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Date: Tue, 14 Nov 95 11:53:10 -0800
From: Marek Strajbl <strajbl@silicon.karlov.mff.cuni.cz>
Message-Id: <9511141953.AA27817@silicon.karlov.mff.cuni.cz>
To: CHEMISTRY@ccl.net
Subject: Summary: force f. and sugar puckering


Dears,
here's summary of responses to following posting:

>Subject: force field and sugar puckering
>
>Dear netters,
>
>can someone give hints, what force field or semiempirical method are
>best for predicting sugar puckering of ribose (deoxyribose) in 
>nucleosides.
>
> Thanks,

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

	From csonka@web  Fri Nov 10 18:12:56 1995
	<strajbl> Subject: Re: CCL:force field and sugar puckering
	Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii
	Status: RO

	Marek

	MM3(92) will do. See the Dowd, French paper in Carbohydr. Res.
	264 (1994) 1.  I think MM2 will be ok too.

	Gabor

	--

	Gabor I. Csonka                 Budapest University of
	Technology FAX: (361) 463.36.42            Inorganic Chemistry
	Dept. Ch. Bldg csonka@web.inc.bme.hu           H-1111, Bp.
	Szent Gellert ter 4
	http://www.fsz.bme.hu/bme/chemical/csonka.html
-------------------------------------------------------------------

	From box@scisun.sci.ccny.cuny.edu  Fri Nov 10 19:34:03 1995
	CHEMISTRY@ccl.net, strajbl Subject: Re:  CCL:force field and
	sugar puckering Status: RO

	Hi

	You can try STR3DI.EXE which has a new force field specifically
	designed to incorporate lone pairs into molecular mechanics.

	Look at the web page for Exorga Inc., who are the distributors
	of the program.

	http://pages.prodigy.com/NJ/exorga/exorga.html


	VB

------------------------------------------------------------------------
	From scott@sciencemedia.com  Fri Nov 10 20:28:52 1995
	scott@sciencemedia.com (Scott Struthers) Subject: Re: CCL:force
	field and sugar puckering Status: RO


	Contact Carl Ewig (carl@biosym.com) or Arnie
	Hagler(arnie@biosym.com).  They recently finished a whole bunch
	of work on exactly this subject, both quantum and force field
	based.

	================================================================
	   R. Scott Struthers, Ph.D.    (e-mail:
	   scott@ScienceMedia.com) Co-Founder Director, Business
	   Development

	   ScienceMedia Inc.                     Phone: (619) 943-0545
	   1827 Autumn Place                     Fax:   (619) 943-9714
	   Encinitas, CA  92024
	================================================================


-----------------------------------------------------------------------
	From chpajt@bath.ac.uk  Fri Nov 10 22:19:31 1995

	I would suggest Charmm - I would avoid AM1 or PM3.  I would be
	very interested in any other replies - please sould you summery
	to the list.

	All the best

	Alex (see my web page about comformational errors in AM1)


	+--------------------------------------------------+ |Alternate
	E-mail A.J.Turner@Bath.ac.uk            | |www home @
	http://www.bath.ac.uk/~chpajt/home.html|
	+--------------------------------------------------+
---------------------------------------------------------------------------

	From al@bob.usuf2.usuhs.mil  Fri Nov 10 23:20:23 1995

	Alfred French uses MM3 almost exclusively for his carbohydrate
	work.  He is perhaps the expert in the field;  he has edited an
	ACS symposium volume.
					Alfred Lowrey


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


From owner-chemistry@ccl.net  Tue Nov 14 09:34:10 1995
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Date: Tue, 14 Nov 1995 09:25:54 -0500 (EST)
From: Cheol Choi <choic@gusun.acc.georgetown.edu>
To: CHEMISTRY@ccl.net
Subject: Force Constant in G94?
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Dear Netters:

Recently, we got the Gaussian 94.

