From Pieter.Stouten@EMBL-Heidelberg.DE  Sun Oct  7 12:22:35 1992
Date: 07 Oct 1992 11:22:35 +0100
From: Pieter Stouten <Pieter.Stouten@EMBL-Heidelberg.DE>
Subject: Re: Ribbons v2.0
To: chemistry@ccl.net
Organization: European Molecular Biology Laboratory, Heidelberg


Reply-To: Stouten@EMBL-Heidelberg.DE

In article <9210061456.AA01134@sagi.wistar.upenn.edu> Curtis Wahlgren
<curtis@sagi.wistar.upenn.edu> wrote:

|>Where does one obtain a copy of Ribbons? 

The Ribbons 2.0 manual says it is written by Mike Carson, University
of Alabama at Birmingham, Center for Macromolecular Crystallography,
252 BHS, 79 THT University Station, Birmingham, AL 35294. E-mail:
carson@uabcmc.bitnet. 

References:
* M Carson & CE Bugg, "Algorithm for Ribbon Models of Proteins,"
  J. Mol. Graphics, 4 (1986) 121-122.
* M Carson, "Ribbon Models of Macromolecules," J. Mol. Graphics 5
  (1987) 103-106.

Hope this helps, Pieter Stouten.

#### #   # ###  #     European Molecular Biology Laboratory
#    ## ## #  # #     Protein Design Group
###  # # # ###  #     Meyerhofstrasse 1, D-6900 Heidelberg, Germany
#    #   # #  # #     e-mail: stouten@embl-heidelberg.de
#### #   # ###  ####  phone: +49-6221-387 472, fax: 387 517

From jkl@ccl.net  Fri Oct  9 20:30:05 1992
From: jkl@ccl.net (Jan Labanowski)
Date: Sat, 10 Oct 1992 00:30:05 -0400
To: chemistry@ccl.net
Subject: quatfit.c - program to fit molecules


Dear Netters,

Remember the fitest.f program by Dave Heisterberg (djh@ccl.net)? The fitest.f
is a FORTRAN program which shows that the quaternion method of fitting two
sets of points is probably the fastest one available. There are several
approaches to the rigid fit of molecules (sorry for no authors and
citations --- I really do not have time to write a review), e.g.:
  1. Iterative methods
     a) points are connected with "springs" of zero length and force constant
        is equal to the statistical weight for a given atom pair, and the
        minimizer optimizes the stretch energy of the springs as a function
        of translation vector and Euler angles,
     b) Taylor expansions of rotation matrix after centers where superimposed,
        and iterative improvement of it.

  2. Methods based on linear algebra
     a) Principal component analysis of the X'Y product
     b) Quaternion method

Methods 1a, and 1b are O.K. but slow (iterative). Method 2a will perform
inversion if needed to get a better fit (i.e., can change chirality).
Method 2b is fast (one step) and will not inverse coordinates.

So now is the quatfit.c program, It uses quaternion method to fit molecules.
This method was developed before the Kearsley paper was published:
Kearley, S.K., J. Comput. Chem, 11, 1187-1192 (1990),  and is actually
slightly different. One day Dave may publish a paper on this, but he really
does not have time to do it now.

The program quatfit.c is placed in our archives on www.ccl.net in
/pub/chemistry/quatfit directory. The following files are there:
  quatfit.c      --- source of the program. Compile it with:
                        cc -o quatfit quatfit.c -lm
  quatfit.roff   --- (t|n|dit|pt)roff source of man page. To process it, use
                     your version of roff with -man. It is intended to be
                     installed on Unices with the Documenter's Workbench
                     option.
  quatfit.ps     --- a PostScript version of the man page.
  quatfit.txt    --- a pure text version of the man page.
  quatfit.ascii  --- a text version of man page as came from nroff (with
                     underlines and backspaces for printer or terminal
                     display
  readme         --- this file.
  rm.xyz         --- example of reference molecule
  fm.xyz         --- example of fitted molecule
  fmmod.xyz      --- example of the fit result
  stat.txt       --- example of fit statistics file
  pairs.tab      --- example of pairs and weights file

How to get it?

Via ftp:
ftp www.ccl.net  (or ftp 128.146.36.48)
Login: anonymous
Password: Your_email_address
ftp> ascii
ftp> cd /pub/chemistry/quatfit
ftp> mget *
ftp> quit

Via e-mail:
Send message:
   send ./quatfit/quatfit.c     from chemistry        
   send ./quatfit/quatfit.roff  from chemistry        
   send ./quatfit/quatfit.ps    from chemistry        
   send ./quatfit/quatfit.txt   from chemistry        
   send ./quatfit/quatfit.ascii from chemistry        
   send ./quatfit/readme        from chemistry        
   send ./quatfit/rm.xyz        from chemistry
   send ./quatfit/fm.xyz        from chemistry
   send ./quatfit/fmmod.xyz     from chemistry
   send ./quatfit/stat.txt      from chemistry
   send ./quatfit/pairs.tab     from chemistry
to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET and the files will be
automatically sent to your mailbox.

