From BORKENT@caos.caos.kun.nl Mon Oct 4 10:08:35 1993
Date: Mon, 4 Oct 1993 10:52:08 METDST
From: BORKENT@caos.caos.kun.nl
Subject: entropy of methyl group
To: CHEMISTRY@ccl.net
Message-Id: <01H3PN4OEON694DS47@caos.caos.kun.nl>
Dear netters,
Is there somebody outthere who can educate me on the following:
I'm using AMPAC to reproduce a racemization path, starting from
the transition state, down to one enantiomer.
In the molecule there is a methyl group, rotating (almost) freely
in the TS and enantiomer, but hindered halfway.
As an organic chemist I've always been told that this causes an
entropy effect, increasing the energy of the system, maybe even
creating another TS? So I would like
to make this correction to the enthalpy (heat of formation) values
obtained from AMPAC, but the question is, how?
The manual states that a FORCE/THERMO calculation only makes sense in
stationary points, not halfway.
I can trace some frequencies of the CH3 oscillations, but can these be
used to calculate an entropy contribution at any point of the curve?
So far the problem, no need to elaborate further and to bore the
general audience. I would be grateful to people giving this case a
thought and I am of course willing to provide more details if needed.
Please contact me directly to discuss the issue and I'll summarize
anything useful.
Hens Borkent
CAOS/CAMM Center
University of Nijmegen
The Netherlands
Tel +31-80-652137
borkent@caos.caos.kun.nl
From chp1aa@surrey.ac.uk Mon Oct 4 10:36:06 1993
From: Mr Andrew D Allen <chp1aa@surrey.ac.uk>
Message-Id: <9310040957.AA28977@central.surrey.ac.uk>
Subject: DFT: SUMMARY
To: chemistry@ccl.net
Date: Mon, 4 Oct 93 10:57:52 BST
Here it is at last. Thanx to all who contributed, I will leave the summary on
our local ftp server (131.227.110.2 : login anonymous, etc) for a while, in
postscript and ascii form.
Density functiional theory
An introduction to DFT may be found in:
J.Weber, H.Huber and H.P.Weber,
Chimia vol 47, 57-59 (1993)
Computational Chemistry: All you ever wanted to know about
density functional theory.
Dear Andy,
Springer-Verlag published a couple of book on density functional
methods. I attach the respective information for you. The book
edited by J.K. Labanowski is in high demand and might be out of
print (only few copies were available when I last looked into
the sales figures). There have also been several contributions
to Theor. Chim. Acta.
Sincerely yours,
Dr. Rainer Stumpe
Chemistry Editorial
Springer-Verlag
Tiergartenstr. 17
D-69121 Heidelberg
Phone: +49-(0)6221-48 73 10
Fax: +49-(0)6221-41 39 82
INTERNET:stumpe@spint.compuserve.com
Lecture Notes in Chemistry Vol. 50
D. MUKHERJEE, Calcutta, India (Ed.)
Aspects of Many-Body Effects in Molecules and Extended Systems
Proceedings of the Workshop-Cum-Symposium Held in Calcutta,
February 1-10, 1988
1989. VIII, 565 pp. Soft cover DM 128,-. ISBN 3-540- 50765-5
Contents:
Separability in Many-Electron Problem;
Size Extensivity and Size-Consistency.
Many-Body Perturbation Theory and Coupled-Cluster Theory of
Atomic and Molecular Electronic Structure.
Propagators in Bound States and Resonances.
Condensed Matter and Related Topics.
Many- Body Methods in Dynamical Processes.
Relativistic Methods with Applications.
Group-Theoretic Techniques.
Few-Body Methods, Large-N Expansion and Other Mathematical
Topics.
Densities and Density-Functionals.
List of Participants.
Subject Index.
This volume features invited lectures presented in the
workshop-cum-symposium on aspects of many-body effects in
molecules and extended systems, Calcutta, February 1 - 10,
1988. The organizers invited leading experts to present recent
developments of many-body methods as applied to molecules and
condensed systems. The panorama portrayed is quite broad, but by
no means exhaustive. The emphasis is undoubtedly on a "molecular
point of view".
U. Harms, Industrieanlagen-Betriebsgesellschaft (IABG)
Ottobrunn, FRG (Ed.)
Supercomputer and Chemistry
IABG Workshop 1989
1990. Approx. 150 pp. 46 figs. 38 tabs. Softcover DM 98,- ISBN
3-540-52915-2
This volume represents the contributions of the 1989 IABG
workshop on supercomputers and chemistry.
>From the CONTENTS :
Transputer Graphic Supercomputing MIMD Type Computers Drug
Design Peptide and Protein Engineering Density Functional
Calculations
Computational Chemistry, Theoretical Chemistry, Drug Design,
Protein Engineering, Super and Parallel Computing, Transputer
Applications
For industrial and academic researchers, research managers in
industry and computer manufacturers and vendors in the
above-mentioned fields
J.K. Labanowski, Ohio Supercomputer Center, Columbus, OH; J.W.
Andzelm, Cray Research Inc., Eagan, MN (Eds.)
