From chemistry-request@server.ccl.net Sun Nov 10 22:43:34 2002 Received: from pacific-carrier-annex.mit.edu ([18.7.21.83]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAB3hYQ12127 for ; Sun, 10 Nov 2002 22:43:34 -0500 Received: from grand-central-station.mit.edu (GRAND-CENTRAL-STATION.MIT.EDU [18.7.21.82]) by pacific-carrier-annex.mit.edu (8.9.2/8.9.2) with ESMTP id WAA07443 for ; Sun, 10 Nov 2002 22:43:34 -0500 (EST) Received: from melbourne-city-street.mit.edu (MELBOURNE-CITY-STREET.MIT.EDU [18.7.21.86]) by grand-central-station.mit.edu (8.9.2/8.9.2) with ESMTP id WAA29916 for ; Sun, 10 Nov 2002 22:37:23 -0500 (EST) Received: from bucky.mit.edu (BUCKY.MIT.EDU [18.247.0.116]) by melbourne-city-street.mit.edu (8.9.2/8.9.2) with ESMTP id WAA25204 for ; Sun, 10 Nov 2002 22:37:22 -0500 (EST) Message-Id: <5.1.0.14.2.20021110220929.00a695c0@po12.mit.edu> X-Sender: zhiheng@po12.mit.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Sun, 10 Nov 2002 22:39:05 -0500 To: chemistry@ccl.net From: Zhi-Heng Loh Subject: running PBS with Gaussian 98 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear all, I have a Linux cluster that runs Gaussian 98, and I am having difficulty getting G98 to run with the PBS queuing system. The G98 software and /home directories of each user are mounted via NFS to all the slave nodes. I suspect that my submit script is faulty. Would greatly appreciate if someone could send me a sample PBS submit script that works with G98. Thanks a bunch. Zhi-Heng Loh Department of Chemistry, Rm 2-209 Massachusetts Institute of Technology Cambridge, MA 02139 zhiheng@mit.edu From chemistry-request@server.ccl.net Sun Nov 10 22:28:47 2002 Received: from yakko.cimav.edu.mx ([148.223.46.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAB3SkQ11886 for ; Sun, 10 Nov 2002 22:28:46 -0500 Received: from prima ([148.223.46.121]) by yakko.cimav.edu.mx (8.11.6/8.11.2) with SMTP id gAB4Kk232692 for ; Sun, 10 Nov 2002 21:20:46 -0700 Message-ID: <00ca01c28932$e5764a20$ae00000a@cimav.edu.mx> From: "Dr. Daniel Glossman-Mitnik" To: Subject: a bit more on molecular computational chemistry Date: Sun, 10 Nov 2002 20:30:15 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00C7_01C288F7.FA3B86E0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_00C7_01C288F7.FA3B86E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: As a follow up to my previous e-mail, I would like to explain the = reasons for my questions: Many times, as for example, when applying for funds, we are asked to codify our field of work according to some listings (i.e. UNESCO, etc). We are not going to find Computational Chemistry as a field. Of course, we will find "Whatever" Chemistry, like Organic Chemistry, Physical Chemistry, Polymer Chemistry and the like. Notwithstanding, I believe that Computational Chemistry is a science=20 per se with its own theories, models and techniques, which are, in = principle,=20 independent of the system under study. Following this reasoning, I = conclude that Computational Chemistry should be a science in its own right. In = that=20 case the system(s) under study should be specified, as for example, in Molecular Computational Chemistry. Is this reasoning correct, or is the "Computational" merely an add-on = like in Computational Materials Science, meaning that the computer is an aid in Materials Science ? Thanks again for your attention. Dr. Daniel Glossman-Minik=20 ********************************************************************** Dr. Daniel Glossman-Mitnik CIMAV - Centro de Investigacion en Materiales Avanzados LAQUICOM - Laboratorio de Quimica Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Tel: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com ********************************************************************** ------=_NextPart_000_00C7_01C288F7.FA3B86E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
Dear netters:
 
As a follow up to my previous = e-mail, I=20 would like to explain the reasons for
my questions:
 
Many times, as for example, = when applying=20 for funds, we are asked to
codify our field of work = according to=20 some listings (i.e. UNESCO, etc).
We are not going to find = Computational=20 Chemistry as a field. Of course,
we will find  "Whatever" = Chemistry,=20 like Organic Chemistry, Physical
Chemistry, Polymer Chemistry = and the=20 like.
 
Notwithstanding, I believe = that=20 Computational Chemistry is a science
per=20 se  = with=20 its own theories, = models and=20 techniques, which are, in principle,
independent of the system = under study. Following this reasoning, I = conclude
that Computational Chemistry = should be a=20 science in its own right. In that
case the system(s) under = study should be=20 specified, as for example,
in Molecular Computational=20 Chemistry.
 
Is this reasoning correct, or = is the=20 "Computational" merely an add-on like
in Computational Materials = Science,=20 meaning that the computer is an aid
in Materials Science = ?
 
Thanks again for your=20 attention.
 
