Subject: MGMS EC-1 Announcement

From: Steve Doughty <[email-masked]>
Date: Fri, 12 Jul 1996 10:33:05 +0000 (GMT)

FIRST ELECTRONIC MOLECULAR GRAPHICS AND MODELLING SOCIETY CONFERENCE
  ********************************************************************

  The First Electronic Molecular Graphics and Modelling Society
Conference (MGMS EC-1) will be held on the Internet (the Net) and 
World Wide Web (the Web) from Oct 7-18, 1996.  The conference
is sponsored by Elsevier and the Molecular Graphics and Modelling 
Society and will be co-organized by Graham Richards, Art Olson,
Rod Hubbard and Barry Hardy.

  MGMS EC-1 will be a fully international event open to all members of 
the scientific community and will cover a broad range of disciplines 
related to molecular modelling, graphics and simulation methods
and applications.
     
  Conference subject areas are: Protein Structure; Membranes and Membrane
Proteins; Bioinformatics; Computational Nanotechnology; Protein Folding;
Modelling of In Vivo Activity; Knowledge-based Library Design;
Surface Science; Host-guest interactions; Carbohydrates;
Enzyme Mechanisms; Conformational Analysis; Nucleic Acids;
Quantum Chemistry; Car-Parrinello Methods and Applications; 
Structure-based Design; Visualization; and Perspectives.

  Each subject area has a section convener who will screen 
abstracts sent by authors for suitability.  Authors can opt to submit 
a non-permanent presentation like a normal conference poster or
a presentation which will be refereed and considered for publication
in the Journal of Molecular Graphics.  Referees will be appointed 
by the section conveners. 
  
  Presentations must be prepared in Hypertext Markup Language (HTML), 
graphics (GIF,JPEG) and other web-compatible formats (VRML,Java,PDF) 
so that participants can view the papers via the World Wide Web.  
Aid and consultation will be provided to participants in the weeks 
prior to the event to help them with their presentation 
(Email:[email-masked]). Further details will be given in the 
authors' guide accessible via the URL: http://bellatrix.pcl.ox.ac.uk/mgms/

  During the conference discussions will take place via the Internet 
in real-time using a virtual conference centre based on a MOO 
(multiple-user domain, object oriented) and via Internet-accessible 
electronic mailing lists. Trial sessions for those not familiar with 
MOOs will be held before the conference. Before the conference, a 
timetable for MOO discussion sessions of each section will be posted. 
Since these realtime discussions are an integral part of the 
conference, authors will be expected to attend one for their subject; 
the right is reserved not to referee submissions by authors who do 
not attend one of these sessions. 

  The Conference will feature a Virtual Trade Center where commercial
vendors, software and hardware developers, consultants, and contractors 
will be able to display their goods and services and provide software 
demonstrations in return for exhibition fees to support conference 
activities. Any potential exhibitors should contact Barry Hardy at
[email-masked]

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

DEADLINES AND DATES               

1) DO NOW - The MGMS mailing list

Conference-related news and announcements will be posted regularly 
to the MGMS mailing list (http://bellatrix.pcl.ox.ac.uk/hypermail/mgms/).

If you wish to subscribe to the MGMS list send the following
one line message to [email-masked]:

subscribe [email-masked] your_email@address
your_name 

2) DO NOW - Registration

The deadline for registration is Sept 15th 1996. Early registration is 
strongly encouraged to aid the efficient operation of the conference 
including the establishment of timely access to the conference.

If you intend to participate in MGMS EC-1 please use the registration 
form accessible via http://bellatrix.pcl.ox.ac.uk/mgms/ 
which is available for electronic registration.  The 
registration will be used to construct a registrant database 
for the conference which will generate the conference mailing list and 
handle assignment of userids and passwords.

In addition it is necessary to pay for registration via ordinary 
means: The conference fee will be 35 pounds sterling (50 US dollars) 
with a special rate for students of 20 pounds sterling (30 US 
dollars). A copy of a suitable student identification or a letter from 
the supervisor will be required to be charged at the lower rate.

Registration payments can be accepted by credit card, 
direct bank transfer, cheque or bank draft. 
Regardless of method of payment we ask you to
supply accompanying correspondence with your complete name,
address, fax and phone number, and email address which
should be mailed directly to:

Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory,
University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK

Payment Instructions:                       

a) Credit Card

We can currently accept Visa, Mastercard, Switch or JCB.
We cannot yet accept American Express as our application with
them has still to be processed.

