From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de  Thu Feb 26 06:14:22 1998
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From: "Emadeddin Tajkhorshid" <tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de>
Message-Id: <9802261121.ZM21820@mbp-sgi7.inet.dkfz-heidelberg.de>
Date: Thu, 26 Feb 1998 11:21:17 -0800
Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de
X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail)
To: chemistry@www.ccl.net (Computational Chemistry List)
Subject: R-C=C-R atom type
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Dear CCLers

I have a ligand which contains two conjugated doule bonds in its dtructure.

R-C=C-C=C-R

I am wondering for the proper atom type for the SP2 carbons and their hydrogens
in AMBER. Is there any explicit atom type for these atoms or do I have to
consider one of the available SP2 carbons which is normally used for the
aromatic rings or carbonyl group?

Thanx

-- 
Emad
*********************************************************************
E. Tajkhorshid				
German Cancer Research Center; DKFZ             Tel: +49 6221 42 2340
Dept. Molecular Biophysics (0810)               FAX: +49 6221 42 2333
P.O.Box 101949			   
69009 Heidelberg, FRG         Email: E.Tajkhorshid@DKFZ-Heidelberg.de 
*********************************************************************
* "Never express yourself more clearly than you think." -Niels Bohr *
*********************************************************************

From pang@iris.chem.cuhk.edu.hk  Thu Feb 26 07:14:23 1998
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Date: Thu, 26 Feb 1998 19:15:48 +0800 (HKT)
From: Pang Siu Kwong <pang@iris.chem.cuhk.edu.hk>
To: chemistry@www.ccl.net
Subject: VShift in Gaussian 94
Message-ID: <Pine.SGI.3.91.980226185751.18138A-100000@iris.chem.cuhk.edu.hk>
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Hello!  'VShift' in Gaussian 94 is a common method to solve the 
convergence problem.  How to know the value of VShift which is 
suitable?  
Thank you for your attention!

Patrick Pang 

From root@liposome.genebee.msu.su  Tue Feb 24 13:18:07 1998
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Date: Tue, 24 Feb 1998 21:03:11 +0300 (MSK)
From: root <root@liposome.genebee.msu.su>
To: chemistry@www.ccl.net
Subject: automatical generation of polypeptide / oligo coordinates?
Message-ID: <Pine.LNX.3.95.980224204431.7376G-100000@liposome.genebee.msu.su>



Dear CCLers,

I'm fairly certain there is a program/script capable of generating a
polypeptide / oligo e.g. in linear conformation just from the primary
structure (amino acid sequence) data somewhere out there. Corina-generated
structures from SMILES seem to lack important data, preventing both XPLOR
and Solvate from reading them (? -- feel free to correct me). I wanted to
generate pdb/psf pairs 10-30 residue-oligos for subsequent MD runs. 

In the CCL archive there seems to be no mentioning of such an animal,
which is strange.

Before I start reinventing the wheel: anybody aware of such a thing? It
can be an XPLOR script, but a simple language such as C/Perl/Python would
be preferable.

Regards,

Eugene Leitl

P. S. When compensating protein polyelectrolyte (e.g. polylysine)
      charges with counterions (e.g. chloride) is using HETATM the
      canonical thing to do, or do ATOMs suffice?

P. P. S. Anybody knows why RasMol chooses to kill CONECT when saving a
         just-read pdb file?



From Jan.R.Karlson@eu.apbiotech.com  Wed Feb 25 09:14:17 1998
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From: Jan.R.Karlson@eu.apbiotech.com (Jan R Karlson)
Subject: modified aminoacids/peptides....
To: chemistry@www.ccl.net


     Is there any program wich can calculate different parameters for 
     peptides like hydrophobisity, pI, charges. Exist programs which take 
     into account modified aminoacids????? I am intrested in interaction 
     with peptides and surfaces on chromatographic media. 
     
     Jan Roger karlson


From katalin@pharma.univ-montp1.fr  Wed Feb 25 12:14:14 1998
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From: katalin@pharma.univ-montp1.fr (Katalin KESERU)



dear netters!

I'm interested in the calculation (prediction) the values logP or water 
solubility of the quaterner ammonium compounds. 
best regards

katalin



From root@liposome.genebee.msu.su  Wed Feb 25 14:14:22 1998
Date: Wed, 25 Feb 1998 09:51:52 -0800
From: Elaine Tschorn <office@foresight.org>
To: office@foresight.org
Subject: Foresight Conference on Molecular Nanotechnology
Resent-Date: Wed, 25 Feb 1998 21:51:07 +0300 (MSK)
Resent-From: Eugene Leitl <eugene@liposome.genebee.msu.su>
Resent-To: root <root@liposome.genebee.msu.su>




Sixth Foresight Conference on Molecular Nanotechnology
http://www.foresight.org/conference/MNT6/

Call for Abstracts

November 12-15, 1998 at the Westin Hotel in Santa Clara, CA.
An intensive Tutorial on Critical Enabling Technologies for
Nanotechnology will be held on November 12.