          &nbs= p;            = ;            =  =20 Dr. Daniel Glossman-Minik 
 
****************************************************************= ******
Dr.=20 Daniel Glossman-Mitnik
CIMAV - Centro de Investigacion en Materiales=20 Avanzados
LAQUICOM - Laboratorio de Quimica Computacional
Miguel = de=20 Cervantes 120 - Complejo Industrial Chihuahua
Chihuahua, Chih. = 31109 =20 -  Mexico
Tel: (52) 614 4391151      = FAX: (52)=20 614 4391112
E-mail: daniel.glossman@cimav.edu.mx=
           = ;=20 glossman@hotmail.com
 &n= bsp;         =20 dglossman@yahoo.com
**********= ************************************************************
= ------=_NextPart_000_00C7_01C288F7.FA3B86E0-- From chemistry-request@server.ccl.net Mon Nov 11 01:40:21 2002 Received: from nmr-v.ioc.ac.ru ([193.233.3.213]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAB6eKQ16830 for ; Mon, 11 Nov 2002 01:40:20 -0500 Received: from ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.9.3/8.9.3) with ESMTP id JAA24302; Mon, 11 Nov 2002 09:41:25 GMT Sender: val@nmr-v.ioc.ac.ru Message-ID: <3DCF7B45.140ED1B8@ioc.ac.ru> Date: Mon, 11 Nov 2002 09:41:25 +0000 From: Valentin Ananikov Reply-To: val@ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.13 i686) X-Accept-Language: ru, en MIME-Version: 1.0 To: "Dr. Daniel Glossman-Mitnik" CC: chemistry@ccl.net Subject: Re: CCL:a bit more on molecular computational chemistry References: <00ca01c28932$e5764a20$ae00000a@cimav.edu.mx> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit > Many times, as for example, when applying for funds, we are asked to > codify our field of work according to some listings (i.e. UNESCO, > etc). > We are not going to find Computational Chemistry as a field. Of > course, > we will find "Whatever" Chemistry, like Organic Chemistry, Physical > Chemistry, Polymer Chemistry and the like. > > Notwithstanding, I believe that Computational Chemistry is a science > per se with its own theories, models and techniques, which are, in > principle, > independent of the system under study. Following this reasoning, I > conclude > that Computational Chemistry should be a science in its own right. In > that > case the system(s) under study should be specified, as for example, > in Molecular Computational Chemistry. In principle you are correct and nowadays computational chemistry meets the necessary criteria. However, as far as funds application are concerned computational chemistry projects very often turn to: 1) we have computers, programs, etc. and want to do something in chemistry; 2) we have very good experience and can calculate everything; None of the foundations may be happy with such projects. Whatever Computational Chemistry project must show chemical benefits, while just adding computers to research work does not seem to be very valuable. This could be the reason why Computational Chemistry is not in the listings yet. Note, however, that Theoretical Chemistry is usually in the lists. It looks like one has to draw a clear border between Applied Computational Chemistry (to Organic, Inorganic, Polymer etc. chemistry) and pure Computational Chemistry itself. best regards, Valentin. PS. Classifying Computational Chemistry into Atomic, Molecular, Supramolecular, etc. again means application to specific problems and may not claim to "a science per se". ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow, 119991 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Mon Nov 11 04:43:20 2002 Received: from dedalus.lcc.ufmg.br ([150.164.65.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAB9hJQ22719 for ; Mon, 11 Nov 2002 04:43:20 -0500 Received: from localhost (noronha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with ESMTP id HAA60408; Mon, 11 Nov 2002 07:43:08 -0200 Date: Mon, 11 Nov 2002 07:43:08 -0200 (BDB) From: antonio luiz oliveira de noronha X-X-Sender: noronha@dedalus To: chemistry@ccl.net cc: rkrocha@dedalus.lcc.ufmg.br Subject: CURVES Program Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all Does anyone have some experience with the DNA analysis program called CURVES? Ie been trying to find the meaning of some parameters in the output, but I could not find so far any answer ( specifically, I wish to know the difference between what is called global parameters and the local ones ). Thank you ______________________________________________________________________ | | |Antonio Luiz Oliveira de Noronha - noronha@dedalus.lcc.ufmg.br | |EEPEMM - Eletronic Spectra and Electromagnetic Properties of Molecules| |Theoretical Physical Chemistry | |Chemistry Departament - DQ | |UFMG - Federal University of Minas Gerais - Brazil | |Av. Antonio Carlos, 6627 - Campus Pampulha | |CEP 31270-901 - Belo Horizonte - MG - Brazil | |VOICE +55 31 499 5757 - FAX +55 31 499 5700 | |______________________________________________________________________| From chemistry-request@server.ccl.net Mon Nov 11 05:44:21 2002 Received: from mum.mans.edu.eg ([193.227.50.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gABAiJQ24241 for ; Mon, 11 Nov 2002 05:44:20 -0500 Received: by mum.mans.edu.eg with Internet Mail Service (5.5.2656.59) id ; Mon, 11 Nov 2002 12:00:39 +0200 Message-ID: <4C7A402190F4BD4385075D6B739AB414139502@mum.mans.edu.eg> From: Tarek Mamoun El-Gogary To: "'CHEMISTRY@ccl.net'" Subject: H-bond strength and stacking forces in DNA-base Date: Mon, 11 Nov 2002 12:00:38 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: text/plain Dear CCLer's Could any one, please, point me to references (Articles, webs and books) about H-bond strength and stacking forces in DNA-base. Thanks in advance Tarek From chemistry-request@server.ccl.net Mon Nov 11 05:34:17 2002 Received: from roche.bath.ac.uk ([138.38.32.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gABAYHQ24025 for ; Mon, 11 Nov 2002 05:34:17 -0500 Received: from mmdf by roche.bath.ac.uk with pleasure id 18BBtY-0005o0-02 for chemistry@ccl.net; Mon, 11 Nov 2002 10:34:16 +0000 Received: from amos.bath.ac.uk ([138.38.32.36] ident=mmdf) by roche.bath.ac.uk with smtp id 18BBtX-0007WP-02; Mon, 11 Nov 2002 10:34:15 +0000 Received: from prpcn144 ( prpc-n144.bath.ac.uk [138.38.128.144] ) by bath.ac.uk id aa15204 ; 11 Nov 2002 10:34 +0000 From: James Robinson To: chemistry@ccl.net, "Dr. Daniel Glossman-Mitnik" Subject: RE: a bit more on molecular computational chemistry Date: Mon, 11 Nov 2002 10:36:20 -0000 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_002E_01C2896E.2C989440" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: <00ca01c28932$e5764a20$ae00000a@cimav.edu.mx> Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_002E_01C2896E.2C989440 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit As the field expands and grows, it will have to be taught as a separate degree course. Whoever gets there first will do well. In the field of molecular modelling, one needs to understand QSAR (maths), biochemistry (proteins), more maths for the methods involved, chemistry to understand the results. Computational chemistry textbook look like lessons in hieroglyphics.. physics..maths… then when one has some understanding.. up pops Unix, Fortran, Java, Windows/Dos… The science seems to be about simulating the natural world on a computer, that runs many millions of calculations a second. So to learn all the bits required, it would easily fill a four year degree course… Of course academia pick the bits they like and ignore the bits that oddly, industry likes. There is a difference in the activities of academics and industrial modellers. Some evolution is required and the academics needs to catch up with the industrial modellers, then people need to start doing a undergraduate degrees in the subject and there we are; a recognisable science.. I daresay it is that now. Just look at the whole.. its applications, its foundations and is popularity.. and its successes and failures. Its either a science or I merely create pictures for posters…would that be science imitating art? James -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Dr. Daniel Glossman-Mitnik Sent: 11 November 2002 03:30 To: chemistry@ccl.net Subject: CCL:a bit more on molecular computational chemistry Dear netters: As a follow up to my previous e-mail, I would like to explain the reasons for my questions: Many times, as for example, when applying for funds, we are asked to codify our field of work according to some listings (i.e. UNESCO, etc). We are not going to find Computational Chemistry as a field. Of course, we will find "Whatever" Chemistry, like Organic Chemistry, Physical Chemistry, Polymer Chemistry and the like. Notwithstanding, I believe that Computational Chemistry is a science per se with its own theories, models and techniques, which are, in principle, independent of the system under study. Following this reasoning, I conclude that Computational Chemistry should be a science in its own right. In that case the system(s) under study should be specified, as for example, in Molecular Computational Chemistry. Is this reasoning correct, or is the "Computational" merely an add-on like in Computational Materials Science, meaning that the computer is an aid in Materials Science ? Thanks again for your attention. Dr. Daniel Glossman-Minik ********************************************************************** Dr. Daniel Glossman-Mitnik CIMAV - Centro de Investigacion en Materiales Avanzados LAQUICOM - Laboratorio de Quimica Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Tel: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com ********************************************************************** ------=_NextPart_000_002E_01C2896E.2C989440 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