Please send your credit card type, number and expiration date
via regular mail to:
Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory,
University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK

b) Bank Transfer

Your payment can be made in sterling by direct bank transfer
into the folowing account:

Account Number: 20-6518 50772712
Account Name: Greenlea Communications
Bank: Barclays Bank, Oxford City Centre Branch,
P.O. Box 333, Oxford, OX1 3HS, UK

--Please ensure your full name is listed with the transfer details.
--You are responsible for any bank charges associated with the
transfer from your bank. 
--Please notify us directly of your transfer payment.

3) Cheque/Bank Draft

Cheques or bank orders (in pounds or dollars) should be made out to
Greenlea Communications and mailed to:

Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory,
University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK

Acknowledgement of Registration and Payment:

When you first register at the conference site you should
receive an acknowledgement email with a password and userid.

After receipt of your registration fee you will
receive a further acknowledgement and your userid and password
will be validated to allow access to the conference site
(when it opens). 

(Note: Registration payments received during the period July 23-
August 14 will not be immediately processed and acknowledged. They will
be processed as soon after August 14 as possible.)

Academic registrants from economically-disadvantaged countries can 
write to Barry Hardy requesting an exemption to the registration fee. 
Exemptions will be made on a discretionary basis taking into account 
the reasons given for the request and will be dependent on suitable 
funds being available.  We will consider economically disadvantaged 
countries to include those of Eastern Europe, Africa, Central and 
South America, Indian sub-continent, etc. 

3) DEADLINE for receipt of ABSTRACT.  

The deadline for receipt of presentation abstracts is August 1. Email 
your abstract directly to the appropriate section convener listed 
below.  Fuller details of the scope of each section will be given in the 
authors' guide accessible via http://bellatrix.pcl.ox.ac.uk/mgms/

Your abstract should be no longer than 300 words. And remember to 
state which category of presentation (non-permanent poster or refereed
paper) you wish.

If you are unsure as to which section your abstract is suitable for, 
please email a possible section convener or Barry Hardy 
([email-masked]). Section conveners do have the discretion 
to reject abstracts, ask for revisions to an abstract or to send the 
abstract to the convener of a more suitable section.

4) DEADLINE for receipt of PRESENTATION

The deadline for receipt of papers and posters is Sept 15th.  You 
must deposit your text and graphics files at the conference ftp site for
presentation at the conference. Ftp instructions will be provided at the
conference site.  Hard copies of final refereed papers
following the format of the Journal of Molecular Graphics
should be sent by Dec 1 to: 

Graham Richards, Journal of Molecular Graphics, 
Physical & Theoretical Chemistry Lab, Sth Parks Rd,
University of Oxford, Oxford, OX1 3QZ, UK.  

Journal guidelines are posted at 
http://bellatrix.pcl.ox.ac.uk/mgms/

Although there is no limit to the graphics authors choose
to display in their conference presentation, the editor
reserves the right to limit the number of free colour
figures in each printed journal article. 

5) Refereeing Period

The refereeing period will commence upon completion of the conference.
If you have a presentation at MGMS EC-1 you may be requested to contribute
a refereeing evaluation on another conference presentation.  Referee reports 
will be due November 15. 

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

                  SECTIONS AND SECTION CONVENERS 

(Please email section conveners with questions related to 
your particular section and presentation. Details on the 
sections are accessible via http://bellatrix.pcl.ox.ac.uk/mgms/)

Any general emails (such as registration queries, maillist queries, 
HTML queries, password queries, timetable queries, general technical 
advice on browsers and graphics, MOO queries, etc.) should be sent to:
[email-masked]

1. Protein Structure 
Rod Hubbard
University of York, UK
Email:[email-masked]

2. Nucleic Acids
David Beveridge and Dennis Sprous
Wesleyan University, USA
Email:[email-masked],[email-masked]

3. Membranes and Membrane Proteins
Alan Robinson 
University of Oxford, UK
Email:[email-masked]
and
Terry Stouch
Bristol-Myers Squibb, USA
Email:[email-masked]