In G92 geometry optimization, it actually calculates the
Hessian matrix and force. 
Since G94 uses the redundant coordinate, there might be a big
change in geometry optimization.
But what I still need is the Hessian matrix in Cartesian Coordinate.
Since frequency calculation is expensive, I don't like to try it.

So I used the opt=z-matrix option to get hessian matrix in cartesian 
coordinate.
That option gave me the hessian matrix with sto-3g basis set but not with
larger basis sets.

I don't know why larger than sto-3g basis set didn't give me the hessian
metrix. (In fact, the hessian only can be extracted from checkpoint file.)

Please, let me know how to get hessian metrix with larger basis sets.

Thanks a lot.


Cheolho Choi
Georgetown Univ.

From goeller@organik.uni-erlangen.de  Tue Nov 14 09:49:10 1995
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From: Andreas Goeller <goeller@organik.uni-erlangen.de>
Message-Id: <199511141445.PAA09529@derioc1.organik.uni-erlangen.de>
Subject: Thiirenes
To: chemistry@www.ccl.net
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Dear CCLers,

I would appreciate to get some references on Thiirenes (=Ethylenesulfit)
, Thiiranes (=Acetylenesulfite), Bisoxothiirenes and Bisoxothiiranes for
an ab initio study. Experimental as calculational results.
Also derivatives are very welcome.


                                   O     O            O     O
                                    \\ //              \\ //
         S            S               S                  S
        / \          / \             / \                / \
       C___C        C===C           C___C              C===C

Thanks in advance




				Bye, AHG...

---------------------------------------------------------------
   Andreas Goeller               Computer Chemie Centrum der
   Dipl.-Chem.    	        Universitaet Erlangen/Nuernberg
                                      Naegelsbachstr. 25
phone: +49(0)9131-856583               D-91052 Erlangen 
  fax: +49(0)9131-856565                   Germany
email: goeller@organik.uni-erlangen.de      
http://www.organik.uni-erlangen.de
---------------------------------------------------------------

From qojskd@uscmail.usc.es  Fri Nov 10 13:03:00 1995
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Date: Fri, 10 Nov 1995 18:32:51 +0100
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From: "Javier Sardina"  <qojskd@uscmail.usc.es>
To: chemistry@www.ccl.net
Subject: Freeware NMR proccesing




  Dear netters:

  It is a pleasure to announce that version 3.0.4 of the NMR processing program 
SwaN-MR is available, as three compressed-self-expanding files, (via anonymous 
ftp) from :

sfdzuma.usc.es (193.144.75.69)
directory: /pub/NMR/SwaN-MR.304

SwaN-MR is a FREEWARE program for the Macintosh and PowerMac. It processes and 
analyzes NMR spectra (1D to 4D, from Varian Gemini, Bruker nad TecMag 
spectrometers). It is also very useful in annotating, printing and presenting 
spectra. The program has been written by:

Dr. Giuseppe Balacco
MENARINI s.r.l.
Via Sette Santi, 3
I-50131 Firenze
ITALY

In order to use SwaN-MR you need to write a SIGNED LETTER (no fax or e-mail 
messages) to Dr. Balacco requesting a LICENSE. With the license you will receive
a password to decompress the program file.

  If you want to check out the program before asking for the license you can try
Snail-MR (included in the demo file). It does everything that SwaN-MR does but 
much more slowly.

The program's capabilities include:
Weighting (9 different window functions)
FFT (real, complex, hypercompex, etcI)
Phase Correction (1 manual and 2 automatic options)
Magnitude representation
Baseline Correction (6 options, including 5th degree polynomials and 
trigonometric series)
BasePlane correction
Integration (manual and automatic)
Least Squares Fitting (to Lorentzian or Gaussian functions)
Quanto-mechanical simulations
Fast Linear Prediction
Digital Solvent Suppression
T1 calculation (inversion recovery)
Spectral Editing (algebraic addition and much more)
Symmetrization

What's in the files?

Swan.sea contains the main application. It is protected with a password.