As the field expands and grows, it will have to be taught as a separate = degree course. Whoever gets there first will do well. =

 

In the field of molecular modelling, one needs to understand QSAR (maths), biochemistry (proteins), more maths for the methods involved, chemistry = to understand the results. Computational chemistry textbook look like = lessons in hieroglyphics.. physics..maths… then when one has some understanding.. up pops = Unix, Fortran, Java, Windows/Dos…

 

The science seems to be about simulating the natural world on a computer, = that runs many millions of calculations a second. So to learn all the bits = required, it would easily fill a four year degree course… Of course academia = pick the bits they like and ignore the bits that oddly, industry likes. There is a = difference in the activities of academics and industrial modellers. Some evolution = is required and the academics needs to catch up with the industrial = modellers, then people need to start doing a undergraduate degrees in the subject = and there we are; a recognisable science.. I daresay it is that now.  Just look at the whole.. its applications, its foundations and is popularity.. and its successes and failures.

Its either a science or I merely create pictures for posters…would = that be science imitating art?

 

James

-----Original Message-----
From: Computational = Chemistry List [mailto:chemistry-request@ccl.net]On = Behalf Of Dr. Daniel Glossman-Mitnik
Sent: 11 November 2002 = 03:30
To: chemistry@ccl.net
Subject: CCL:a bit more = on molecular computational chemistry

 

 <= /p>

Dear netters:<= /p>

 <= /p>

As a follow up to my previous e-mail, I would like to = explain the reasons for

my questions:<= /p>

 <= /p>

Many times, as for example, when applying for funds, we are = asked to<= /p>

codify our field of work according to some listings (i.e. = UNESCO, etc).

We are not going to find Computational Chemistry as a = field. Of course,

we will find  "Whatever" Chemistry, like = Organic Chemistry, Physical

Chemistry, Polymer Chemistry and the = like.<= /p>

 <= /p>

Notwithstanding, I believe that Computational Chemistry is = a science

per se  with its own theories, models and = techniques, which are, in principle, <= /p>

independent of the system under study. Following this = reasoning, I conclude

that Computational Chemistry should be a science in its own = right. In that

case the system(s) under study should be specified, as for example,

in Molecular Computational Chemistry.<= /p>

 <= /p>

Is this reasoning correct, or is the = "Computational" merely an add-on like

in Computational Materials Science, meaning that the = computer is an aid

in Materials Science ?<= /p>

 <= /p>

Thanks again for your attention.<= /p>

 <= /p>

          =             &= nbsp;           &n= bsp;  Dr. Daniel Glossman-Minik <= /p>

 <= /p>

************************************************************= **********
Dr. Daniel Glossman-Mitnik
CIMAV - Centro de Investigacion en Materiales Avanzados
LAQUICOM - Laboratorio de Quimica Computacional
Miguel de Cervantes 120 - Complejo Industrial Chihuahua
Chihuahua, Chih. 31109  -  Mexico
Tel: (52) 614 4391151      FAX: (52) 614 = 4391112
E-mail: daniel.glossman@cimav.edu.mx=
            glossman@hotmail.com
            dglossman@yahoo.com
**********************************************************************<= /p>

------=_NextPart_000_002E_01C2896E.2C989440-- From chemistry-request@server.ccl.net Mon Nov 11 06:38:35 2002 Received: from gate1.ggr.co.uk ([193.128.25.13]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gABBcYQ25573 for ; Mon, 11 Nov 2002 06:38:35 -0500 From: mike.m.hann@gsk.com Received: (uucp@localhost) by gate1.ggr.co.uk; Mon, 11 Nov 2002 11:38:10 GMT Received: from uk-stv-mhub1.ggr.co.uk(147.184.2.7) by gb-stv-fw3.ggr.co.uk via smap (V5.5) id xma016612; Mon, 11 Nov 02 11:37:05 GMT Received: from gbgms02.sb.com ([166.71.155.102]) by mailhub.ggr.co.uk; Mon, 11 Nov 2002 11:37:28 GMT Received: from SBHSNSM1.sb.com (sbhsnsm1 [166.71.155.16]) by sb.com (8.8.6 (PHNE_17135)/8.8.6) with ESMTP id LAA03588 for ; Mon, 11 Nov 2002 11:21:33 GMT Subject: MGMS meeting on "DISTRIBUTED AND GRID COMPUTING FOR MOLECULAR MODELLING", London, Dec 13th. MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.6a January 17, 2001 Message-ID: Date: Mon, 11 Nov 2002 11:27:57 +0000 X-MIMETrack: Serialize by Router on SBHSNSM1/SERVERS/SB_PLC(Release 5.0.6a |January 17, 2001) at 11/11/2002 11:36:46, Serialize complete at 11/11/2002 11:36:47, Serialize by Router on SBHSNSM1/SERVERS/SB_PLC(Release 5.0.6a |January 17, 2001) at 11/11/2002 11:36:47 Content-Type: multipart/alternative; boundary="=_alternative 003EFBB580256C6E_=" This is a multipart message in MIME format. --=_alternative 003EFBB580256C6E_= Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable DISTRIBUTED AND GRID COMPUTING FOR MOLECULAR MODELLING=20 The Molecular Graphics and Modelling Society (MGMS) is organising a one=20 day meeting on Friday 13th December 13th 2002 on the different ways in=20 which commodity chips can be utilised in distributed computing=20 environments. Anyone interested in gaining more compute power should=20 attend this meeting. Full details and registration are available at the MGMS web-site, http://w= ww.mgms.org/dist=5Fcomp=5Fmeeting.htm . And it is free* (unlike similar com= mercial conferences which will set you back =A31100!!).=20 The meeting will take place at the new Brunei Gallery of the School of=20 Oriental and African Studies on Russell Square in London (http://www.soas.a= c.uk/gallery/conference.html).=20 Timetable and speakers are:=20 9-10 Registration and coffee=20 10-10.45 Pat Leach - Inpharmatica =20 10.45-11.20 Keith Davies - Trewern Consultants/Oxford=20 University=20 11.20-11.40 Davin Potts - United Devices=20 11.40-12.00 Maya Natarajan - Entropia=20 12.00-1.30 Lunch and Vendor exhibits=20 1.30-1.50 Stuart Henderson - IBM=20 1.50-2.10 Bob van Steenberg - RLX=20 2.10-2.30 Richard Groves - Blackstone Computing=20 2.30-2.50 Richard Watkins - Platform Computing. 2.50-3.10 Tea=20 3.10-3.45 Phil Butcher - Sanger Centre, Cambridge=20 3.45-4.20 David Boyd - CLRC e-Science Centre =20 There will also be a trade/vendor exhibition during the lunch break.=20 * FREE thanks to our sponsors for this meeting =3D United Devices, Entropia= ,=20 Platform Computing, Inpharmatica, GlaxoSmithKline, RLX, IBM, Blackstone=20 Computing, Accelrys, CCG, CCDC, Tripos, Bladetec -------------------------------------------------------------------------- Dr Mike Hann Computational and Structural Sciences GlaxoSmithKline Medicines Research Centre Gunnels Wood Rd Stevenage Herts SG1 2NY UK tel: (44)-1438-763392 fax: (44)-1438-764918 email: Mike.M.Hann@gsk.com --=_alternative 003EFBB580256C6E_= Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

