipid headgroup, along side other lipid molecules.  But -83.49 should give
you at least a reasonable starting estimate.  For more information you might
want to consult the following references:

H. E. Alper, D. Bassolino, and T. R. Stouch., J. Chem. Phys. 98, 9798 (1993).

H. E. Alper, D. Bassolino, and T. R. Stouch., J. Chem. Phys. 99, 5547 (1993).


  Howard Alper

-- 

  Dr. Howard Alper
  Moldyn Inc.
  1033 Massachusetts Avenue
  Cambridge, MA 02138
  617-354-3124 x19

- helping molecules find happiness for over a 10th of a century.


From mwtcc@chem.nwu.edu  Fri Apr 21 17:02:04 1995
Received: from mercury.chem.nwu.edu  for mwtcc@chem.nwu.edu
	by www.ccl.net (8.6.10/930601.1506) id QAA10102; Fri, 21 Apr 1995 16:54:47 -0400
Received: by mercury.chem.nwu.edu (AIX 3.2/UCB 5.64/4.03)
          id AA24916; Fri, 21 Apr 1995 15:54:57 -0500
From: mwtcc@chem.nwu.edu (Midwest Theoretical Chemistry Conference)
Message-Id: <9504212054.AA24916@mercury.chem.nwu.edu>
Subject: MWTCC !! (VERY IMPORTANT INFORMATION)
To: chemistry@ccl.net
Date: Fri, 21 Apr 1995 15:54:56 -0500 (CDT)
X-Mailer: ELM [version 2.4 PL23alpha2]
Content-Type: text
Content-Length: 1021      


This note is intended for people interested in the 28th Midwest Theoretical
Chemistry Conference.
Sorry to the rest of you.



Dear MWTCC people;

This note is IMPORTANT to those of you who sent abstracts or registration 
forms to mwtcc@chem.nwu.edu during FRIDAY, APRIL 21th, BEFORE 3PM only.

Due to an unfortunate computer and human error (fingers faster than brain)
we have lost all your abstract and registration information. If you
submitted something during that period, please send it again.

IF YOU KNOW OF ANYONE IN THIS SITUATION, PLEASE FORWARD THIS E-MAIL TO THEM.


We appreciate your cooperation and understanding on this matter.

Best regards


Dr. Adrian Roitberg


============================================================================
For Information About the Midwest Theoretical Chemistry Conference
please contact Prof. George Schatz (708-491-5657) or Prof. Mark Ratner
(708-491-5652) or just e-mail to this address.
===========================================================================

From aholder@CCTR.UMKC.EDU  Fri Apr 21 17:32:12 1995
Received: from axp1.umkc.edu  for aholder@CCTR.UMKC.EDU
	by www.ccl.net (8.6.10/930601.1506) id RAA10497; Fri, 21 Apr 1995 17:23:24 -0400
From: <aholder@CCTR.UMKC.EDU>
Received: by CCTR.UMKC.EDU (MX V4.1 AXP) id 791; Fri, 21 Apr 1995 16:23:22 CST
Date: Fri, 21 Apr 1995 16:23:22 CST
To: CHEMISTRY@ccl.net
Message-ID: <0098F38C.AF3637C9.791@CCTR.UMKC.EDU>
Subject: MNDO vs. AM1


Netters,

A question was recently posted as to the difference between MNDO
and AM1.  I'll be happy to give my take on this.

1.  The basic difference between the two methods is the addition of 
Gaussian functions to some of the core repulsion functions (CRFs) 
for certain elements.  These functions have a position, a width, 
and an intensity, all of which can be taken as parameters.  They 
were initially intended to adjust the SHAPE of the CRF so that it 
would more closely correspond to "reality", whatever that is.  In 
essence, they were used as patches for specific types of systems 
that could not be handled in general parameterization without 
disrupting other chemically important items.  In my experience, 
the Gaussians were added one at a time and with great deliberation, 
and only after the other parameters were pretty much settled on.  
This is because they could potentially have such a large effect
on the chemistry of the elements.

An example of this are the Al-Cl systems for AM1.  When I was
finishing parameters for Al in AM1, these systems would simply not
come out correctly.  A carefully placed Gaussian solved the problem.
Another example of a "problem" Gaussian function is the one found
at about 3.0 angstroms in the phosphorous parameters for AM1.
This Gaussian can cause extensive problems when there are TWO P
atoms at about this distance in a compound.

All in all, Gaussians MUST be used with extreme care and anytime
one is added to repair a problem, it will almost certainly cause
another.  As with all things, it is a matter of trade-offs.
The above discussion has led to my conclusion (tongue firmly in
cheek) that Gaussians are "evil."  I think I would amend that to
be a "neccessary evil."

2.  Another difference that must be mentioned is additional flex-
ibility in the parameters for the lighter elements in the case of
AM1.  For instance, for most of the lighter elements (rows 1 and 2)
only one zeta value (exponent of the slater orbitals) and one beta
value (resonance) was used for both s and p orbitals in the valence
shell within MNDO.  This approximation was abandoned for the heavier
elements in MNDO and completely for AM1.  This assumption was made
in the case of MNDO for computational efficiency.

3.  The third difference is the added computational power available
for parameterization searches when AM1 was parameterized.  Much more
extensive grid searches and trial parameter examination could be
carried out more quickly as timne went by.  Most of the AM1 parameter
sets are substantially different than the MNDO ones indicating that
definitely different parameter minima were located.

All in all, the methods are basically the same in theory differing
only in the details.  The same can be said about PM3, in that it
was a different parameterization method, not a different theory.
For most cases, the performance of AM1 is considered to be generally
superior to MNDO.


 Regards,  Andy Holder

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
 
UUUU  UUU MMM   MMKK KKKK   CCCC   |           ANDREW J. HOLDER
 UU    U   MM   MMK   K    CC  CC  | Asst. Prof. of Comp./Org. Chemistry
 UU    U   MMM M MK KK    CCC      |          Dept. of Chemistry
 UU    U   M MM  MK   KK   CC  CC  |  University of Missouri-Kansas City
  UUUUU   MMM M MMKK   KK   CCCC   |         Kansas City, MO  64110
                        KK         |          aholder@cctr.umkc.edu
                          K        |  (816) 235-2293, FAX (816) 235-5502
 
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
 

From leoh@maple.lemoyne.edu  Fri Apr 21 17:47:03 1995
Received: from maple.lemoyne.edu  for leoh@maple.lemoyne.edu
	by www.ccl.net (8.6.10/930601.1506) id RAA10927; Fri, 21 Apr 1995 17:43:56 -0400
Received: by maple.lemoyne.edu (MX V4.1 VAX) id 11; Fri, 21 Apr 1995 17:42:41
          EST
Date: Fri, 21 Apr 1995 17:42:37 EST
From: "Leo, Howard" <leoh@maple.lemoyne.edu>
To: chemistry@ccl.net
Message-ID: <0098F397.C17FA900.11@maple.lemoyne.edu>
Subject: Solaris on a PC question


Is anyone running Sun Solaris on a PC? If so, could you tell me
	1) how well does it execute DOS programs?
	2) will it support additional terminals on one CPU?
	3) will it run GAMESS or MOPAC?
Thanks!                             Howard Leo
				    Leoh@LeMoyne.edu