Density Functional Methods in Chemistry
1991. XII, 443 pp. 68 figs. Hardcover DM 128,- ISBN 3-540-97512-8
Predicting molecular structure and energy and explaining the
nature of bonding are central goals in quantum chemistry. In
this volume, which is based on a 1990 workshop at the Ohio
Supercomputer Center, leading experts on the density functional
(DF) method and its chemical applications demonstrate how their
work contributes to these goals and has come into its own as an
advanced method of computational chemistry. Density functional
theory emerged as an alternative to the traditional ab initio
and semiempirical approaches of quantum chemistry for studying
the ground state properties of molecular systems. Advantages of
the method are its high accuracy and efficiency, which make it
particularly well suited for the realistic study of large
molecular systems of practical importance. It describes with
consistent reliability organic, in organic, metallic, and
semiconductor systems consisting of elements throughout the
periodic table. For these reasons, density functional
methodology is used increasingly in pharmaceutical,
agrochemical, and biotechnology research; materials and polymer
science; catalysis, surface and solid state research; and
electrochemistry and microelectro nics. The wealth of
applications presented in this book will make it a valuable tool
for researchers faced with a growing choice of software and
theoretical approaches.
Structure and Bonding Volume 80
Chemical Hardness
K. Sen, University of Hyderabad, India; D.M.P. Mingos, Imperial
College of Science, Technology and Medicine, London, UK (Eds.)
With contributions by numerous experts
1993. Approx. 280 pp. 52 figs. Hardcover DM 228,- ISBN
3-540-56091-2
Contents:
R.G. Pearson, Santa Barbara, CA: Chemical Hardness - An
Historical Int roduction.
P.K. Chattaraj, Karagpur, India; R.G. Parr, Chapel Hill, NC:
Density Functional Theory of Chemical Hardness.
J.L. Gazqu z, Mexico, Mexico: Hardness and Softness in Density
Functional Theory.- L. Komorowski, Wroclaw, Poland: Har dness
Indices for Free and Bonded Atoms.
N.H. March, Oxford, UK: The GroundStat e Energy of Atomic and
Molecular Ions and Its Variation with the Number of Elect rons.
K. Sen, Hyderabad, India: Isoelectronic Changes in Energy,
Electronegativ ity, and Hardness in Atoms via the Calculations
of <r-1>.
P. Politzer, J.S. Mur ray, M.E. Grice, New Orleans, LA: Charge
Capacities and Shell Structures of Atoms.
R. F. Nalewajski, Cracow, Poland: Hardness Based Molecular
Charge Sensitivit ies and Their Use in the Theory of Chemical
Reactivity.
B.G. Baekelandt, R. A. Schoonheydt, W.J. Mortier,
Leuven-Heverlee, Belgium: The EEM Approach to Chemica l Hardness
in Molecules and Solids: Fundamentals and Applications.
J.A. Alonso, L.C. Balbas, Valladolid, Spain: Hardness of
Metallic Clusters.
Z. Zhour, P.K. Chattaraj, R.G. Parr, C. Lee
First-order gradient correction for the exchange-energy density
functional for atoms
Theoretica Chimica Acta Volume 84 Number 3, p 237
P. Politzer, J. M. Seminario, M. C. Concha, J. S. Murray
Some applications of local density functional theory to the
calculation of reaction energetics
Theoretica Chimica Acta Volume 85 Number 1-3, p 127
D. Heinemann, A. Rosen
Basis-independent potential energy curves for the neutral
diatomics of Li, Na and K evaluated by means of Hartree-Fock
and different density functional potentials
Theoretica Chimica Acta Volume 85 Number 4, p 249
Here are a few references which contain systematic comparisons
of various properties of small molecules by DFT and conventional
ab initio (HF, MP2, QCI) as well as experiment. Some of the
references therein are also useful along these lines. I hope
you find them helpful.
B. G. Johnson, P. M. W. Gill and J. A. Pople, J. Chem. Phys. 98,
5612 (1993).
A. D. Becke, J. Chem. Phys. 98, 5648 (1993).
A. D. Becke, J. Chem. Phys. 97, 9173 (1992).
A. D. Becke, J. Chem. Phys. 96, 2155 (1992).
J. Andzelm and E. Wimmer, J. Chem. Phys. 96, 1280 (1992).
Benny Johnson
Department of Chemistry
Carnegie Mellon University
Message 39/53 from rec@ncifcrf.gov Aug 5 '93
at 12:04 (noon)
Reply-To: cachau@ncifcrf.gov
A good reference book is:
"Density Functional Methods in Chemistry"
Jan K. Labanowski & Jan W. Andzelm Ed.
Springer-Verlag Berlin ISBN 3-540-97512-8
We have made a systemmatic comparison of polarizabilities and
hyperpolarizabilities calculated at the HF level (with HONDO8),
with 2 different DFT programs (deMon and DMol), and with
experiment.
The reference is ...
J. Guan, P. Duffy, J.T. Carter, D.P. Chong, K.C. Casida, M.E.
Casida,
and M. Wrinn, J. Chem. Phys. 98 (1993) 4753.
``Comparison of local-density and Hartree-Fock calculations of
molecular polarizabilities and hyperpolarizabilities''
The results are quite encouraging. An interesting point is that
comparisons between HF and DFT with overly small basis sets (valence
triple zeta in our case) are dominated by basis set effects instead
of the treatment of exchange and correlation. Thus the quantitative
advantages of DFT only became apparent as the basis sets became more complete.
Of course, convergence rates will depend on the property.
... Mark E. Casida
Return-Path: <casida@CHIMCN.UMontreal.CA>
From CHUCK@psipsy.uct.ac.za Mon Oct 4 12:08:36 1993
Message-Id: <MAILQUEUE-101.931004092748.288@psipsy.uct.ac.za>
To: "Wojciech Galazka" <wgalazka@chem.uw.edu.pl>, chemistry@ccl.net
From: "Marais, Charles F. , Dr" <CHUCK@psipsy.uct.ac.za>
Date: Mon, 4 Oct 1993 09:27:49 SAST-2
Subject: Re: C.I. on MOPAC 6.0 problem
> When using keyword 'C.I =n' (n - any valid number). I get results
>with 'charge on system = 1', although charge of the molecule
>calculated is 0 !