DISTRIBUTED AND GRID COMPUTING FOR MOLECULAR MODELLING

The Molecular Graphics and Modelling Society (MGMS) is organising a one day= meeting on Friday 13th December 13th 2002 on the different ways in which c= ommodity chips can be utilised in distributed computing environments. Anyon= e interested in gaining more compute power should attend this meeting.

Full details and registration are availab= le at the MGMS web-site,  http://www.mgms.org/dist=5Fcomp=5Fmeeting.ht= m . And it is free* (unlike similar commercial co= nferences which will set you back =A31100!!).

The meeting will take place at the new Brunei Gallery of the School of Orie= ntal and African Studies on Russell Square in London (http://www.soas.ac.uk= /gallery/conference.html). <= br>
Timetable and speakers are: =

9-10          = ;                Registration and c= offee
10-10.45                   &nb= sp;     Pat Leach - Inpharmatica        
10.45-11.20                Keith Da= vies - Trewern Consultants/Oxford University
11.20-11.40                Davin Po= tts - United Devices
11.40-12.00                Maya Nat= arajan - Entropia
12.00-1.30                   &= nbsp;    Lunch and Vendor exhibits
1.30-1.50                   &n= bsp;   Stuart Henderson -  IBM
1.50-2.10                   &n= bsp;    Bob van Steenberg - RLX
2.10-2.30                   &n= bsp;    Richard Groves - Blackstone Computing
2.30-2.50                   &n= bsp;    Richard Watkins - Platform Computing.
2.50-3.10                   &n= bsp;   Tea
3.10-3.45                   &n= bsp;    Phil Butcher - Sanger Centre, Cambridge
3.45-4.20                   &n= bsp;    David Boyd - CLRC e-Science Centre  

There will also be a trade/vendor exhibition during the lunch break.=

* FREE thanks to our sponsors for this meeting =3D United Devices, Entropia= , Platform Computing, Inpharmatica, GlaxoSmithKline, RLX, IBM, Blackstone C= omputing, Accelrys, CCG, CCDC, Tripos, Bladetec
--------------------------------------------------------------------------<= br> Dr Mike Hann
Computational and Structural Sciences
GlaxoSmithKline Medicines Research Centre
Gunnels Wood Rd
Stevenage
Herts
SG1 2NY
UK