Note, the program has a copyright notice, so if you want to sell it  (:-)},
you have to ask us first.

Jan Labanowski
Ohio Supercomputer Center
jkl@ccl.net


From shen@athena.cs.uga.edu  Sat Oct 10 06:51:24 1992
Date: Sat, 10 Oct 92 10:51:24 EDT
From: Mingzuo Shen <shen@athena.cs.uga.edu>
To: chemistry@ccl.net
Subject: Analytic energy 2nd deriv. in the presence of ECP - the answer


Hi all,

    In case anyone else is interested (I have one request for 
information): the analytic energy second derivative technique in the
presence of ECP has been coded in the program system GRADSCF,
which is known to run on the Cray family of computers.

    Contact information:

	Dr. Andrew Komornicki
 	komornick@jupiter.arc.nasa.gov;
	Polyatomics Research Institute
	415-964-4013

    Literature:

	@article{breidung88,
        	author  = {J. Breidung and W. Thiel and A. Komornicki},
	        title   = {Analytical second derivatives for effective core potentials},
        	journal = {Chem. Phys. Lett.},
	        year    = {1988},
	        volume  = {153},
	        pages   = {76-81},
	}

    Thanks to the following quantum chemists for answering my inquiry:

	jan@si.fi.ameslab.gov (Jan Jensen)
	mike@si.fi.ameslab.gov (Mike Schmidt)
	george@archimedes.cray.com (George Fitzgerald)

    Mingzuo Shen

From u926135@minke.iasos.utas.edu.au  Sun Oct 11 12:22:42 1992
Date: Sun, 11 Oct 92 02:22:42 +1000
From: Adrian Hassal Lewis <u926135@minke.iasos.utas.edu.au>
To: CHEMISTRY@ccl.net
Subject: Computational chemistry on the RS/6000



I originally posted this message on the internet news, so I apologise 
if you've seen this before.  However, it was recommended by a 
respondent to my post that I try here.  And as I'm still looking for 
quite a bit of information, I've decided to do so.

However there is one alteration, I *am* trying to get electronic 
addresses for Biosym.  The problem is that BIOSYM.COM (also 
146.202.0.0 & 146.202.0.2) is dead. Specifically, email (to the 
postmaster) either bounces or there is no response when it doesn't. 
Also, direct connection gives a time-out or 'host unreachable'.  So if 
anyone could help me on that specific problem, it would be greatly 
appreciated.

************************original post follows************************

IBM advertises the companies listed below as having computational 
chemistry packages for its RS/6000 workstations.

Aspen Technology Inc - Cambridge, MA, USA
            Ph: (617) 497-9010 Fax: (617) 497-7806
Biosym - San Diego, CA, USA
            Ph: (619) 597-9707 Fax: ??
Chemical Design - ??, UK
            Ph: (201) 529-3323 Fax: 44-865-250-270
Gaussian Inc - Pittsburgh, PA, USA
            Ph: (412) 621-2050 Fax: (412) 621-3563
Molecular Simulation Inc - Sunnyvale, CA, USA
            Ph: (408) 732-9090 Fax: (408) 732-0831
Simulation Sciences Inc - Fullerton CA, USA
            Ph: (714) 879-9180 Fax: (714) 447-4107
Tripos - St. Louis, MO, USA
            Ph: (314) 647-1099 Fax: (314) 647-9241
Wavefunction Inc - Irvine, CA, USA
            Ph: (714) 955-2120 Fax: ??

Unfortunately, I haven't been able to get any information on the 
various packages on offer; the information below is about all I've 
been able to get.  Yes, I have talked to IBM locally, but whilst being 
very helpful, they weren't very helpful (if you know what I mean) (the 
list is from IBM).

Primarily, I'm trying to find contact addresses (preferably e-mail) 
for AUSTRALIAN distributors of these packages.  But _not_ Biosym, I 
have theirs (Insight II is the only one of these packages that I've 
used - on the SG Iris).  In addition, it would be great if there are 
any reviews/comparisons of these packages that anyone knows of.  Also, 
any comments are welcome.

The sorts of molecules I'm interested in are small polycyclic aromatic 
and aliphatic (cage) systems, with heteroatoms in the rings.  The 
types of investigations would include looking at thermal and kinetic 
stabilities, decomposition pathways, and especially the molecular 
orbitals (for example - are the 'aromatic' systems 
aromatic/antiaromatic/non-aromatic?).

The workstation is a basic RS/6000 320 (maybe a 220 as well), and I 
want to know what sort of system upgrades are advisable. 

Please e-mail any responses to u926135@minke.iasos.utas.edu.au
Thanks in advance,
                  ajax

(relatively) new user, please excuse any bludners.