Yes, I saw this in 1991, and asked James Stewart about it - he said that
there seems "to be a bug in MOPAC regarding C.I. = 4" , and said he'll
look into it.
I assume that became part of the changes in MOPAC 7/93, but I haven't
installed any of those.
It would be most helpful if someone could try it out with the new
version....
Charles Marais
Department of Chemistry
University of Cape Town
Private Bag
Rondebosch chuck@uctvax.uct.ac.za
South Africa 7700 chuck@psipsy.uct.ac.za
------------------------------------------------------------------
From JKONG@ac.dal.ca Mon Oct 4 06:19:39 1993
Date: Mon, 04 Oct 1993 09:19:39 -0300
From: JKONG@ac.dal.ca
Subject: Re: "POKING" OUTPUT FILES ON VAX/VMS
To: chemistry@ccl.net
Message-Id: <01H3PK03J27C000R2G@AC.DAL.CA>
From: DAL1::JKONG 4-OCT-1993 09:18:22.46
To: IN%"fredvc@esvax.dnet.dupont.com"
CC: JKONG
Subj: RE: "POKING" OUTPUT FILES ON VAX/VMS
You can try to open the output file as SHARED. This should allow more
than one processes to open the file at the same time.
Good luck!
Jing
From jabs@chemie.uni-halle.d400.de Mon Oct 4 14:44:20 1993
Date: Mon, 4 Oct 1993 13:44:20 +0100
From: jabs@chemie.uni-halle.d400.de
Message-Id: <931004134419*/S=jabs/OU=chemie/PRMD=UNI-HALLE/ADMD=D400/C=DE/@MHS>
To: chemistry@ccl.net
Subject: normal coord.
Hi,
i am looking for normal coordinate analysis for small alcohols
(methanol, ethanol, 2-propanol, 2-phenylethanol) with ab initio
or semiempiric (PM3/AM1) methods. Can anybody help me with literature
or some results ?
Thanks in advance
Andreas
From mckelvey@Kodak.COM Mon Oct 4 04:50:35 1993
Date: Mon, 4 Oct 93 08:50:35 -0400
Message-Id: <9310041250.AA19118@Kodak.COM>
From: mckelvey@Kodak.COM
To: osc@Kodak.COM
Subject: scanning output from unit 6 on VMS...
If the job is submitted to batch, then do not explicitly open unit 6. As a
result, unit-6 info will appear in the logfile bearing the name of the batch-com. That file can be searched readily, or even just copied, I believe. On a unixmachine a similar result wil occur...if the nohup command is used, then unit-6
info will appear in nohup.out.
John McKelvey
From mikes@bioch.ox.ac.uk Mon Oct 4 15:10:53 1993
Date: Mon, 4 Oct 93 14:10:53 +0100
From: mikes@bioch.ox.ac.uk
Message-Id: <9310041310.AA07959@nmrpcd.ocms.bioch.ox.ac.uk>
To: chemistry@ccl.net
Subject: Cluster Analysis
Dear Comp-Chemers,
Does anybody know how one goes about dividing 100 structures (say) with the same
amino acid sequences into groups of similar structures.
The way I would envisage doing this would be to say that two structures are in
the same group if their rmsd (say) is less than 1 Angstrom, and that this
relationship is transitive, but this is only guessing!
Mike Smith
From gl@beta.mdy.univie.ac.at Mon Oct 4 14:26:01 1993
Message-Id: <199310041358.AA00278@oscsunb.ccl.net>
From: Gerald Loeffler <gl@beta.mdy.univie.ac.at>
To: CHEMISTRY@ccl.net
Subject: SUMMARY: force fields for biomolecules
Date: Mon, 4 Oct 93 14:13:44 MEZ
On September 28 I asked what force fields people were using for
the Molecular Dynamics study of biomolecules.
(original posting appended to this mail)
I like to thank
David Case
Arne Elofsson
Peter Reinert and
Don Williams
very much for their replies!
Here is what they conributed:
==============================
David Case: (case@scripps.edu)
==============================
uses AMBER and AMBER/OPLS for proteins. Implemented in Tripos, Discover, Chem-X,
AMBER, SPASMS, WESDYN codes. An improved version is due to come out by the end of 1993.
He also points to the newer all-atom CHARMM force fields, e.g. CHARMM22 implemented
in CHARMM only.
Older CHARMM force fields are used in X-PLOR, moil, md92.
He considers it very hard to compare force fields but points to an article in the November issue
of Chemical Reviews by Charles Brooks and David Case.
========================================
Arne Elofsson: (arne@ewald.mbi.ucla.edu)
========================================
thinks that other parameters than the force field are more important, like correct
treatment of electrostatic cutoffs, switching/shifting and water implementations.
He cites two papers by Guenot & Kollman: Protein Science 1992, 1185 - ?
and Journal of Comp. Chem. 14, 3, 295 - 311, 1993
and three papers by Schreiber/Steinhauser -- which are in fact from our group
that's why I don't cite them here.