tel: (44)-1438-763392  fax: (44)-1438-764918
email: Mike.M.Hann@gsk.com
 --=_alternative 003EFBB580256C6E_=-- From chemistry-request@server.ccl.net Mon Nov 11 11:29:24 2002 Received: from kula.geosc.psu.edu ([128.118.174.177]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gABGTOQ02438 for ; Mon, 11 Nov 2002 11:29:24 -0500 Received: from doris.psu.edu (doris.geosc.psu.edu [128.118.174.247]) by kula.geosc.psu.edu (8.9.3/8.9.3) with ESMTP id LAA24312 for ; Mon, 11 Nov 2002 11:29:20 -0500 (EST) Message-Id: <5.1.0.14.2.20021111102645.00bc98d8@email.geosc.psu.edu> X-Sender: kubicki@email.geosc.psu.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 11 Nov 2002 10:27:22 -0600 To: chemistry@ccl.net From: James Kubicki Subject: What is Omega in G98? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hello, all! I am trying to optimize octahydroxy-silsesquioxane in water using Gaussian 98. However, the job stops and gives this error message. Could you help me with this, what is omega? My input was hf/3-21g** scf=tight SCRF=(IEFPCM,Solvent=Water) opt Error was PEDRA: too many spheres; increase Omega Error termination via Lnk1e in /usr/apps//g98/l502.exe. Thank you SO MUCH, in advance. James Kubicki Dept. of Geosciences The Pennsylvania State University University Park, PA 16802 814-865-3951 814-863-8724 From chemistry-request@server.ccl.net Mon Nov 11 10:18:00 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gABFI0Q32212 for ; Mon, 11 Nov 2002 10:18:00 -0500 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id KAA11755; Mon, 11 Nov 2002 10:17:59 -0500 (EST) Message-ID: <3DCFCA24.CC8B2632@cornell.edu> Date: Mon, 11 Nov 2002 09:17:56 -0600 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:a bit more on molecular computational chemistry References: Content-Type: multipart/alternative; boundary="------------9E05E1985BBA7E9E90ECBC63" --------------9E05E1985BBA7E9E90ECBC63 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi all Not to be snotty, but why can't it all be lumped under "physical chemistry"? I happen to consider myself a physical chemist, with my specialty being doing computations. I think that there are enough sub-disciplines in chemist such that we don't need to unnecessarily create more. As James said, one needs to understand the math and the chemistry, which is what physical chemistry is all about, no? Richard James Robinson wrote: > As the field expands and grows, it will have to be taught as a > separate degree course. Whoever gets there first will do well. > > In the field of molecular modelling, one needs to understand QSAR > (maths), biochemistry (proteins), more maths for the methods involved, > chemistry to understand the results. Computational chemistry textbook > look like lessons in hieroglyphics.. physics..maths… then when one has > some understanding.. up pops Unix, Fortran, Java, Windows/Dos… > > The science seems to be about simulating the natural world on a > computer, that runs many millions of calculations a second. So to > learn all the bits required, it would easily fill a four year degree > course… Of course academia pick the bits they like and ignore the bits > that oddly, industry likes. There is a difference in the activities of > academics and industrial modellers. Some evolution is required and the > academics needs to catch up with the industrial modellers, then people > need to start doing a undergraduate degrees in the subject and there > we are; a recognisable science.. I daresay it is that now.Just look at > the whole.. its applications, its foundations and is popularity.. and > its successes and failures. > > Its either a science or I merely create pictures for posters…would > that be science imitating art? > > James > > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request@ccl.net]On Behalf Of Dr. Daniel > Glossman-Mitnik > Sent: 11 November 2002 03:30 > To: chemistry@ccl.net > Subject: CCL:a bit more on molecular computational chemistry > > Dear netters: > > As a follow up to my previous e-mail, I would like to explain the > reasons for > > my questions: > > Many times, as for example, when applying for funds, we are asked to > > codify our field of work according to some listings (i.e. UNESCO, > etc). > > We are not going to find Computational Chemistry as a field. Of > course, > > we will find "Whatever" Chemistry, like Organic Chemistry, Physical > > Chemistry, Polymer Chemistry and the like. > > Notwithstanding, I believe that Computational Chemistry is a science > > per sewith its own theories, models and techniques, which are, in > principle, > > independent of the system under study. Following this reasoning, I > conclude > > that Computational Chemistry should be a science in its own right. In > that > > case the system(s) under study should be specified, as for example, > > in Molecular Computational Chemistry. > > Is this reasoning correct, or is the "Computational" merely an add-on > like > > in Computational Materials Science, meaning that the computer is an > aid > > in Materials Science ? > > Thanks again for your attention. > > Dr. Daniel Glossman-Minik > > ********************************************************************** > > Dr. Daniel Glossman-Mitnik > CIMAV - Centro de Investigacion en Materiales Avanzados > LAQUICOM - Laboratorio de Quimica Computacional > Miguel de Cervantes 120 - Complejo Industrial Chihuahua > Chihuahua, Chih. 31109 - Mexico > Tel: (52) 614 4391151 FAX: (52) 614 4391112 > E-mail: daniel.glossman@cimav.edu.mx > glossman@hotmail.com > dglossman@yahoo.com > ********************************************************************** > -- Richard L. Wood, Ph. D. Physical/Computational Chemist --------------9E05E1985BBA7E9E90ECBC63 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi all

Not to be snotty, but why can't it all be lumped under "physical chemistry"?
I happen to consider myself a physical chemist, with my specialty being
doing computations.

I think that there are enough sub-disciplines in chemist such that we don't need to unnecessarily create more.

As James said, one needs to understand the math and the chemistry, which is what physical chemistry is all about, no?

Richard

James Robinson wrote:

As the field expands and grows, it will have to be taught as a separate degree course. Whoever gets there first will do well. 

In the field of molecular modelling, one needs to understand QSAR (maths), biochemistry (proteins), more maths for the methods involved, chemistry to understand the results. Computational chemistry textbook look like lessons in hieroglyphics.. physics..maths… then when one has some understanding.. up pops Unix, Fortran, Java, Windows/Dos… 

The science seems to be about simulating the natural world on a computer, that runs many millions of calculations a second. So to learn all the bits required, it would easily fill a four year degree course… Of course academia pick the bits they like and ignore the bits that oddly, industry likes. There is a difference in the activities of academics and industrial modellers. Some evolution is required and the academics needs to catch up with the industrial modellers, then people need to start doing a undergraduate degrees in the subject and there we are; a recognisable science.. I daresay it is that now.Just look at the whole.. its applications, its foundations and is popularity.. and its successes and failures.

Its either a science or I merely create pictures for posters…would that be science imitating art?

James

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Dr. Daniel Glossman-Mitnik
Sent: 11 November 2002 03:30
To: chemistry@ccl.net
Subject: CCL:a bit more on molecular computational chemistry

Dear netters:

As a follow up to my previous e-mail, I would like to explain the reasons for

my questions:

Many times, as for example, when applying for funds, we are asked to

codify our field of work according to some listings (i.e. UNESCO, etc).

We are not going to find Computational Chemistry as a field. Of course,

we will find  "Whatever" Chemistry, like Organic Chemistry, Physical

Chemistry, Polymer Chemistry and the like.

Notwithstanding, I believe that Computational Chemistry is a science 

per sewith its own theories, models and techniques, which are, in principle, 

independent of the system under study. Following this reasoning, I conclude

that Computational Chemistry should be a science in its own right. In that 

case the system(s) under study should be specified, as for example,

in Molecular Computational Chemistry.

Is this reasoning correct, or is the "Computational" merely an add-on like

in Computational Materials Science, meaning that the computer is an aid

in Materials Science ?

Thanks again for your attention.

                                     Dr. Daniel Glossman-Minik

**********************************************************************
Dr. Daniel Glossman-Mitnik
CIMAV - Centro de Investigacion en Materiales Avanzados
LAQUICOM - Laboratorio de Quimica Computacional
Miguel de Cervantes 120 - Complejo Industrial Chihuahua
Chihuahua, Chih. 31109  -  Mexico
Tel: (52) 614 4391151      FAX: (52) 614 4391112
E-mail: daniel.glossman@cimav.edu.mx
            glossman@hotmail.com
            dglossman@yahoo.com
**********************************************************************