Two annual $5000 Feynman Prizes in Molecular Nanotechnology, one each for
experimental and theoretical work, will be presented.
See http://www.foresight.org/FI/1997Feynman.html for details on
last year's prize.

Nobel Laureate Richard Smalley, keynote speaker at the 1997
conference, says: "The idea behind nanotechnology is ultimately, and
maybe sometime very soon, to custom design the materials around us atom by
atom, much like an architect designs a building."

Topics Covered

This conference is a meeting of scientists and technologists
working in fields leading toward molecular nanotechnology:
thorough three-dimensional structural control of materials and devices
at the molecular level. The conference will cover topics relevant to the
pursuit of molecular control including:

molecular electronics
biochemical molecular engineering
scanning probe microscopy
supramolecular chemistry and self-assembly
materials science
mechanosynthesis
natural molecular machines
artificial molecular machines
artificial self replicating systems
computational chemistry and molecular modeling
computer science
mechanical engineering and robotics applications
relevant chemical systems (fullerenes, diamond, biomolecules, etc.)

Submission information:
Extended abstracts          30 June 1998
Acceptance notices          early August 1998
Full papers                 15 October 1998
Text format                 HTML
Image formats               JPEG and GIF
Video format                MPEG

Send extended abstracts (1-4 pages plus figures) to
inform@foresight.org,globus@nas.nasa.gov, and deepak@nas.nasa.gov.

Authors are encouraged to include the data where relevant and practical.
All accepted abstracts and papers will be permanently archived on the
conference's or author's web server.

Proceedings:

As in previous years, proceedings are expected to be published as a
special issue of the Institute of Physics journal Nanotechnology.
http://www.iop.org/Journals/na

Conference Co-chairs: Al Globus and Deepak Srivastava, MRJ
Technology Solutions, Inc. at NASA Ames Research Center.

Cosponsors:

Caltech Materials and Process Simulation Center
Institute for Molecular Manufacturing
Lawrence Berkeley National Laboratory NERSC
NASA Ames Numerical Aerospace Simulation Systems Division
Rice Univ. Center for Nanoscale Science and Technology
Washington Univ Lab. for the Study of Novel Carbon Materials

See URL http://www.foresight.org/conference for additional details,
including complete information on the previous meeting in this series:
http://www.foresight.org/conference/MNT05/Nano5.html

Sponsors and Exhibitors at Foresight Institute Conferences

AMP, Apple Computer, ARCO, Autodesk, Beckman Instruments, CaChe
Scientific, Cambridge Scientific, Digital Equipment Corporation,
Digital Instruments, Ford Motor Company, JEOL, Institute of Physics
Publishing, Loral Systems Manufacturing Company, Mitsubishi, Molecular
Manufacturing Enterprises Inc., Molecular Simulations Inc., Niehaus Ryan
Haller Public Relations Inc., Park Scientific, Tripos Associates,
Schrodinger, Inc., Silicon Graphics, Inc., Sun Microsystems, TopoMetrix,
Xerox, Zyvex

Foresight Institute
P.O. Box 61058
Palo Alto, CA  94306 USA
tel.  650-917-1122  fax 650-917-1123
inform@foresight.org




From varnai@bellatrix.pcl.ox.ac.uk  Wed Feb 25 16:14:16 1998
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From: varnai@bellatrix.pcl.ox.ac.uk (Peter Varnai)
Message-Id: <199802252059.UAA24535@bellatrix.pcl>
Subject: extended electrostatics in CHARMM
To: CHEMISTRY@www.ccl.net
Date: Wed, 25 Feb 1998 20:59:31 +0000 (GMT)



Dear CCLers,

"Extended" electrostatic calculation can provide an efficient way to approximate
the total electrostatic interaction. The electrostatic term has two contribution:
1, conventional pairwise summation (spatially close particles)
2, multipole approximation (spatially distant particles)
To reproduce the electrostatic energy calculated without cutoff, one adds the above
terms. In the first term there is NO smoothing. 
Here comes my questions: in CHARMM manual it is written that 
"The interactions between particles within CUTNB are truncated
rather than having a SHIFt or SWITch function applied."
Unfortunately, the code uses switch function in the electrostatic calculation.

Does anybody know how to get around this problem?
Does anybody have positive/negative experiences with this model?