Extra.sea contains:
- instructions for the program;
- the library "ObjectSupportLib";
- instructions and utilities for transferring Gemini files;
- other small applications.
This file is not protected (it is freely accessible).

Demo.sea contains:
- a few demo spectra.
- Snail-MR.
This file is not protected (it is freely accessible).

  Happy NMR processing.




        F. Javier Sardina
                                                  phone: (34)-81-591085
  Departamento de Quimica Organica                (34)-81-563100-Ext 4249
Universidad de Santiago de Compostela      fax:   (34)-81-595012
15706 Santiago de Compostela. SPAIN        e-mail: qojskd@usc.es



From cletner@remcure.bmb.wright.edu  Tue Nov 14 10:04:10 1995
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Date: Tue, 14 Nov 1995 12:50:17 -0500 (EST)
From: Charles Letner <cletner@remcure.bmb.wright.edu>
Subject: Center of coordinates
To: Computational Chemistry List <CHEMISTRY@www.ccl.net>
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Hello all,
	This is probably a basic question for anyone who is a
crystallographer.  I'm not and keep wondering about this.  The coordinates
of crystal structure give positive and negative values in the x, y,
and z dimensions (i'm mainly speaking of pdb format files).  This inidates
that the origin of the crystal is located someplace!  What I want to know
is, is there a standard/specification of where the origin is located?
Thanks for your response,
Chuck

Charles Letner
Wright State University
Department of Biochemistry
Dayton, OH 45435
e-mail: cletner@remcure.bmb.wright.edu



From moshe_o@VNET.IBM.COM  Tue Nov 14 10:19:11 1995
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Date: Tue, 14 Nov 95 15:52:09 IST
From: "Moshe Olshansky" <moshe_o@VNET.IBM.COM>
To: chemistry@www.ccl.net
Subject: Combining different basis sets


Dear CCL'ers!
We are working on computational aspects of the Hartree-Fock procedure.
For this purpose we would like to have some f-type basis functions
but not too many of them,  while all the basis sets we have either
do not have f functions at all or have too many of them (our trial
molecule contains H C N and O atoms).
Since we are not chemists I would like to ask the following
(possibly very trivial) question:  does it make any sense to combine
two different basis sets (for example,  take a smaller basis set for
H and C and a larger one - containing d and f functions - for N and O)?

Thank you very much and please forgive my ignorance
Moshe Olshansky
IBM Israel Science and Technology
<moshe_o@vnet.ibm.com>

From toukie@zui.unizh.ch  Tue Nov 14 10:34:11 1995
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	id AA13422; Tue, 14 Nov 95 16:01:20 +0100
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Date: Tue, 14 Nov 1995 17:01:45 +0100 (MET)
From: "Hr Dr. S. Shapiro" <toukie@zui.unizh.ch>
Sender: toukie@zui.unizh.ch
Reply-To: toukie@zui.unizh.ch
Message-Id: <61305.toukie@zui.unizh.ch>
To: chemistry@www.ccl.net
Subject: ? re MOPAC keywords for COSMO


Dear Colleagues;

     I would like to obtain solvated geometries for some molecules of inter-
est.  I can take the Z-matrix for a molecule whose geometry has been "opti-
mised" in the gas phase and use that as an input for either MOPAC7 or MOPAC93
running the COSMO subroutine.  Using the keywords

                   pm3 ef precise nointer eps=78.4 nspa=60

I get an output geometry in a short time, satisfying SCF criteria and with
GRAD values <2.  My questions are as follows:

     (i) Do I need the keyword "precise" for COSMO runs, particularly
         since the final value of GRAD obtained is rarely <0.5?

    (ii) Should I use any _other_ keywords to improve the prediction of
         the solvated geometries I am seeking?  If so, which additional
         keywords would you recommend, and how would they advantageously
         contribute to the calculation of the solvated geometries that
         I seek?

     Thanks in advance to all responders.