--
Richard L. Wood, Ph. D.
Physical/Computational Chemist
 
  --------------9E05E1985BBA7E9E90ECBC63-- From chemistry-request@server.ccl.net Mon Nov 11 11:38:48 2002 Received: from pc16154.pharmazie.uni-marburg.de ([137.248.161.154]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gABGclQ02797 for ; Mon, 11 Nov 2002 11:38:47 -0500 Received: from localhost (localhost.pharmazie.uni-marburg.de [127.0.0.1]) by pc16154.pharmazie.uni-marburg.de (Postfix) with ESMTP id D6EE62F993; Mon, 11 Nov 2002 17:38:42 +0100 (CET) Received: from mailer.uni-marburg.de (pc16113.Pharmazie.Uni-Marburg.DE [137.248.161.113]) by pc16154.pharmazie.uni-marburg.de (Postfix) with ESMTP id D2E1C2F992; Mon, 11 Nov 2002 17:38:39 +0100 (CET) Message-ID: <3DCFDD0E.B7B3CFFA@mailer.uni-marburg.de> Date: Mon, 11 Nov 2002 17:38:38 +0100 From: Dirk Dettmering Organization: Institut f. Pharmazeutische Chemie - Philipps =?iso-8859-1?Q?Universit=E4t?= Marburg X-Mailer: Mozilla 4.8 [en] (Windows NT 5.0; U) X-Accept-Language: de,en MIME-Version: 1.0 To: Miroslava Cuperlovic-Culf , CCL ML Subject: Re: CCL:SwissProt Pdb viewer on Linux RedHat References: <3DC7EA86.30301@health.nb.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS 0.3.12pre8 with H+BEDV AntiVir/Linux Version 6.16.0.15 on pc16154.pharmazie.uni-marburg.de Hy, Miroslava Cuperlovic-Culf wrote: > I recently became a proud owner of Linux RedHat PC but now I am having > few problems. I am trying to run DeepView (SwissProt Pdb viewer). I > installed it without any errors but now when I try to run it I get a > message: > > "No response from any other spdbv process. > Becoming master." > > and screen comes up without any text. > Any idea what can be wrong here. > Thanks a lot for your help sorry to bother eveybody with this. > Mira You haven't mentioned your version of RH. So I tell you what I have done to get DeepView runnung on RH 7.2 and 7.3: I had the same problem last week and could chase the problem down to the absence of the package openmotif. For RH 7.3 I could easily install openmotif21 from the CDs. But there are no openmotif packages for RH 7.2 and when I tried to install the package from RH 7.3 I got a conflict with the installed packages lesstif and lesstif-devel which are needed by nedit, my favourite editor. I finally got everything running by installing openmotif-2.2.2-5 and openmotif-devel-2.2.2-5 and rebuilding from the SRPMs and installing lesstif-0.93.18-2, openmotif21-2.1.30-1 and nedit-5.2-2 from RH 7.3. HTH and Bye Dirk -- ================D=i=r=k===D=e=t=t=m=e=r=i=n=g=================== http://pc16154.pharmazie.uni-marburg.de/dettmering/index.html Tel.: +49 6421 28 21332 Fax: +49 6421 28 25828 Philipps University Marburg - Germany - Department of Pharmacy Enjoy drugs in 3D and read some basic facts gathered by students Visit our drug database WisDa: http://www.wisda.de From chemistry-request@server.ccl.net Mon Nov 11 10:44:37 2002 Received: from mail.rpi.edu ([128.113.22.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gABFibQ00776 for ; Mon, 11 Nov 2002 10:44:37 -0500 Received: from rpi.edu (omniocular-22.dynamic.rpi.edu [128.113.135.31]) by mail.rpi.edu (8.12.1/8.12.1) with ESMTP id gABFiaEr251156 for ; Mon, 11 Nov 2002 10:44:36 -0500 Message-ID: <3DCFD10C.DF0E78AA@rpi.edu> Date: Mon, 11 Nov 2002 10:47:24 -0500 From: "Curt M. Breneman" X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: ACS Division of Computers in Chemistry CCG Award Winners for 2003. Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Scanned-By: MIMEDefang 2.3 (www dot roaringpenguin dot com slash mimedefang) The ACS Division of Computers in Chemistry and the Chemical Computing Group would like to announce the latest winners of the CCG Excellence Awards for the Spring 2003 ACS National Meeting in New Orleans. Congratulations to the winners! IVANOV, Ivaylo N. (Mr.) Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania “Relative pKs from First Principles Molecular Dynamics: The Case of Histidine Deprotonation” Michael L. Klein, Director and Hepburn Professor of Physical Science, University of Pennsylvania KORMOS, Bethany Department of Chemistry, University of Minnesota “Utilizing Density Functional Theory to Study Nucleophilic Substitution Reactions: Optimization of an Adiabatic Connection Method and its Application” Christopher J. Cramer, Department of Chemistry, University of Minnesota AIKENS, Christine Department of Chemistry, Iowa State University “Molecular Electronic Structure and Magnetic Properties of Y2Ti(?