==================================================
Peter Reinert: reinert@vax.mpiz-koeln,mpg.d400.de)
==================================================
thinks that AMBER is the most popular force field for biomolecules, the older
version of which (AMBER 3.x) is implemented in HYPERCHEM, SYBYL, PROSIMULATE,
INSIGHT/DISCOVER)
The reference is: Weiner, S.J. et al "A new force field ... " JACS, 106, 765 - 784, 1984
He also expects GROMOS to be upgraded.
============================================
Don Williams: (williams%xray2@ulkyvx.bitnet)
============================================
points to a commercial program that calculates net atom charges and other
electric multipoles from the molecular electric potential obtained by ab initio
calculations.
=====================================================================
If you would like to add some comments, here is the original posting:
=====================================================================
Dear Chemist!
We have been using the GROMOS force field implemented in the program gromos itself and in a
home-made program for the MD-simulation of proteins in water for a long time.
Since I consider this force field somewhat dated by now, I am asking you for your experience
with FORCE FIELDS FOR BIOMOLECULES.
I would very much appreciate answers to the following questions:
1) what is the force field you would recommend and which program you are
using implements this force field
2) why would you recommend this force field - e.g. are there published
comparisons between different force fields?
3) is source code for a program using this force field available?
What I ideally would like to get is a reference to a paper describing the force field
in detail and a 'sample implementation' by the developers of the force field
including source code.
Using that I will probably write a program that uses this force field on my own, since we
are usually doing a lot of algorithmic tuning.
I THANK YOU VERY MUCH FOR YOUR RESPONSES IN ADVANCE,
Gerald
--
+------------------------+ +-----------------------------------+
|Gerald Loeffler | |Theoretical Biochemistry Group |
|gl@beta.mdy.univie.ac.at| |Department of Theoretical Chemistry|
+------------------------+ |University of Vienna |
+-----------------------------------+
+--------------------------------------------------------------------------+
|Institut fuer Theoretische Chemie und Strahlenchemie der Universitaet Wien|
|Arbeitsschwerpunkt Theoretische Biochemie |
|Waehringerstrasse 17/Erdgeschoss |
|A-1090 Wien, Austria |
+--------------------------------------------------------------------------+
From wgalazka@chem.uw.edu.pl Mon Oct 4 09:57:58 1993
Organization: Department of Chemistry, University of Warsaw
From: "Wojciech Galazka" <wgalazka@chem.uw.edu.pl>
Date: Mon, 4 Oct 93 15:57:58 CST
Message-Id: <621.wgalazka@zoolook.chem.uw.edu.pl_POPMail/PC_3.2.3_Beta_2>
To: chemistry@ccl.net
Subject: Semiempirical programs with d,f orbitals
Hi
Does anybody know if there are any quantum semiempirical programs
with d, f orbitals included? The only one I know is SINDO1 (for reference
see K.Jug R.Iffert J.Schulz 'Development and Parametrization of SINDO1
for Second-row Elements' Int.J. Quant. Chem. 32 265-277 (1987)}.
I have heard about MNDO-like methods with artificially included d
orbitals but results obtained by them are not good for hypervalent
sulphur compounds.
////////////////////////////////////////////////////////////
// //
// Wojciech Galazka //
// Computer Center //
// Chemistry Department, University of Warsaw //
// Pasteura 1, 02-093 Warsaw, Poland //
// //
// wgalazka@zoolook.chem.uw.edu.pl //
////////////////////////////////////////////////////////////
From combariz@rouge.phys.lsu.edu Mon Oct 4 05:55:58 1993
Date: Mon, 4 Oct 93 10:55:58 CDT
From: combariz@rouge.phys.lsu.edu (Jaime Combariza)
Message-Id: <9310041555.AA16669@rouge.phys.lsu.edu>
To: CHEMISTRY@ccl.net
Subject: SCRF for ions
Hi all:
I have been working with Gaussian 92 and Gamess using the SCRF method
to study solvated anions. First, I found out that the two programs
would give me different results for similar input decks!!!
A closer look revealed that this
difference is roughly equal to the molecular Born energy, which
apparently is not accounted for in the Gaussian implementation of the
self-consistent-reaction-field.
Question for all of you G92 users/gurus: Is this right? If it is,
especifically for ions, should one not account for this energy?
I should add that in some small test cases this energy is about 40 Kcal/mol.
I will appreciate your comments,
Jaime E. Combariza
From leoh%lemoyne.BITNET@phem3.acs.ohio-state.edu Mon Oct 4 10:44:04 1993
Date: Mon, 04 Oct 1993 14:44:04 -0400 (EDT)
From: "Leo, Howard" <leoh%LEMOYNE.BITNET@phem3.acs.ohio-state.edu>
Subject: MOPAC6 FOR PC?
To: CHEMISTRY@ccl.net
Message-Id: <0097384D.5F4F9F80.31956@lemoyne>
Dear Netters,
Does anyone have, or know of, a ported version of MOPAC 6
for a PC?
Howard Leo
LEOH@LEMOYNE
From EDGECOMK@QUCDN.QUEENSU.CA Mon Oct 4 11:22:00 1993
Message-Id: <199310041924.AA05870@oscsunb.ccl.net>
Date: Mon, 4 Oct 1993 15:22 EDT
From: EDGECOMK@QUCDN.QueensU.CA
To: chemistry@ccl.net
Subject: DFT-HF comments
Jing is right about the boundary conditions with
DFT, however, I think people are trying to work around
that in various ways... One problem with HF is of course
basis set selection and limits... then to get correlation
MP theory also is nonvariational (illustrated quite well
by Nick Handy at last years NATO ASI in Vancouver).