4. Bioinformatics
Steve Gardner
Oxford Molecular, UK
Email:[email-masked]          

5. Computational Nanotechnology
Al Globus
NASA-Ames, USA
Email:[email-masked]

6. Protein Folding
Jeffrey Skolnick
Scripps Institute, USA
Email:[email-masked]

7. Modelling of In Vivo Activity
Edward Hodgkin
Wyeth-Ayerst Research, USA
Email:[email-masked]

8. Knowledge-based Library Design
Mike Hann
GlaxoWellcome, UK
Email:[email-masked]

9. Surface Science
Donald Brenner
North Carolina State, USA
Email:[email-masked]

10. Host-Guest interactions
Jon Essex
Southampton University, UK
Email:[email-masked]

11. Carbohydrates and Protein-Carbohydrate Interactions
Anne Imberty
CNRS, France
Email:[email-masked]

12. Enzyme Mechanisms
Guy Grant
University College Dublin, Ireland
Email:[email-masked]

13. Stochastic Methods for Conformational Sampling
Robert Topper
The Cooper Union, USA
Email:[email-masked]

14. Quantum Chemistry
Tim Clark
University of Erlangen, Germany
Email:[email-masked]

15. Structure-based Design
David Winkler
CSIRO, Australia
Email:[email-masked]

16. Car-Parrinello Methods and Applications
Michele Parrinello
Max-Planck Institute, Germany
Email:[email-masked]

17. Visualization
Art Olson
Scripps Institute, USA
Email:[email-masked]

18. Perspectives in Molecular Modelling
Graham Richards
University of Oxford, UK
Email:[email-masked]

------------------------------------------------------------------ 
//                                       ||                     \\
//  Stephen Doughty                      || "The best and most  \\
//  Physical & Theoretical Chemistry Lab.||beautiful things in  \\
//  Oxford University,                   ||this world cannot be \\
//  South Parks Road, OXFORD, OX1 3QZ, UK||seen or even touched.\\
//                                       ||They must be felt    \\
//  Tel: +44 1865 275475                 ||with the heart."     \\
//--------------------------------------------------------------\\ 
//  Email : [email-masked]                        \\
//   WWW  : http://bellatrix.pcl.ox.ac.uk/people/steve/         \\
------------------------------------------------------------------

>From [email-masked] Fri Jul  5 12:44 EDT 1996
From: "Steve Gwaltney" <[email-masked]>
Date: Fri, 5 Jul 1996 11:43:44 -0500
To: [email-masked]
Subject: Re: CCL:MCSCF freq. + scaling factors
Cc: [email-masked]
Content-MD5: jkxo4rPvdNWiF4B5b5LYew==
Content-Length: 2949
Status: RO

>   Dear CCL Netters   [email-masked]
> 
>   Ref: CAS vs HF frequencies, vibration scaling factors,
> 
>   I would like to add my grain of salt to these 2 threads.
> 
>   1/ I would tend to think that MCSCF ( and then CAS ) frequencie are
>    much better than HF and ALSO MP2.
>   In the case, where static correlation is important, no doubt MCSCF
>  is better. It has been argued (in the CCL discussion)
>   than MP2 might be better to describe dynamic correlation, why ?
>  In fact, I begun to be suspicious of MP2 schemes, when I realized
>  that most MP2 energy is coming from the highest virtual MOs, which
>  feature extremely bizarre contours ( plot them !) and also
>  very large MO coefficients. 
> 
>   2/ For frequencies computed within the harmonic approximation,
>  scaling factors might correct both for
>  lack of proper correlation treatment,and
>  lack of anharmonicity. 
> 
>  It is safer, whenever possible, to try to separate these 2 issues.
>  In fact MP2 frequencies, often seem better than MCSCF frequencies
>  but this might come from a compensation of error with anharmonicity.
> 

Most of the MP2 energy does not come from the highest virtual MO's.  The
MP2 energy formula is

                             2
 (2)   1           |<ij||ab>|
E    = _ sum(ijab) ___________
       4           e +e -e -e
                    i  j  a  b

where e  and e  are the energies of the occupied (spin) orbitals,
       i      j
and e  and e  are the energies of the virtual orbitals.  What this
     a      b
shows is that when you are exciting out of very low lying occupied
orbitals or you are exciting into very high lying virutal orbitals,
the denominator is large, and therefore that term contributes very
little to the total energy correction.  The large energy corrections
come when you are exciting from high lying occupied orbitals into low
lying virtual orbitals.

