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From: Fernando Luis Barroso da Silva <fernando@melba.fkem2.lth.se>
To: chemistry@www.ccl.net
Subject: Re: CCL:computational chemistry of polymers 
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On Mon, 07 Dec 1998, Dr. Daniel Glossman  wrote:

>  Dear netters:
> 
>  Can somebody point me to any book related to computational chemistry 
>  and/or molecular modeling of polymers?
> 
>  Also, in what journals are published the articles related to this subject?
> 
>  Thanks in advance
> 
> 
> 					Daniel Glossman
> 

  
  Dear Daniel,

  There is a book written by K. Binder. It is called "Monte Carlo and
  Molecular Dynamics Simulation in Polymer Science" (Oxford University
  Press, New York, 1995). The topic is also covered in some limited
  detail by other molecular modeling books and reviews. Binder has
  one relatively recent review about Monte Carlo. If I am not wrong, 
  few examples were related with polymers. The reference is K.Binder,
  Rep.Prog. Phys. 60, 487(1997). Yesterday, I saw a short review
  written by C.Holm and K.Kremer with emphasis in Molecular
  Dynamics. It was available at lanl server
  (http://xxx.lanl.gov). Its number is cond-mat/9812152. 

  I think several journals are publishing articles in this topic.
  For example, Macromolecules, Biopolymers, JCP, Mol.Phys., etc..

  Best regards,

    Fernando.



--

Fernando Luis Barroso da Silva
Physical Chemistry II - Chemical Center  
POB 124 - Lund University                  Fax: +46 (46) 2224543
S-221 00 Lund, Sweden                    Phone: +46 (46) 2228241 (lab)
E-mail: fernando@melba.fkem2.lth.se             +46 (46) 2220381 (office)
        Fernando_Luis.Barroso_da_Silva@fkem2.lth.se 

         http://www.fkem2.lth.se/personnel/fernando/dasilva.html
         http://idefix.ffclrp.usp.br/barroso/fernando.html



From chemistry-request@server.ccl.net  Thu Dec 17 05:15:22 1998
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From: Fernando Luis Barroso da Silva <fernando@melba.fkem2.lth.se>
To: glossman@overnet.com.ar, CHEMISTRY@www.ccl.net
Subject: Re: CCL:computational chemistry of polymers (fwd)
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On Mon, 07 Dec 1998, Dr. Daniel Glossman  wrote:

>  Dear netters:
> 
>  Can somebody point me to any book related to computational chemistry 
>  and/or molecular modeling of polymers?
> 
>  Also, in what journals are published the articles related to this subject?
> 
>  Thanks in advance
> 
> 
> 					Daniel Glossman
> 

  
  Dear Daniel,

  There is a book written by K. Binder. It is called "Monte Carlo and
  Molecular Dynamics Simulation in Polymer Science" (Oxford University
  Press, New York, 1995). The topic is also covered in some limited
  detail by other molecular modeling books and reviews. Binder has
  one relatively recent review about Monte Carlo. If I am not wrong, 
  few examples were related with polymers. The reference is K.Binder,
  Rep.Prog. Phys. 60, 487(1997). Yesterday, I saw a short review
  written by C.Holm and K.Kremer with emphasis in Molecular
  Dynamics. It was available at lanl server
  (http://xxx.lanl.gov). Its number is cond-mat/9812152. 

  I think several journals are publishing articles in this topic.
  For example, Macromolecules, Biopolymers, JCP, Mol.Phys., etc..

  Best regards,

    Fernando.



--

Fernando Luis Barroso da Silva
Physical Chemistry II - Chemical Center  
POB 124 - Lund University                  Fax: +46 (46) 2224543
S-221 00 Lund, Sweden                    Phone: +46 (46) 2228241 (lab)
E-mail: fernando@melba.fkem2.lth.se             +46 (46) 2220381 (office)
        Fernando_Luis.Barroso_da_Silva@fkem2.lth.se 

         http://www.fkem2.lth.se/personnel/fernando/dasilva.html
         http://idefix.ffclrp.usp.br/barroso/fernando.html


From chemistry-request@server.ccl.net  Thu Dec 17 09:26:01 1998
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From: Christoph.Helma@univie.ac.at
Cc: dalke@bioreason.com
To: chemistry@www.ccl.net
Subject: SUMMARY: Looking for an utility to generate unique SMILES
Reply-to: Christoph.Helma@univie.ac.at
Date: Thu, 17 Dec 1998 15:22:38 +0100
Sender: ch@helma.cancer.univie.ac.at


Some weeks ago I was asking for a tool for the generation of unique
SMILES under Linux. A source for the SMILES uniquetizer is available
from

       outreach@superior.dul.epa.gov

I was able to compile it without problems, but did not have time
enough to test it thoroughly.