Thank you,

Peter Varnai
Oxford University
UK



From HILAL2@FRCU.EUN.EG  Thu Feb 26 10:14:25 1998
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 id <01IU1IGTKOGW0009UV@FRCU.EUN.EG> for chemistry@www.ccl.net; Thu,
 26 Feb 1998 16:31:45 +0200
Date: Thu, 26 Feb 1998 16:31:37 +0200
Subject: energy partitioning
To: chemistry@www.ccl.net, CHEMISTRY@www.ccl.net
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Dear CClers
  I am appreciated greatly if any one give me some information how I calculate 
completely the energy 
patitioning of a structure  or geometry which is optimized under GAMESS 
program using split-valence basis sets, 31-6G. 

Thank In advance
Ahmad Omar
Cairo university
Chem. Dep.


From jkl@ccl.net  Thu Feb 26 10:22:32 1998
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Message-Id: <199802261506.KAA16908@krakow.ccl.net>
To: chemistry@www.ccl.net
Subject: 98.04.20-22 Workshop: Comp. Methods in Toxicology, Dayton, OH
Cc: jkl@ccl.net



The text of this announcement is also available at Computational Chemistry
Conference List at:

             http://www.ccl.net/cca/info/conferencelist.html
-----------------------------------------------------------------------------

              COMPUTATIONAL METHODS IN TOXICOLOGY
                       April 20-22, 1998
              Holiday Inn/I-675, Dayton, Ohio, USA


                    Organizing Committee:
  John Frazier (AFRL/HEST)           Ruth Pachter (AFRL/MLPJ & ASC)
  Kevin Geiss (AFRL/HEST)            Steven Trohalaki (AFRL/MLPJ)
  Jan Labanowski (ASC/ARL & OSC)     Theresa Windus (ASC & OSC)

International workshop: "Computational Methods in Toxicology" organized by: 
   -  Air Force Research Laboratory (Operational Toxicology Branch of the
      Human Effectiveness Directorate, Materials & Manufacturing Directorate,
      and Air Force Office of Scientific Research.) 

   -  Aeronautical Systems Center (Major Shared Resource Center for High
      Performance Computing) through the Programming Environment and
      Training Program. 
will be held at Holiday Inn/I-675, Dayton, Ohio, USA. The workshop is open to
all US and international participants from Industry, Government, or
Academic/Non-profit sectors but is limited to 60 participants. Please register
promptly since the priority will be given to preregistered participants.

                     Topic Areas:
      Research applications of QSAR/SARs, 
      Tools for development of new QSAR/SARs, 
      Molecular modeling and simulation in toxicology, 
      Commercially available software products. 

                     Workshop Format:
      Oral presentations by invited speakers, 
      Roundtable discussion with panel of invited speakers, 
      Poster session open for presentations by attendees. 

                     Deadlines:
      Registration Deadline: March 31, 1998. 
      Abstract Submission Deadline: March 16, 1998. 


                     List of invited speakers: 
           Marilyn Arnott - LogiChem 
           Subhash Basak - University of Minnesota 
           Romualdo Benigni - Instituto Superiore di Sanita, IT 
           Doug Bristol - NIH/NIEHS, RTP 
           James Devillers - CTIS, Lyon, FR 
           Kurt Enslein - Health Designs, Inc, NY 
           Nigel Greene - LHASA , UK 
           William C. Herndon - University of Texas-El Paso 
           Peter Jurs - Penn State University 
           Douglas J. Klein - Texas A&M 
           Bob Lipnick - EPA, Washington, DC 
           Edwin Matthews - FDA, Rockville 
           Rich Purdy - 3M, St. Paul
           Milan Randic - Drake University, IA 
           Ann Richard - EPA, RTP 
           Herb Rosenkranz - University of Pittsburgh 
           Paul Seybold - Wright State University 
           Alex Tropsha - UNC-Chapel Hill 

Detailed information about registration, location, and program is available
on the Web at:

           http://www.ccl.net/CCM/toxicology/

or can be requested from:
           Toxicology Workshop
           c/o Ms. Jill Robertson
           ASC/HP
           2435 Fifth Street
           Bldg. 676, Room 114
           Wright-Patterson AFB, OH 45433-7802
              FAX: (937) 255-4585
              E-mail: toxicology@ccl.net

Since we do not have much time in advertizing this workshop,
we would be grateful if you could forward this message to your
colleagues who may be interested in participating.