As to the quality of MP2 vibrational frequencies:  in R.J. Bartlett and
J.F. Stanton, _Reviews_in_Computational_Chemistry_ Vol. 5, K.B. Lipkowitz
and D.B. Boyd, eds. (VCH, New York) 1994, the authors give the following
figures.  For eight small molecules for which experimental harmonic
vibrational frequencies are known, here are the average percent errors
for various methods using a DZP basis:

SCF                          8.7
CISD                         3.7
MBPT(2) (also known as MP2)  3.2
SDQ-MBPT(4)                  2.5
CCSD                         2.2
MBPT(4)                      3.1
CCSD(T)                      2.4

By the time we get to CCSD(T), the basis set error is probably larger
than the method error.  No MCSCF values were given, so it is not possible
to directly compare the quality of MP2 and MCSCF frequencies.  However,
it is clear that the quality of MP2 frequencies does not come from a
cancellation of method and anharmonicity errors.

Steve

Steven Gwaltney
[email-masked]
Quantum Theory Project
University of Florida

>From [email-masked] Sat Jul 13 05:29 EDT 1996
Date: Fri, 12 Jul 1996 13:45:46 -0400 (EDT)
From: Alexander J Ropelewski <[email-masked]>
To: [email-masked]
Subject: CCL:biomedical workshop announcement

                      BIOMEDICAL WORKSHOPS
                   PITTSBURGH SUPERCOMPUTING CENTER
                      August 25-28, 1996

The Pittsburgh Supercomputing Center is offering an
"ADVANCED NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS" workshop.
The workshop is open to researchers who have previously attended one of the
PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who
have previous experience with computerized sequence analysis.  The
workshop will build on previous experience to teach techniques for
what is commonly referred to as "homology modeling", specifically the methods
known as threading techniques. This involves fitting the sequences of
proteins whose structure is not known to the known three-dimensional structure
of another protein. The workshop will feature the threading techniques
developed by Dr. Stephen H. Bryant of the Computational Biology Branch,
National Center for Biotechnology Information, National Library of Medicine.
Dr. Bryant's work focuses on empirical energy functions that measure the
complementarity of sequence and folding motif and on algorithms for
rapid threading. His group is also developing computer programs for
automatically creating homology models derived from core structural motifs
identified by other sequence analysis techniques.

Instructors are:
Dr. Stephen H. Bryant, National Center for Biotechnology Information,
   National Library of Medicine
Dr. Michael Gribskov, San Diego Supercomputer Center and
Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center.

APPLICATION DEADLINE: July 17, 1996.

For additional information, please refer to
     http://www.psc.edu/biomed/workshops.html
CONTACT INFORMATION: Nancy Blankenstein, Biomedical Program Assistant,
(412)268-4960, [email-masked]

                               **********

                     PITTSBURGH SUPERCOMPUTING CENTER
                     ADVANCED SEQUENCE ANALYSIS WORKSHOP

                               APPLICATION

Name:          
________________________________________________________________

Affiliation:   ________________________________________________________________

Address:       ________________________________________________________________
           (Business)
           ________________________________________________________________

           ________________________________________________________________
           (Home)
           ________________________________________________________________

Telephone:  ____________________________         ______________________________
               (Business)                     (Home)

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

Electronic Mail Address:_______________________________________________________

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

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 vitae.  Graduate students must have a letter
of recommendation from a faculty member.

Please return all application materials to:
          Biomedical Workshop Applications Committee
          Pittsburgh Supercomputing Center
          4400 Fifth Avenue, Suite 230C
          Pittsburgh, PA 15213

Direct inquiries to: Nancy Blankenstein, [email-masked] 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 [email-masked] Thu Jul 11 06:30 EDT 1996
From: <[email-masked]>
Date: Thu, 11 Jul 1996 12:30:28 +0200
To: [email-masked]
Subject: CCL: random stops in G94
Content-Length: 1042
Status: RO

Dear All,

We have a strange and random problem :
we are running Gaussian 94 on a IBM 43P (Power PC) under AIX4.1.4 with
128 Meg of memory and 284 Meg of pagingspace. Gaussian 94 was compiled
with IBM Fortran 3.2.
We run Gaussian with : nohup 'script-in-csh'  
and it stops mysteriously with no error message (nor in the output file 
nor in the errlog), no core dump...just stops (the scratch files  
are not removed by Gaussian). 
Sometimes after a re-start of the script it goes to the end and 
sometimes it stops again after one or more optimisation steps.
It happens after writing the energy on the output file. 
There is enough temporary scratch space available.

Does anyone have had the same problem ? or have an idea what it
could be and/or what to do ?