The pros and cons can be bothersome. For example, DFT
does not give you a 'wavefunction' you can put to one
side and look at later... you have to calculate everything
then and there. Of course, some will argue that as DFT is
much faster so you just recalculate everything again...
Also, what about excited states?... a sore point with DFT.
WHich code and approximations are best?... are results
found with one approximation (functional) comparable to
those found with another?
Once again the problem is choosing the method, code, approximations
etc that suits the research problem. DFT may be able to give
results in some areas that HF just cannot handle. However,
coming back to some discussion that took place earlier, maybe
for some systems of interest (polypeptides etc) MM is best!
Just some thoughts...
Ken Edgecombe
Dept. of Chemistry
Queen's University
Kingston, ON CDN
From adit@Kodak.COM Mon Oct 4 11:51:42 1993
Date: Mon, 4 Oct 93 15:51:42 EDT
From: adit@Kodak.COM (Adi Treasurywala)
Message-Id: <9310041951.AA02712@bcc9.kodak.com>
To: chemistry@ccl.net
Subject: MM/MD WORKSHOP ANNOUNCEMENT.
FIRST ANNOUNCEMENT
FOURTH BIENNIAL WORKSHOP ON
MOLECULAR MECHANICS AND MOLECULAR DYNAMICS
Sponsored by
The Supercomputer Computations Research Institute
Florida State University
Tallahassee
Florida
Monday Feb 21 to Friday Feb 25 1994
Plenary Speaker who have accepted invitations so far:
D.L.Beveridge Jack Dunitz
Thomas Halgran Warren Hehre
Kendall Houk Adi Treasurywala
Invited Speakers who have accepted invitations so far:
J.E.Anderson, J.Phillip Bpwen, Helena Dodzuik, Frank Leusen,
Wayne Mattice, Dora Schnur, Terry Stouch, S.Swaminathan,
Henk van der Plas, Bastian van de Graaf, David M. Gagne, David C. Doherty, Douglas A. Smith, Hubert Bodot.
TOPICS: New developments in the quantitative computational modeling of
molecular structure, molecular dynamics, energies (thermodynamics)
including solvent effects, polymers, including biopolymers, inorganic
systems. It is expected that the studies will reflect new approaches in
the use of molecular mechanics or molecular dynamics rather than
applications of well-developed techniques. Developments in the use of
ab initio calculations in modeling are appropriate.
PROGRAM: Monday evening: Reception.
Tuesday through Friday noon: Scientific sessions
Tuesday through Thursday: Vendor exhibits combined with
electronic posters (see below)
POSTERS: Contributed conventional posters will be displayed.
ELECTRONIC POSTER SESSION:Please send all requests to take part in this
new event no later than October 31 1993 to
Adi M Treasurywala,Sterling Winthrop Inc,1250 South Collegeville Road,
PO Box 5000, Collegeville, PA 19426-0900,Voice (215)983-6610 FAX
(215)983-5559, INTERNET adit@kodak.com
stating the software, hardware and approximate time requirements.
ALL OTHER INQUIRES TO
DELOS DETAR,
DEPT. OF CHEMISTRY,
FLORIDA STATE UNIVERSITY,
TALLAHASSEE FL 32306-3006
TEL (904)644-3709.
FAX (904)644-8281
detar@mailer.fsu.edu
Acceptance cannot be guaranteed. Deadline January15 1994.
CONTRIBUTED TALKS: A few additional contributed talks may be accomodated.
FEES: The workshop fee is $350 ($325 if received before January 15
1994). For those whose talks/posters have been accepted the fees will
be $250. Student rate $150. Fees will cover a hospitality reception on
March 26 continental breakfasts 4 days lunches 3 days coffee breaks and
conference banquet.
Registration Form
Molecular Mechanics and Molecular Dynamics 1994
Program # 1902994
To register, please complete this form and mail it with your payment (checks
made payable to Florida State University) to: Conference Registrar, Florida
State Conference Center, Florida State University, Tallahassee FL 32306-2027.
For registration information, please call 904-644-3806. For information about
the program, please call Pat Meredith at 904-644-1866, or by e-mail at
meredith@scri.fsu.edu..
Name:____________________________________
Social security #: _______________________(This is not essential, but will speed
the process if you require a reimbursement of fees)
Organization: _________________________________________
Address: _____________________________________________
_________________________________________________
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Fees: $325 before January 15, 1994
$350 after January 15, 1994
$150 for students
$250 for those whose contributed talks or posters are accepted
I wish to pay my fee of $______by ___MasterCard, or ___Visa
Acct. # _________________________ Exp. Date ________________
Signature: __________________________________________
Please note, the university adds a 2% service fee for credit card payments.
From st-amant@theory.chem.uottawa.ca Mon Oct 4 14:52:29 1993
Date: Mon, 4 Oct 1993 18:52:29 -0400
From: st-amant@theory.chem.uottawa.ca (alain st-amant)
Message-Id: <9310042252.AA04953@theory.chem.uottawa.ca>
To: chemistry@ccl.net, mikes@bioch.ox.ac.uk
Subject: Re: Cluster Analysis
> Dear Comp-Chemers,
>
> Does anybody know how one goes about dividing 100 structures (say) with the
> same amino acid sequences into groups of similar structures.
>
> The way I would envisage doing this would be to say that two structures are
> in the same group if their rmsd (say) is less than 1 Angstrom, and that this
> relationship is transitive, but this is only guessing!
>
> Mike Smith
A very nice piece of work has recently come out of Charlie Brooks' group.