Sincerely,

(Dr.) S. Shapiro
Inst. f. orale Mikrobiol. u. allg. Immunol.
Zent. f. Zahn-, Mund- u. Kieferheilkd. der Univ. ZH
Plattenstr. 11
Postfach
CH-8028 ZH 3

Internet: toukie@zui.unizh.ch
FAX-nr: ( ... + 1) 261'56'83

From guillem@gauss.uib.es  Tue Nov 14 12:49:12 1995
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To: chemistry@www.ccl.net
Subject: IGLO program 
Date: Tue, 14 Nov 95 18:34:33 +0000
X-Mts: smtp


Dear Netters,

I would like to obtain information regarding the IGLO program (or MOLPRO 
package?) since my aim is to buy it. Could anybody to help me with related info?

Many thanks in advance.

Guillermo A Suner

------------------------------------------------------------------------ 
Dr Guillermo A. Suner; Dep. de Quimica, UNIVERSITAT DE LES ILLES BALEARS
E-07071-Palma de Mallorca, SPAIN.
E-mail: guillem@gauss.uib.es    Tel: + 34 71 173498  Fax: + 34 71 173426 
WWW URL: http://www.uib.es/depart/dqu/dquo/suner.html

From mas@qc.ag-berlin.mpg.de  Tue Nov 14 13:04:12 1995
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Date: Tue, 14 Nov 1995 18:57:01 +0100
From: mas@qc.ag-berlin.mpg.de (Marek Sierka)
Message-Id: <9511141757.AA13603@gea.qc.ag-berlin.mpg.de>
To: CHEMISTRY@www.ccl.net
Subject: BSSE



Dear Moshe,

        Good basis set has to be properly balanced, otherwise it introduces
so called Basis Set Superposition Error. In case of the unbalanced basis set,
it leads to the artificial charge transfer, and also gives nonphysical,        
stabilizing contributions to the enery of molecule. This stabilizing will
then occure irrespective of whether there is any genuine binding interaction
in the molecule or not. It will give a spurious increase in the binding 
energy.The choice of proper basis set is kind of art, so you have to be
very careful about it. Try this:                                               
  
http://www.emsl.pnl.gov:2080/forms/basisform.html
This www server contains several basis sets, so maybe you can find
something useful.

Marek Sierka
Max-Planck Society
Quantum Chemistry Group at the Humboldt Univ.
Joegerstrasse 10/11
D-10117 Berlin, Germany
e-mail: mas@gea.qc.ag-berlin.mpg.de

From wtwinter@mailbox.syr.edu  Tue Nov 14 15:19:14 1995
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Date: Tue, 14 Nov 1995 15:03:36 -0500 (EST)
From: "William T. Winter" <wtwinter@mailbox.syr.edu>
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To: Charles Letner <cletner@remcure.bmb.wright.edu>
Cc: Computational Chemistry List <CHEMISTRY@www.ccl.net>
Subject: Re: CCL:Center of coordinates
In-Reply-To: <Pine.3.07.9511141217.C29626-a100000@remcure.bmb.wright.edu>
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The choice of origin in a crystal structure is dependent upon the space 
group symmetry.  For example, in space group P2sub1 2sub1 2sub1 it is midway 
between the three sets of non-intersecting two fold screw axes.  Origin 
positions for different space groups may be found in vol I of the International
 Tables for X-ray Crystallography in each space group description.  Of 
course in P1,  which has no symmetry, the choice is arbitrary and in other 
cases individuals have elected to use a non-conventional origin for various 
reasons 

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
William T. Winter                      Phone: (315)470-6876
315 Baker Lab                          FAX:   (315)470-6856
SUNY-ESF                               Internet: wtwinter@mailbox.syr.edu
Syracuse, NY 13210-2786                URL     http://www-chem.esf.edu


From owner-chemistry@ccl.net  Tue Nov 14 18:34:16 1995
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Date: Tue, 14 Nov 1995 15:18:53 -0800
From: David Case <case@scripps.edu>
To: chemistry@ccl.net
Subject: New version of NAB now available


ANNOUNCE: version 1.1 of the NAB molecular manipulation language now available.