Thanks in advance

 Anne Milet

===========================================================
Anne Milet
Laboratoire de Chimie quantique
UPR 139
4, rue Blaise Pascal
67000 Strasbourg
e-mail : [email-masked]
===========================================================

>From [email-masked] Wed Jul 10 05:40 EDT 1996
Date: Wed, 10 Jul 1996 11:38:52 +0200 (MET DST)
From: Massimo Trotta <[email-masked]>
Subject: basic fluorescence information
To: [email-masked]
Content-Length: 929
Status: RO

 Dear All,
 this is probably not exactly a question for a computational chemistry list,
 but it is possible that some of you have experience in basic fluorescence
 spectroscopy:
 	I am looking for literature or any suggestion regarding the
 fluorescenze of substituted benzoquinones: Should they fluoresce or not?
 
 Also indication on Electronic Lists on fluorescence related topics.
 
 thank you in advances
 
 massimo trotta 

-- 
!==============================================================!
!   Massimo Trotta                                             ! 
!   Centro Studi Chimico Fisici sull'Interazione Luce Materia  !
!   c/o Dept. of Chemistry                                     !  
!   V. Orabona, 4  I-70126 Italy                               !
!   e-mail: [email-masked]                            !
!   http://www.ba.cnr.it/~csilmt12
!==============================================================!

>From [email-masked] Mon Jul 15 23:44 EDT 1996
Date: Tue, 16 Jul 1996 09:00:03 -0500
From: [email-masked] (Dr.A.K.Chandra)
To: [email-masked]
Subject: Norrish
Content-Length: 511
Status: RO

Dear netters,
Does anybody have an idea of NORRISH TYPE II (Intramolecular gamma-Hydrogen
abstraction processes) in ORGANO-THIO (C=S) compounds in ground or excited
states? If so, please send me a reference/s.  Thanks in advance,

V.SREEDHARA RAO

****************************************
V. SREEDHARA RAO
Department of Inorganic and Physical Chemistry
Indian Institute of Science (I.I.Sc)
BANGALORE - 560 012. India.

E-mail : [email-masked]   (or)
         [email-masked]

>From [email-masked] Wed Jul 10 10:26 EDT 1996
Date: Wed, 10 Jul 1996 09:26:36 -0500 (CDT)
From: Rino Ragno <[email-masked]>
To: [email-masked]
Subject: Conf. space & RBs
Content-Length: 1326
Status: RO

Dear Netters,

any of you out there knows if there is any program/routine that is able 
to compute both the number of rotatable bonds and the number of 
geometrically possible number of conformers of a given molecules?

Thank in advance to every one is going to answer.

Rino Ragno

++---------------------------------------------------------------------------++
++---------------------------------------------------------------------------++
||                                                                           ||
||  Dr. Rino Ragno                            E-mail: [email-masked]   ||
||  Institute for Biomedical Computing            or: [email-masked]     ||
||  Center for Molecular Design               Phone : 314-362-2273           ||
||  Box 8036, Washington University           FAX   : 314-362-0234           ||
||  700 South Euclid Avenue                                                  ||
||  St. Louis, Missouri 63110                                                ||
||  U. S. A.                                                                 ||
||                                                                           ||
++---------------------------------------------------------------------------++
++---------------------------------------------------------------------------++

>From [email-masked] Thu Jul  4 14:15 EDT 1996
Date: Tue, 28 May 1996 10:00:24 +0100
To: [email-masked]
From: "B. Kallies" <[email-masked]>
Subject: CCL:autoprotolysis constant of alcohols
CC: [email-masked]
Content-Length: 1381
Status: RO

Dear Dr. Trotta,

Christian Reichardt collected some pK(auto) for amphiprotic solvents in

"Solvents and Solvent Effects in Organic Chemistry"
2nd. ed., VCH 1990, p. 431 ff.

There will be found for 2 ROH =3D R(OH)2(+) + RO(-)

Solvent         R       pK(auto) at 25=B0C
-----------------------------------------
Methanol        CH3      17.20
Ethanol         C2H5     18.88
1-Propanol      C3H7     19.43
1-Butanol       C4H9     21.56
1-Pentanol      C5H11    20.65

and some others. Original references and some other original literature
citations are given, too.

Yours sincerely

B. Kallies

---------------------------------------------------
DC Bernd Kallies
Institut fuer Physikalische und Theoretische Chemie
Universitaet Potsdam
Am Neuen Palais 10
14469 Potsdam
GERMANY
e-mail: [email-masked]
Fax: ++49 / 0331 977 1315
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