It should be just what you want. The reference is:
M. E. Karpen, D. J. Tobias, and C. L. Brooks, "Statistical Clustering
Techniques for the Analysis of Long Molecular Dynamics Trajectories --
Analysis of 2.2 ns Trajectories of YPGDV," Biochemistry, Volume 32,
pages 412-420.
Sincerely,
Alain St-Amant
st-amant@theory.chem.uottawa.ca
From shenkin@still3.chem.columbia.edu Mon Oct 4 15:04:10 1993
Date: Mon, 4 Oct 93 19:04:10 -0400
From: shenkin@still3.chem.columbia.edu (Peter Shenkin)
Message-Id: <9310042304.AA06034@still3.chem.columbia.edu>
To: mikes@bioch.ox.ac.uk, chemistry@ccl.net
Subject: Re: Cluster Analysis
> From: mikes@bioch.ox.ac.uk
> Does anybody know how one goes about dividing 100 structures (say)
> with the same
> amino acid sequences into groups of similar structures.
> The way I would envisage doing this would be to say that two structures
> are in
> the same group if their rmsd (say) is less than 1 Angstrom, and that this
> relationship is transitive, but this is only guessing!
I'm glad you asked that question. :-)
Quentin McDonald and I have written a program that does exactly
what you describe: cluster analysis of molecular conformations. An
article that covers the approach we used, as well as the implementation,
has been submitted to J. Comput. Chem.
The program is called XCluster. It begins by constructing
the matrix of inter-conformational "distances" between all
pairs of conformations read in. There are several choices
of "distance" available, including RMS of interatomic distances
following rigid-body superposition (which is what I assume you mean
by "rmsd"). Molecular symmetry can be taken into account, and
clustering can, if desired, be performed on only a subset of the
atoms -- for example, the ring atoms of a cyclic system.
> The way I would envisage doing this would be to say that two structures
> are in
> the same group if their rmsd (say) is less than 1 Angstrom, and that this
> relationship is transitive, but this is only guessing!
The relationship does satisfy the triangle inequality, but I don't
think the term "transitivity" is applicable, if I remember its
definition correctly (which I may not :-) ). A very nice proof of
the satisfaction of the triangle inequality for RMS interatomic distance
following best rigid-body interatomic superpostion is given in our paper.
The proof is due to Dr. Mathis Thoma of the CIBA-Geigy Corporation.
XCluster allows you to perform clustering based either on an a-priori
distance criterion (eg, the 1 Angstrom RMS distance you propose), or
else based on statistical criteria (some of which we devised ourselves)
for determining whether there is some "natural" clustering distance
inherent in the data. Our statistical criteria are imperfect, but they
work in many cases -- especially where the clustering is especially
clear-cut.
XCluster has been distributed along with the molecular modeling package
MacroModel since Release 4.0 of MacroModel, which came out in July.
The package does cost money, but is inexpensive to academic institutions.
For pricing, availability and an overview of its capabilities, issue the
following command::
finger mmod@still3.chem.columbia.edu
Sorry, but XCluster is available only with MacroModel.
As the name implies, XCluster has a spiffy X interface, including
some nice visualization tools (eg, visualization of the inter-
conformational distance matrix). XCluster can also write out the
clusters of conformations, superimposed and colored by cluster, in
MacroModel format. This format is understood by several other
programs as well as MacroModel itself.
XCluster is a standalone program, but it also can "talk to"
MacroModel. For example, if you display a compound in MacroModel,
the set of atoms to be used in the cluster analysis may be "picked"
with the mouse, and thereby transmitted to a simultaneously running
XCluster program.
XCluster can also run in a mode which accepts not molecular structures,
but rather the N(N-1)/2 non-redundant distance-matrix elements, then
applies the cluster-analysis to that matrix. Thus it can be used to
visualize and analyze arbitrary distance data. We have additional
facilities planned for future releases.
I hope I have not been "tooting my own horn" too loudly in this posting.
Obviously, I have an intimate association with MacroModel and with
XCluster, and am thrilled to hear of interest in the subject of
clustering of molecular conformations.
-P.
************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************
Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ.,
New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143
********************** Wagner, Beame, Screvane in '93! **********************
From states@ibc.wustl.edu Mon Oct 4 13:26:37 1993
Date: Mon, 4 Oct 93 18:26:37 CDT
From: states@ibc.wustl.edu (David J. States)
Message-Id: <9310042326.AA10458@ibc.WUStL.EDU>
To: chemistry@ccl.net, mikes@bioch.ox.ac.uk
Subject: Re: Cluster Analysis
|> Does anybody know how one goes about dividing 100 structures (say) with the same
|> amino acid sequences into groups of similar structures.
|>
|> The way I would envisage doing this would be to say that two structures are in
|> the same group if their rmsd (say) is less than 1 Angstrom, and that this
|> relationship is transitive, but this is only guessing!
|>
|> Mike Smith
There are several issues here. If you do not know how many clusters
there should be, then you don't want to use an algorithm that imposes
a particular answer. This can happen either explicitly (for example
a binary classification halted at 3 divisions by definition will give 8
classes) or implicitly in a leader-mean classification of the sort you
describe (the number of classes is inversely dependent on the cutoff
radius).
To avoid biasing the results of the classification by class number, you
need a method that allows you to compare classifications with different
numbers of classes. This leads to the general field of Bayesian
classification where a classification is viewed as a model for the
observed distribution and the optimal classification is that
classification which optimally describes the data. Larry Hunter and I
used this to derive a classification of protein secondary structure
several years ago (Hunter and States (1991), "Bayesian classificaiotn
of protein structural motifs.", in Proceedings of HICSS-24, IEEE Press,
Los Alamitos CA, 595-604).