On a SGI it is possible to use the Daylight toolkit or TSAR (Oxford
Molecular) to generate unique SMILES.


Christoph Helma

----
Christoph Helma                               christoph.helma@univie.ac.at
Institut fuer                            http://helma.cancer.univie.ac.at/
Tumorbiologie-Krebsforschung
Borschkegasse 8a                                      tel +43-1-4277-65147
A-1090 Wien, Austria                                  fax +43-1-4277-9651

From chemistry-request@server.ccl.net  Thu Dec 17 09:57:58 1998
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Hi ccl'ers,
Does anyone know of a free or relatively cheap interactive 
visualisation package to enable crystallographic coordinates with 
thermal parameters (to form ellipsoids) to be read. I'd be most 
grateful for any information.
Many thanks
Shaqil


From chemistry-request@server.ccl.net  Thu Dec 17 10:12:35 1998
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Arthur Wang recently posted a message to CCL announcing avaiability of
SPL programs which "improve" CoMFA analyses by exhaustively searching
the possible orientations and placements of molecules on the lattice and
using that which gives the highest q^2.  Users should be aware that when
this is done, that highest q^2 ceases to be a valid test statistic for
the significance of the model and no longer accurately reflects the
expected external predictivity, just as is the case for variable
selection methods in general( see U Norinder J. Chemonetrics 1996, 10,
95-105 and recent reports by other groups).  This is because compounds
are no longer completely "left out" of the analysis - each contributes
to identifying the highest q^2.

A lattice shift represents a random perturbation of the CoMFA
descriptors.  Though neither the highest nor the lowest q^2 value are of
interest in and of themselves, the AOS and APS programs may nonetheless
be useful for determining the distribution of values and hence how
robust a particular model (the scheme used to align each molecule with
the others) is.  When this is done, however, the appropriate test
statistic is the median or mode q^2 or, better, the mean cross-validated
standard error and the q^2 calculated therefrom. 

Lattice placements which give q^2 values at either extreme - high or low
- are misleading and therefore undesirable.  It turns out, however, that
good representative lattice orientations can reliably be obtained simply
by applying ORIENT BEST to a prototypical molecular (usually the most
extended of the more active compounds) and aligning other molecules in
the training set on that prototype (RD Clark, M Cline & TW Heritage
(1998) Making 3D QQSAR Both Simple and Robust, 215 ACS Natl Meeting,
Abstract COMP 057). In fact, this is now the default option in the
DATABASE ALIGNMENT dialog in SYBYL QSAR. 

Bob Clark
Tripos Inc.
1699 S. Hanley Road
St. Louis MO 63144

bclark@tripos.com

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From: "Andruski, Stephen W." <StephenA@albmolecular.com>
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Shaqil asked:
>>Hi ccl'ers,
>>Does anyone know of a free or relatively cheap interactive 
>>visualisation package to enable crystallographic coordinates with 
>>thermal parameters (to form ellipsoids) to be read. I'd be most 
>>grateful for any information.
>>Many thanks

For Windows 3.1, 95 and NT look at:
http://www.chem.gla.ac.uk/~louis/ortep3/ 
Ortep-3 for Windows is a MS-Windows version of the current release of
ORTEP-III (1.0.2), which incorporates a Graphical User Interface (GUI)
to make production of thermal ellipsoid plots much easier. 

I have used versions of this program and it is easy to use and free.  It
supports a variety of crystallographic file formats and generates
graphics files which can be brought into a word processor for inclusion
in reports and publications.