-X)2TiY2(X,Y=H,F,Cl,Br) Isomers” Mark S. Gordon, Department of Chemistry, Iowa State University DONG, Haitao (Mr.) Department of Chemistry and Biochemistry, The University of Oklahoma “Quasiharmonic Vibrations of Water, Water Clusters, and Liquid Water > from Principal Component Analysis of Quantum or QM/MM Trajectories” Ralph A. Wheeler, Department of Chemistry and Biochemistry, The University of Oklahoma CUI, Guanglei (Mr.) Department of Chemistry, SUNY at Stony Brook “The Complicated Folding of a Simple Peptide Studied by Multiple Folding Simulations and Replica Exchange Approach” Carlos Simmerling, Department of Chemistry, SUNY at Stony Brook KATT, William B. Department of Chemistry, Rensselaer Polytechnic Institute “Optimization of Molecular Properties Through Structural Mutation and Virtual Screening with QSAR Models” Curt M. Breneman, Department of Chemistry, Rensselaer Polytechnic Institute ZHOU, Zhigang (Mr.) Department of Chemistry, Duquesne University “Resistant Effect Exploring of HIV-1 RT Mutation by Molecular Dynamics” Jeffrey D. Madura, Department of Chemistry and Biochemistry, Duquesne University STROCKBINE, Bentley Department of Pharmacological Sciences, Stony Brook University “Advances in Structure Prediction Techniques” Carlos Simmerling, Department of Chemistry, SUNY at Stony Brook WU, Min (Ms.) Department of Chemistry, New York University “Structural Studies of an Environmental Carcinogen within a Y Family Bypass DNA Polymerase” Suse Broyde, Department of Biology, New York University BUCHETE, Nicolae-Viorel Department of Chemistry, Boston University “The Effect of Relative Side Chain Orientations on the Ability of Statistical Potentials to Identify Native-Like Structures of Proteins” John E. Straub, Boston University From chemistry-request@server.ccl.net Mon Nov 11 11:58:16 2002 Received: from dknt2.acadia-pharm.com ([80.77.66.146]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gABGwFQ03670 for ; Mon, 11 Nov 2002 11:58:15 -0500 Received: by DKNT2 with Internet Mail Service (5.5.2653.19) id ; Mon, 11 Nov 2002 17:52:42 +0100 Message-ID: <47583DB3ED46D61193E6000102A191932E478A@DKNT2> From: Vladimir Sherbukhin To: "'chemistry@ccl.net'" Subject: low cost 3D graphics program wanted Date: Mon, 11 Nov 2002 17:52:42 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, I need a low cost (ideally free) front-end graphics program which can manipulate with 3D structures (both small molecules and proteins) and save them in the MacroModel format. Must be able to run under Linux or Windows on a PC. Please let me know if there is any software matching these requirements. Many thanks in advance! Yours sincerely, Vlad Vladimir Sherbukhin, PhD tel. 45 4329 3000 (switchboard) ACADIA Pharmaceuticals A/S tel. 45 4329 3017 (direct) Fabriksparken 58 fax 45 4329 3030 DK-2600 Glostrup e-mail VSherbukhin@acadia-pharm.com Denmark http://www.acadia-pharm.com ICQ 171831717 From chemistry-request@server.ccl.net Mon Nov 11 12:26:05 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gABHQ5Q04304 for ; Mon, 11 Nov 2002 12:26:05 -0500 Received: from tempest.sd.lionbioscience.com (tempest.sd.lionbioscience.com [10.8.0.8]) by so.sd.lionbioscience.com (8.11.3/8.11.3) with ESMTP id gABHPPg19313; Mon, 11 Nov 2002 09:25:25 -0800 (PST) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Mon, 11 Nov 2002 09:25:24 -0800 Message-ID: From: Stephen Bowlus To: "'James Robinson'" , chemistry@ccl.net, "Dr. Daniel Glossman-Mitnik" Subject: RE: a bit more on molecular computational chemistry Date: Mon, 11 Nov 2002 09:25:17 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C289A7.4DA296C0" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C289A7.4DA296C0 Content-Type: text/plain; charset="iso-8859-1" Some evolution ... To a degree, the academics face different problems. As an industrial modeller (not a "computational chemist"), I have the constant challenge of - - "Real-time modelling." I must be able to address a problem, adopt a methodology, develop a trial model and make a useable prediction faster than the chemists with whom I work can come up with "good ideas." Otherwise a model is useless (or at least unused). These time constraints limit suitable techniques encountered in the academic-biased literature - computations of biological systems at high levels of theory, for example, are largely not practically useful to me. - Talking to chemists. As a synthesis chemist-turned-modeller, I have some appreciation of what goes on in the laboratory, the biases and preferences of chemists, and so on. To a degree, I am plugged in to the experimental program. "How to talk to the lab chemists" seems to be one of the weaker points in the academic training of new computational chemists. As the field becomes increasingly specialized ("a recognizable science"), I wonder how this connection, important to the industrial side, will be maintained? sb The science seems to be about simulating the natural world on a computer, that runs many millions of calculations a second. So to learn all the bits required, it would easily fill a four year degree course... Of course academia pick the bits they like and ignore the bits that oddly, industry likes. There is a difference in the activities of academics and industrial modellers. Some evolution is required and the academics needs to catch up with the industrial modellers, then people need to start doing a undergraduate degrees in the subject and there we are; a recognisable science.. I daresay it is that now. Just look at the whole.. its applications, its foundations and is popularity.. and its successes and failures. ------_=_NextPart_001_01C289A7.4DA296C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Some=20 evolution ... To a degree, the academics face different problems.  = As an=20 industrial modeller (not a "computational chemist"), I have the = constant=20 challenge of - 
 