Another issue is flat vs. hierarchical classification. Are these
proteins derived by an evolutionary process from a common ancestor in
which case a hierarchical model might be more appropriate, or are they
random samples of conformation space in which case a flat
classification would be better. Defining the optimal tree structure
for a set can itself be a demanding problem.
The computational complexity of the problem depends on your class
definition. If you seek connected classes (two structures are in the
same class if there is a path of similarity relationships connecting
them, transitive closure) then this is algorithmically a minimal
spanning tree problem for which linear time solutions exist. On the
other hand, if you demand that all members of a class to fall within
some cutoff of every other member (cliques), then you have a graph
partition problem that is NP-complete.
The sensitivity of the classification to errors or ambiguities in the
data is also dependent on class definition. Transitive closure is
robust to less than perfect sensitivity in defining similarity
relationships but false positive similarity judgements lead directly
to classification errors. On the otherhand, clique definitions are very
sensitive to false negative similarity judgements and robust to false
positives.
David States
Institute for Biomedical Computing / Washington University in St. Louis
From mercie@med.cornell.edu Mon Oct 4 15:37:18 1993
Date: Mon, 4 Oct 1993 19:37:18 -0400 (EDT)
From: Gustavo Mercier <mercie@med.cornell.edu>
Subject: DFT
To: chemistry@ccl.net
Message-Id: <Pine.3.05.9310041918.B16738-d100000@med.cornell.edu>
Hi, Netters!
Recently there have been a few questions about DFT. Although I don't
consider myself an expert, I have been listening to people talk about
DFT for a few years and recently started to do DFT computations on
metalloporphyrins. I hope the following will clarify some points. I certainly
welcome any corrections of my statements below!
DFT (Density Functional Theory) stands as a reformulation of the Schroedinger
Equation. Its origin really dates from the early days of quantum mechanics
(Thomas-Fermi-Dirac, Slater's work, etc), but its "modern" foundation is
based on the theorems of Hohenberg and Kohn developed in the '60's, and its
practical implementation in Quantum Chemistry rests on the Kohn - Sham
equations. For a beautiful and concise description of the historical
development of DFT I suggest you read the article by Hohenberg, Kohn,
and Sham in Advances of Quantum Chemistry v. 21 special ed. S. Trickey
pp 7 -26, 1990.
The HK theorems essentially state:
1) Given a density, rho, the external potential, Vext, is fixed.
For Quantum Chemistry using the electronic molecular hamiltonian
within the Born-Oppenheimer approximation, the Vext is the electrostatic
potential generated by the nuclei.
2) The energy is a UNIQUE Functional of the density.
As originally described, the above applies only to NON-DEGENERATE
GROUND STATE systems!
Following their work, issues described as the V-representability and
N-representability problems were identified and dealt with in a variety
of ways. For an explanation of these and the rigourous foundation of
DFT theory, try Kryachko and Ludena, Energy Density Functional Theory
of Many-Electron Systems by Kluwer Academic Publishers Understanding
Chemical Reactivity Series v. 4, 1990.
For computational chemists the Kohn - Sham equations are the origin of
most implementations of DFT theory. Essentially they apply a variation to
E[rho] = F[rho] + Eext[rho];
F = Ts + Eee + Exc
where Eee is the coulombic electron - electron repulsion and Exc is the
"exchange - correlation" term, a functional of rho. The key point to
understand is Ts. Ts is the kinetic energy for a collection of NON-INTERACTING
electrons!. As you can see the structure is similar to our familiar
Hartree - Fock, but there are subtle differences. In Hartree - Fock, the
Kinetic term is for an INTERACTING set of electrons. The difference is
THROWN into the undefined Exc term. KS showed that if Exc is known exactly,
the KS equations will yield the EXACT density! The KS equations are
generated using the above functional and the HK variational
principle that stems from Theorem #2. The key result is that due to the
choice of reference state, the KS equation is identical to the HARTREE
equation, the Schroedinger Eq. for a system of non-interacting electrons,
but with a new potential:
Veff = Vext + Vee + Vxc
Following the Hartree Eq., the density can be written EXACTLY as
rho = Sumi phi(i)^2
This form of rho is NOT an approximation as is the case when the
density is generated from the HARTREE - FOCK Equation. The rho
looks identical in form, but the phi's are very different!!
In solving the KS equations a Variational Method is used that includes
Lagrangians due to the constraint of the density to integrate to the total N
number of electrons. In Hartree - Fock, these correspond to
the orbital energies as shown through Koopman's Theorem. In DFT, the
Lagrangians do not have the same meaning. THEY DO NOT correspond to
orbital energies. Through some manipulations you can generate "orbital
energies" but they do not come explicitly from the KS equations.
The fact that orbital energies are not generated also means that the phi's
above don't have the same meaning they have within HF theory!
This is one of the most distressing things for us chemist who always
think in terms of orbitals!!! Only the density has "meaning", not its
"components". The physical interpretation associated with the orbitals
in HF theory which is useful in the generation of different configurations
for CI or GVB computations is lost!