Steve Andruski
> *********************************** 
> Dr. Stephen W. Andruski
> Senior Research Chemist II
> Albany Molecular Research, Inc.
> 21 Corporate Circle
> Albany, New York 12203 USA
> Tel. (518) 464-0279, Ext. 3303
> Fax (518) 464-0289
> http://www.albmolecular.com
> E-mail:  stephena@albmolecular.com
>  ************************************ 
> 
> 

From chemistry-request@server.ccl.net  Thu Dec 17 12:28:43 1998
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Date: Thu, 17 Dec 1998 12:25:42 -0500
From: "M. Nicklaus" <mn1@helix.nih.gov>
To: CHEMISTRY@www.ccl.net
cc: "M. Nicklaus" <mn1@helix.nih.gov>
Subject: Parallel G98 on x86/Linux
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According to Gaussian, Inc. (http://www.gaussian.com/parallel.htm),
G98 is available for Shared Memory Parallel execution on [Intel]
Linux systems.

Does anyone have G98 set up like this, and could report some 
performance results?

I am particulary thinking of a Dual-P II 450MHz system, with
G98 compiled with the Portland Group compilers, and using the
tuned BLAS libraries as recommended by Gaussian, Inc.
(see http://www.gaussian.com/g98_req.htm).  This should be 
about the fastest *inexpensive* G98 implementation on
x86/Linux at this time.  (One can certainly get higher
perfomance by using Linda with >2 CPU's, and/or Xeon processors,
but either option would increase the cost substantially.)

If someone has this setup and could run some benchmarks for me
(should be < 1 h), I'd appreciate.

Please contact me directly.  I'll summarize for the list.

Thanks in advance for all responses,

Marc

------------------------------------------------------------------------
 Marc C. Nicklaus                        National Institutes of Health
 E-mail: mn1@helix.nih.gov               Bldg 37, Rm 5B29
 Phone:  (301) 402-3111                  37 Convent Dr, MSC 4255       
 Fax:    (301) 496-5839                  BETHESDA, MD 20892-4255    USA 
      http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm
    Laboratory of Medicinal Chemistry, National Cancer Institute
------------------------------------------------------------------------



From chemistry-request@server.ccl.net  Thu Dec 17 13:10:39 1998
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Date: Thu, 17 Dec 1998 13:07:39 -0500 (EST)
From: Jan Labanowski <jkl@ccl.net>
To: chemistry@www.ccl.net
cc: Jan Labanowski <jkl@ccl.net>
Subject: Happy Holidays and all the best in 1999!!!
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Dear Friends [and Enemies (:-)}],

The holiday season has arrived. For many of us, it is time of joy but also
reflection. Some of us are more reassured at the end of this year,  and some
are more humble; some are at peace with themselves, and some are busily
searching. We already know that one cannot be happy without suffering first.
We also know that nothing lasts forever. The change is what makes it all
fascinating. In any way, life is a process (we, chemists know what process is,
don't we?, though let us not talk about equilibrium at this moment, and beside,
the true equilibrium is never reached, there is this quantum stuff and these
11 or so dimensions, which can leap us always to some new state, and let us
face it, we do not know anything, we are stupid...), and the greatest value
of this process is that each year brings new experience and makes us richer
as unique beings which cannot be cloned. Each year makes us closer to the
ideal of our creator (even if you refuse to personalize a creator, you have
to admit that nature in itself is quite amazing, and will keep us employed
for a long time to come...). We may never be sure why, but it is great to be
a part of this constant struggle of reason and feelings, and fail to control
our basic reflexes and know what others will do. [this is not a voice in
discussion for or against impeachement, though...]. It is fun to be infinitely
more unpredictable than cellular automata or neural networks and jump up and
down. Consider the alternative... This is really better. So use the time
to have some joy, forget about logic, be a party animal, and ask the questions
later... The Y2k bug is a year ahead, so you will be able to read your e-mail
when you come back from holiday break... Do not worry, be happy...

Happy Holidays and the best of everything now and later...