Tom Macke and David A. Case

We have developed a new approach to the modelling of nucleic acids that is
implemented as a computer language called NAB.  The method was
primarily designed to construct models of helical and non-helical nucleic
acids from a few dozen to a few hundred nucleotides in size, and uses a
combination of rigid body transformations and distance geometry to create
candidate structures that match input criteria.  The language is designed
to provide a flexible way to described nucleic acid structures at an atomic
level of resolution, and contains built-in connections to the AMBER
molecular modelling package, the MEAD programs to compute solvation effects
at the Poisson-Boltzmann level, and the AVS visualization system.

NAB is a computer language (specified through lex and yacc) that allows
nucleic acid structures to be described in a hierarchical fashion, using a
language similar to C or awk, but designed especially for the manipulation
of nucleic acid structures.  We have applied NAB to duplex- and triplex- and
tetraplex DNA, to RNA hairpins and pseudo-knots, to closed-circular DNA, and
to models of recombination sites.  Prospects and progress toward
implementation of these methods to larger systems (such as tRNA, the
hammerhead ribozyme, and the Group I intron) look positive.  This language
may also be useful for other molecular modelling tasks, and a protein
library is included in the distribution.  NAB can also be used as a general-
purpose language for writing programs that deal with three-dimensional
biomolecular structures.

New features in version 1.1:

-- better distance geometry performance
-- better error messages
-- new molecule attributes
-- support for peptides and proteins

NAB can be obtained from ftp://ftp.scripps.edu/pub/macke/nab5.v_1_1.tar.Z.
Send questions/comments to macke@scripps.edu.

From scho@quantum.cm.utexas.edu  Tue Nov 14 18:49:17 1995
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From: scho@quantum.cm.utexas.edu (Sarah Schofield )
Message-Id: <9511142345.AA19845@quantum>
Subject: Spartan sigma bond crashes
To: chemistry@www.ccl.net
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Hi Netters: 
I send in this question on behalf of an organic professor here at U. Texas
who has been using Spartan to generate illustrations for his sophmore 
class.  He has a problem related to his upcoming presentation 11am Wed. 
Central US time.  A reply before 10am would be very appreciated.  
Here is the question.  Why does Spartan crash when asked for the HOMO 
of H_2?  He has tried several AM1 and ab initio basis sets.  He has also 
tried other molecules.  Whenever he gets to the point of a sigma bond 
the programs crashes.  Any advice? 
    
-----------------------------------------------------------------
Sarah Ann Schofield                scho@quantum.cm.utexas.edu  

Department of Chemistry and Biochemistry       (512) 471-1023  
University of Texas at Austin             fax: (512) 471-8696  
Austin, Texas 78712             
----------------------------------------------------------------- 

>From E.WEZENBEEK@elsevier.nl Tue Nov 14 06:28 EST 1995
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Subject:  Contents-Alert Fullerenes





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CONTENTS-ALERT FULLERENES: a FREE alerting service

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From bcnlma@hkpucc.polyu.edu.hk  Tue Nov 14 22:34:20 1995
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Date: Wed, 15 Nov 1995 11:29:21 +0800
To: CHEMISTRY@www.ccl.net
Subject: [Q]: How to keep a particular state in G94?


Dear all,

        I had a question that I hope someone on the list can help.  I am
doing some calculations on small transition metal compound using Gaussian
94.  I carried out an SCF calculation which gives me a particular state but
I would like to calculate a DIFFERENT state.  After using
guess=(read,alter) to get to the state I like, the SCF brings it back to
the original state that I do not want.

        My question is: is there anyway I can get Gaussian to keep the same
state from my guess=(read,alter) job?

yours sincerely,
Ida N. L. Ma


Dr. Ida N. L. Ma
Assistant Professor,
GH623, Dept. of Applied Biology and Chemical Technology
Hong Kong Polytechnic University
Hung Hom, Hong Kong
Tel:    852-27665620
FAX:    852-23649932