From br1@inel.gov  Sat Oct 10 12:44:38 1992
Date: Sat, 10 OCT 92 09:47:38
From: br1@inel.gov
To: chemistry@ccl.net
Subject: Grants Overhead





	NRC%"<ravishan@swan.wesleyan.edu>"  "G. Ravishanker"  wrote:

<Folks
<
<I was listening to parts of Bill Clinton's interview with Larry King on
<CNN last night and one question and its answer interested me very much and
<thought people in this list may be interested in discussing about it.
<
<Someone called in with a question to Clinton as to what his strategy is
<towards basic research in academic instituions. The question also
<mentioned that Clinton plan proposes to cut budget for such research. His
<explanation was that he does not intend to cut budget for research per se,
<but plans to cut the adminstrative cost associated with the grants (I
<guess he was referring to indirect costs) and funnel most of it back to
<research grants. Therefore, he claims that his plan actually will funnel
<more money back into research. 
<
<On the surface this looks great, however, how can the Govt. control
<indirect costs, except to say that we will not give beyond a certain
<percent of the direct costs to you. Will the Adminstrators of the academia
<agree to such proposal? (Since the indirect costs can run as high as 70%
<in some cases, the savings from reducing this may be significant...)
<What do people in this newsgroup think of this idea? 
<
<Ravi



	You work in a sheltered setting if you think indirect costs
can be "as high as" 70%.  That may be true for academic institutions,
as the caller directed his question, but I doubt that Clinton was
focusing his answer to the letter of the caller's question.  The
overwhelming majority of government reseach money is not spent by
scientists at academic institutions.  Actually, the share of research 
funds that go to academic institutions is quite small (see the U.S. 
Census Bureau publications).  For example the DOE has about a dozen, 
very large laboratories that it runs.  The indirect costs at the lab 
I am leaving could choke a horse: 250% not (not) including any kind of 
secretarial support (like drawing figures for publications or typing 
papers or letters) or travel or even matching funds for equipment
purchases.  My guess is that all of the federal agencies run with
similar efficiency.  Thus, one has to wonder what portion of the NSF
budget finds its way to the universities.  Bill Clinton is definitely
on the right track by attacking this "fat"; which has ballooned under
the Reagan and Bush administrations.

	As I see it; the (fed) budget allocated for research could be 
cut in half while maintaining an increase real dollars spent on 
research.  The first step is to release most (if not all) of the 
high-priced welfare recepients from their "management" positions in
federal agencies.


                 			Happy Discussions,
					
                                        Randall C. Boehm, Ph. D.
					BR1@INEL.GOV (4 more weeks)


From PA13808@UTKVM1.bitnet  Sat Oct 10 15:07:13 1992
Date: 10 Oct 92   15:06 LCL
From: PA13808%UTKVM1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU
To: CHEMISTRY@ccl.net
Subject: BITNET mail follows


 REFERENCES ON POLARISABILITIES
  Here are some references to uses of dipole polarisabilities. There
 are many more which predate the recent interest in NLO properties.
    1. QUALITATIVE IDEAS. The term polarisability was used for many
 years by physical organic chemists to describe the tendency of a molecul
 e to distort on the approach of a reagent particularly a proton.I sugges
t the paper POLARIZATION AND POLARIZABILITY IN CHEMISTRY by R.J.W.
LE FEVRE REV. PURE and APP. CHEM.vol 20 pages 67-79 (1970) for a good des
cription and refs to earlier work.It includes erf to the KERR effect and
 electric birefringence measurements and a discussion of the stereo
stuctural app of anisotropic polarizabilities. SEE other reviews by this
author.
   2 PKas. It is possible that Doug. Smith was referring to a paper by
POPLE on the inductive effect of alkyl groups in amines.(pubno 139 in the
pople pub list given in INT J QUANT CHEM VOL 37 p355. The Methyl INDUCTIV
E EFFECT ON ACID BASE STRENGTHS TETRAHEDRON LETTERS 34 p2959 1970.At
that time there was a discussion obout what happens when we replace
a H by a CH3 group and it was usually thought the effect on many
properties was due to the grater polarisability of the C-N compared
to the N-H bond since MULL pop indicated the CH3 group attracted electron
s rel to HYD.!
  3.POL (CNDO/2) have been correlated with the Hansch hydrophobic
parameter D.V. Lewis J.of COMP CHEM 10,145-151(1989)
  4.POL and collision induced Infra red Absorption Chem. Phys LETT
 26 474(1974) W.PERSON et al.
  5.for many other app see refs 4-24 in a paper by APPLEQUIST FUND
 relationships in the theory of electrical Multipole Moments and Multipol
e Polarizabilities in Static Fielsd. CHEMICAL PHYSICS VOL 85 279-290       d
  6.BIRGE(J.CHEM. PHYS vol 79 2256(1983) lists a number of phenomena
which require a knowledge of the polarizability tensor.
  7.HANNACHI AND ANGYAN. Ab initio calc together with a microscopic
 modeling of rare gas matrices using experimental ! dipole polarizabiliti
 es. THEOCHEM. vol 232 pages 97-110 1991.
  Should be enough to get you started. JEB(PA13808 at UTKVM1)