Jan Labanowski
The Creator of unpredictable CCL...
jkl@ccl.net

------------------------------------------------------------------------------!
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   \ /          "FELIZ  NATAL"      --O--                     "DOSIEGO!"      !
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   / \       "KALA CHRISTOUGENA"                          "PARI  ARTSAGOURT"  !
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           "FROEHLICHE WEIHNACHTEN"                    "NAYA VARSH SHUBH HO"  !
          "BUON  NATALE-GODT NYTAR"                   "ATHBHLIAIN FAOI MHAISE !
         "HUAN YING SHENG TAN CHIEH"                "IYI YILLAR-HYVAEAE LOMAA !
        "WESOLYCH SWIAT-SRETAN BOZIC"       \ /             "NA  ZDOROVE"     !
       "MOADIM LESIMHA-LINKSMU KALEDU"     --O--          "MERRY CHRISTMAS"   !
      "HAUSKAA JOULUA-AID SAID MOUBARK"     / \          "FELICHAN JARFINON"  !
           "'N  PRETTIG  KERSTMIS"                      "#-SHUB NAYA BARAS-@" !
          "ONNELLISTA UUTTA VUOTTA"      !            "INPAKARAMAANA VIDUMURAI!
         "Z ROZHDESTYOM  KHRYSTOVYM"    >+<          "STASTNY NOVY ROK-CHEERS!!
        "NADOLIG LLAWEN-GOTT NYTTSAR"    !          "CHING CHI SHEN TAN-@@@@@!!
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      "S  NOVYM  GODOM-FELIZ ANO NUEVO"          .-'-.  mmmmmm  !!!!          !
     "GLEDILEG JOL-NOELINIZ KUTLU OLSUM"      .-' .-. '-.!  !   xxxx          !
    "EEN GELUKKIG NIEUWJAAR-SRETAN BOSIC"  .-' .-'   '-. '-.!    .            !
   "KRIHSTLINDJA GEZUAR-KALA CHRISTOUGENA"  .-'         '-. '-.               !
  "SELAMAT HARI NATAL - LAHNINGU NAJU METU"'               '-. '-.            !
       "SARBATORI FERICITE-BUON  ANNO"   !   ___________     !-..!-           !
      "ZORIONEKO GABON-HRISTOS SE RODI"  !   !__o_!__!__!    !                !
     "BOLDOG KARACSONNY- VESELE  VANOCE" !   !_ooo!__@__!    !                !
    "MERRY CHRISTMAS**JOY**HAPPY NEW YEAR"   !ooooo__#__!    !      (\_/)-=)) !
   "ROOMSAID JOULU PUHI -KUNG HO SHENG TEN"     .            !     =('.')=//  !
  "FELICES PASUAS-EIN GLUCKICHES  NEUEJAHR*.-.-' -.._________!	   ( ~~~ )/   !
"PRIECIGUS ZIEMAN SVETKUS  SARBATORI VESLLE"            '-.-''-..  `w---w`    !
"BONNE ANNEE-BLWYDDYN NEWYDD DDA*FELIZ NATAL"                     '-....      !
SHENORAVOR SOORP TSENOONT,SHENORAVOR NOR DARI"
                     XXXXXX                                                   !
                     XXXXXX                                                   !
                     XXXXXX                                                   !





Jan K. Labanowski            |    phone: 614-292-9279,  FAX: 614-292-7168
Ohio Supercomputer Center    |    Internet: jkl@ccl.net 
1224 Kinnear Rd,             |    http://www.ccl.net/chemistry.html
Columbus, OH 43212-1163      |    


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Date: Thu, 17 Dec 1998 13:03:00 -0800
Subject: Web Browser Requirements for CRDB
To: chemistry@www.ccl.net
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Several people have written to say that they were unable to properly
access the web page I mentioned in yesterday's posting.  I've spoken
with the developer.  She decribed the requirements as follows:

The CRDB web page requires Netscape version 4.x to run.  It will not
work with current versions of Internet Explorer.  The page has
been tested on PCs, MacIntoshs, Solaris 2.5.1 and SGI 6.x workstations
primarily with Netscape 4.06.

Dave

-- 

David Feller                                | Mail Stop K1-96
Environmental Molecular Sciences Laboratory | Box 999
Battelle Pacific Northwest National Lab     | Richland, WA 99352
                                            | 
e-mail:d3e102@emsl.pnl.gov                  | Fax: (509)-375-6631