Thank you,

The Organizers: toxicology@ccl.net
=========================================================================

The text of this announcement is also available at Computational Chemistry
Conference List at:

             http://www.ccl.net/cca/info/conferencelist.html


From smb@smb.chem.niu.edu  Thu Feb 26 11:14:38 1998
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The full technical program for the Division of Computers in Chemistry at
the Spring ACS Meeting in Dallas is now available from the COMP web
page:

http://hackberry.chem.niu.edu/COMP/

Steve
-- 
Steven Bachrach				
Department of Chemistry
Northern Illinois University
DeKalb, Il 60115			Phone: (815)753-6863
smb@smb.chem.niu.edu			Fax:   (815)753-4802



From pieter.stouten@dupontmerck.com  Thu Feb 26 11:26:41 1998
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Date: Thu, 26 Feb 1998 10:23:20 -0500
From: Pieter Stouten <pieter.stouten@dupontmerck.com>
Subject: Re: CCL:R-C=C-R atom type
In-reply-to: <9802261121.ZM21820@mbp-sgi7.inet.dkfz-heidelberg.de>
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On 98/02/26 at 11:21 -0800, Emadeddin Tajkhorshid wrote:

>I have a ligand which contains two conjugated doule bonds in its dtructure.
>
>R-C=C-C=C-R
>
>I am wondering for the proper atom type for the SP2 carbons and their
>hydrogens in AMBER. Is there any explicit atom type for these atoms or
>do I have to consider one of the available SP2 carbons which is normally
>used for the aromatic rings or carbonyl group?
>
Sounds like the poly-ene problem. Typically, these systems are not aromatic
and then there is a length difference between the single and double bonds.
If all the carbons have the same atom type, then there is no way to
distinguish between the single and double bonds. There are two principle
solutions (but I have no clue how Amber might handle this):

1) using alternating atom types for adjacent carbon pairs (e.g.
   -Cx=Cx-Cy=Cy-Cx=Cx-Cy=Cy etc.) and use identical (double bond) lengths
   and force constants for "like" atom pairs Cx=Cx and Cy=Cy and different
   (single bond) lengths and force constants for "unlike" pairs Cx-Cy.
2) using explicit bond orders as is done e.g. in MSI's CFF96.

Good luck,

Pieter Stouten                              ||
Computer Aided Drug Design Group            ||   Free advice is
The DuPont Merck Pharmaceutical Company     ||    seldom cheap
P.O. Box 80500, Wilmington, DE 19880-0500   ||
Phone: +1 (302) 695 3515                    ||  (Ferengi Rule Of
Fax: +1 (302) 695 9090                      ||  Acquisition #59)
Internet: pieter.stouten@dupontmerck.com    ||
Web: http://www.halcyon.com/stouten/        ||



From daniel.parish@roche.com  Thu Feb 26 11:32:51 1998
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To: chemistry@www.ccl.net
From: Daniel Parish <daniel.parish@roche.com>
Subject: Summary: Mailing list for MSI's Catalyst software
Cc: daniel.parish@roche.com
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Dear CCLers,

Earlier in the month I asked for feedback concerning the establishment of
an independent Catalyst mailing list.  To date I have received a total of
10 responses in favor of the idea and 1 opposed to it.  I also received
responses from 2 MSI scientists asking to be included, which I believe
would be important for the success of the list.  While not quite the level
of response I expected, I think this is a reasonable number of participants
to get things started.  If the list results in some useful discussions,
etc., I'm sure we will be able to attract more users as time progresses.  

I will now look into where/how to get this set up and will send out another
email when it is ready to go.

Regards,

Daniel


At 09:51 AM 2/10/98 -0800, I wrote:
>Greetings CCLers,
>
>For some time now I have been toying with the idea of starting a mailing
>list specifically for users of the software package Catalyst.  For those of
>you unfamiliar with it, Catalyst is a commercial pharmacophore
>generation/database searching package sold by MSI.  Although MSI maintains
>its own mailing list for Catalyst (catalyst-l), traffic on their list
>appears to be virtually nonexistent.  I'm not sure whether this reflects a
>lack of need for such a list or whether users are uncomfortable with the
>list because it is maintained by MSI.
>
>I'd like some feedback on whether you think an independent catalyst mailing
>list would be useful and who among you would be interested in
>subscribing/contributing to such a list if it were available.  If there is
>sufficient interest I will be happy to maintain this new list and, having a
>great deal of practical (and impractical :^) ) experience using Catalyst,
>happy to share my expertise as well.
>
>Please email your comments directly to me <daniel.parish@roche.com> and I
>will summarize to the list if necessary.
>

__*_____Daniel W. Parish
____*_____Roche Bioscience
______*_____daniel.parish@roche.com
________*_____650/855-6314 (Phone) 650/852-1875 (FAX)