Most of the work in DFT deals with defining Vxc. If it were known exactly,
we would have the exact equation and an exact solution within the
basis set expansion we chose for the phi's. In other words, within
Hartree - Fock we have an exact operator with its approximate solution
(single determinant), but in DFT we have an approximate functional with its
exact solution. The ADVANTAGE is that the approximate part is small, and
the density is a function of only three variables! In fact, using
Mathematica and the output of my DFT runs, I have written the analytic
expression for the the density of a 66 electron system using a double zeta
+ polarization basis set! All computed in an INDIGO R4000. It is satisfying
to actually see the analytic form of your result! Given the functional
associated with a molecular property, you can easily compute
the property. Particularly, standard numerical algorithms can fairly
easily be applied since the dimensionality of the problem has decreased
significantly! For example, in my case from 66*3 to 3.
When does DFT - KS fails? When your choice of Vxc or basis set is bad!
Also, from the practical point of view, many programs expand the
the electron density used to compute the Vee. If this basis is poor you
also get bad results. One thing that has been appreciated is that if
you want to adequately reproduce H-bonds, a critical point for the
many biochemically oriented people in this mailing list, you need
good descriptions of Vxc that include gradient expansions etc.
Sorry for the bandwith, but I hope the above was useful.
good luck
mercie@cumc.cornell.edu
From cramer@maroon.tc.umn.edu Mon Oct 4 16:21:34 1993
Message-Id: <0012cb0da2e011938@maroon.tc.umn.edu>
From: "Christopher J Cramer-1" <cramer@maroon.tc.umn.edu>
Subject: Re: SCRF for ions
To: combariz@rouge.phys.lsu.edu (Jaime Combariza)
Date: Mon, 4 Oct 93 21:21:34 CDT
Jaime,
>
> Hi all:
>
> I have been working with Gaussian 92 and Gamess using the SCRF method
> to study solvated anions. First, I found out that the two programs
> would give me different results for similar input decks!!!
> A closer look revealed that this
> difference is roughly equal to the molecular Born energy, which
> apparently is not accounted for in the Gaussian implementation of the
> self-consistent-reaction-field.
>
Your analysis is exactly correct, the monopole (or Born) term is not
included in the multipole expansion (which is truncated at the dipole in the
Onsager model).
In principle, one can take the G92 calculated spherical radius "a" that
was used in the SCRF and use it to calculate the Born free energy from the
classical Born eqn G = -1/2 ( 1 - 1/dielectric) q^2/a, where q is the charge
on the molecule (all units atomic units).
Of course, in a charged molecule, the dipole is no longer origin
independent, and one needs to worry a bit about where the center of the
sphere is being placed -- center of mass? center of charge?
No matter what, the Born-Onsager model in a spherical cavity approximation
starts to get pretty risky about this point. Of course, it's fast and simple.
CJC
--
Christopher J. Cramer
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
(612) 624-0859
cramer@maroon.tc.umn.edu
From mail Mon Oct 4 16:50:39 1993
Date: Mon, 4 Oct 1993 16:19:02 -0400
From: hyper!ostlund (Neil S. Ostlund)
Message-Id: <9310042019.AA19423@hyper.hyper.com>
To: chemistry@ccl.net
Subject: conjugation in mol mech
John McKelvey has commented here about torsional angles in
biphenyls. HyperChem also gives reasonable values of torsional
angles in molecules such as this, but the issue is a very important
one that is fundamental to the success or failure of molecular
mechanics approaches and although I rarely contribute to
discussions here, I thought that I might briefly comment on this topic.
The standard molecular mechanics methods (MM2, Amber, CHARMm, etc)
assign parameters on the basis of the "atom type" of the relevant
atoms involved (4 atoms,in the case of a torsion) without consideration
of the bond type. This results in the same torsional constants for the
SINGLE BOND in biphenyl at for the AROMATIC RING BONDS of Benzene!!
Thus, all the standard methods mentioned above result in biphenyl
being planar which is unfortunate chemistry. The molecular
mechanics secret is to recognize more of the chemical environment of
a bond torsion than just the 4 "atom types". Alternatively, one might
expand the number of different atom types, but this has its own problems.
For example, in biphenyl it is important that one is trying to describe
the torsion of a "single" bond (bond-order=1) not an "aromatic" benzene
bond (bond-order=1.5). Chemical ideas like this are not recognized by
the simple "atom type" methods, but are recognized by Dreiding, MM+, and
others.
In HyperChem, the MM+ method does standard MM2 calculations when explicit
parameters are available in the parameter file associated with the relevant
atom types. Thus a "standard" calculation results in planar biphenyl for the
reasons described above. However, the MM+ force field in HyperChem falls
back to a Dreiding-like scheme when explicit parameters for the torsion in
question are not available in the parameter file. It then uses information
about the "bond type" to derive default parameters. The result is that you
get a better result when you don't have an explicit MM2 parameter and the
default scheme is used! This points out one of the major defficiencies of
standard molecular mechanics procedures like MM2, Amber, and CHARMm - they
don't recognize the "bond type" of a torsion but only the "atom type" of
the 4 relevant atoms.
For those familiar with HyperChem, if you select the molecule and set all
the atoms types to unknown (**) to dismiss the standard MM2 parameters and
fall back to the default scheme, you will find reasonable geometries for
systems like biphenyl, butadiene, etc.
I don't want to sound as though I am promoting HyperChem here; I only
use it as an example of an important issue for molecular mechanics
calculations. Other programs also recognized this problem associated
with the simple "atom type" approach.
------------
Neil Ostlund
President, Hypercube Inc.
419 Phillip St, Waterloo, Ont, Canada N2L 3X2
(519)725-4040
internet: ostlund@hyper.com