-=20 "Real-time modelling." I must be able to address a problem, adopt a = methodology,=20 develop a trial model and make a useable prediction faster than the = chemists=20 with whom I work can come up with "good ideas."  Otherwise a model = is=20 useless (or at least unused).  These time constraints limit = suitable=20 techniques encountered in the academic-biased literature - = computations of=20 biological systems at high levels of theory, for example, are largely = not=20 practically useful to me.
- Talking to chemists.  As a synthesis=20 chemist-turned-modeller, I have some appreciation of what goes on = in the=20 laboratory, the biases and preferences of chemists, and so on.  To = a=20 degree, I am plugged in to the experimental program.  "How to talk to the lab=20 chemists" seems to be one of the weaker points in the=20 academic training of new computational chemists.  As the = field becomes=20 increasingly specialized ("a recognizable science"), I wonder how this=20 connection, important to the industrial side, will be=20 maintained?
 
sb

The science = seems to be=20 about simulating the natural world on a computer, that runs many = millions of=20 calculations a second. So to learn all the bits required, it would = easily fill a=20 four year degree course… Of course academia pick the bits they = like and ignore=20 the bits that oddly, industry likes. There is a difference in the = activities of=20 academics and industrial modellers. Some evolution is required and the = academics=20 needs to catch up with the industrial modellers, then people need to = start doing=20 a undergraduate degrees in the subject and there we are; a recognisable = science.. I daresay it is that now. =20 Just look at the whole.. its applications, its foundations and = is=20 popularity.. and its successes and failures. 
------_=_NextPart_001_01C289A7.4DA296C0-- From chemistry-request@server.ccl.net Mon Nov 11 22:50:54 2002 Received: from mail.rpi.edu ([128.113.22.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAC3orQ20672 for ; Mon, 11 Nov 2002 22:50:54 -0500 Received: from rpi.edu (vpn-955.nss.rpi.edu [128.113.211.205]) by mail.rpi.edu (8.12.1/8.12.1) with ESMTP id gAC3olEr095530; Mon, 11 Nov 2002 22:50:47 -0500 Message-ID: <3DD07404.3D1829B@rpi.edu> Date: Mon, 11 Nov 2002 22:22:44 -0500 From: "Curt M. Breneman" X-Mailer: Mozilla 4.8 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, qsar_society@accelrys.com Subject: Deadline Approaching - ACS/COMP Symposium on Machine Learning in Computational Chemistry Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.3 (www dot roaringpenguin dot com slash mimedefang) Final Announcement - ** Machine Learning in Computational Chemistry ** A symposium at the Spring ACS National Meeting in New Orleans You are invited to participate in a program designed to showcase a broad range of applications of machine learning methods in chemistry. Presentations in this symposium include the use of classification methods, knowlege-based methods, diversity, regression and statistical learning methods such as neural networks (self-organizing maps), support vector machines, kernel PLS (and other kernel methods) to address a variety of chemically-relevant problems. If you are considering an oral presentation in these or other related areas, please join us. We look forward to seeing you in New Orleans in the Spring. Don't forget - the COMP OASys deadline is approaching on November 15th - get your abstracts in! Curt Breneman RPI Chemistry COMP Treasurer From chemistry-request@server.ccl.net Mon Nov 11 16:41:40 2002 Received: from c001.snv.cp.net ([209.228.32.114]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gABLfeQ10770 for ; Mon, 11 Nov 2002 16:41:40 -0500 Received: (cpmta 28555 invoked from network); 11 Nov 2002 13:41:40 -0800 Received: from 209.228.32.124 (HELO mail.roberttopper.com.criticalpath.net) by smtp.register-admin.com (209.228.32.114) with SMTP; 11 Nov 2002 13:41:40 -0800 X-Sent: 11 Nov 2002 21:41:40 GMT Received: from [199.98.21.51] by mail.roberttopper.com with HTTP; Mon, 11 Nov 2002 13:41:39 -0800 (PST) Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 7bit MIME-Version: 1.0 To: CHEMISTRY@ccl.net Cc: topper@cooper.edu From: topper@cooper.edu Subject: ECCC9 Call for Papers and Proceedings Announcement X-Sent-From: roberttopper@roberttopper.com Date: Mon, 11 Nov 2002 13:41:39 -0800 (PST) X-Mailer: Web Mail 5.1.0-7_sol28 Message-Id: <20021111134140.12816.h010.c001.wm@mail.roberttopper.com.criticalpath.net> *Please forgive us if you receive multiple copies of this message. It is beng sent to several lists to ensure the greatest possible dissemination.* ******************* ECCC9 - 9th Electronic Computational Chemistry Conference Dear colleagues, We are pleased to announce that registration for the 9th Electronic Computational Chemistry Conference is now open. ECCC9 will be held March 1 - March 31, 2003, entirely on the Internet, at http://eccc9.cooper.edu. Abstracts are now being accepted for online submission at the conference website. We are also pleased to inform you that the proceedings will be published in a special issue of the online International Journal of Molecular Sciences (see below). As in previous years, ECCC9 is a multidisciplinary, international conference and covers all aspects of computational and theoretical chemistry and materials science, as well as computational molecular biology, computational and theoretical molecular and atomic physics, visualization, cheminformatics, the history of computational chemistry and all related fields. Participants will be able to view the presentations and discuss them entirely through a web browser. As with the previous eight ECCCs, ECCC9 has NO registration fee and is a completely virtual, online conference. The ECCC was originally developed by Steven Bachrach, who also organized the first five meetings. Abstracts for all contributions to ECCC9 will be reviewed by the Scientific Organizing Committee (SOC) to insure novelty, scientific value, and appopriateness for inclusion in the conference. The members of the ECCC9 SOC are: Robert Topper, Cooper Union (Chair) David Chatfield, Florida International University Thomas Cundari, University of North Texas Olga Dmitrenko, University of Delaware Walter Fabian, Karl-Franzens Universitaet Graz Francis Muguet, ENS Techniques AvanceeUs All presentations must be made in HTML format and ideally will take full advantage of the interactive nature of the World-Wide Web to present their findings and conclusions. Authors may choose to either serve their contributions from their own local web site, or may request us to serve them from our own server. Uploaded contributions will be removed from our server at the end of ECCC9. As in ECCC8, a single weeklong "interactive" session will be part of the conference. This session will be held via asynchronous posting of questions to the conference site, which authors can choose to receive either at the site, at their personal email account, or both. All authors must commit to having at least one coauthor available to answer questions (i.e. by checking the discussion board at least once daily) during the "interactive" session to provide timely responses (within approximately 24 hours) to any questions that conferees may have about their online presentation. Important dates for ECCC9 are: November 11, 2002 - Registration opens; abstracts of papers accepted December 13, 2002 - Abstracts of presentations due February 24, 2003 - Final presentations due online March 1, 2003 - Conference begins March 17, 2003 - Interactive Session begins March 24, 2003 - Interactive Session ends April 1, 2003 - ECCC9 ends May 1, 2003 - Submissions to ECCC9 - IJMS Proceedings due As mentioned above, the Proceedings of the 9th Electronic Computational Chemistry Conference will be published in a special issue of the International Journal of Molecular Sciences (http://www.mdpi.net/ijms/). IJMS is a peer-refereed scientific journal, published online monthly (since September 2001) and CD-ROM yearly. It is indexed and abstracted by several leading indexing and abstracting services, including Chemical Abstracts and CAPLUS, and is physically distributed to various libraries around the world. IJMS articles are freely available to all on the Internet. Authors can distribute an unlimited number of e-reprints via e-mail free of charge. After peer review is completed, accepted papers will be published immediately. Although the IJMS is supported solely by the payment of publication charges by authors, all charges will be waived for all articles published in the ECCC9 Proceedings issue. Waiver support from the "Open Society Institute" ( OSI - SOROS foundation) is acknowledged for authors coming > from one the 67 countries where OSI operates (a list may be found at http://www.mdpi.net/SOROS/osi-countries.html ). The MDPI foundation is gratefully acknowledged for extending the waiver to all authors. We are grateful to the IJMS for their support of the completely free, completely online ECCC. As mentioned above, all ECCC9 presentations must be in HTML format, with their layout and presentation at the discretion of the authors. We would kindly ask authors who plan to submit their work for review and publication in the Proceedings to also prepare their manuscripts in the "Word" format (.DOC) with the help of a template that will be made available. DOC format documents can be prepared using a variety of commercial products (such as Word) and freeware products (such as OpenOffice), following the guidelines of the IJMS template. After peer review and acceptance, the papers will be published online by the IJMS editorial office using the PDF format. In addition to the DOC format paper, authors will also have the option to submit a supplement in HTML format, which may allow a richer graphics content (animation, interactive graphics, java applet, javascript, VRML, etc .. ) and result in a better overall transcription of their original ECCC9 presentation. For HTML supplement man uscripts to be accepted in the online ECCC9 Proceedings issue of the IJMS, they should follow the guidelines of the HTML template which IJMS will make available on its web site in the near future. We look forward to your participation in ECCC9 and the IJMS conference proceedings. Robert Q. Topper, Robert Hopkins and Christopher Lent School of Engineering The Cooper Union for the Advancement of Science and Art 51 Astor Place New York, NY 10003 topper@cooper.edu http://eccc9.cooper.edu ***************************************************************************** 9th ELECTRONIC COMPUTATIONAL CHEMISTRY CONFERENCE MARCH 2003 http://eccc9.cooper.edu ***************************************************************************** Robert Q. Topper, Ph.D. Associate Professor of Chemistry School of Engineering The Cooper Union for the Advancement of Science and Art 51 Astor Place New York, NY 10003 phone: (212) 353-4378 fax: (212) 353-4341 ***************************************************************************** http://www.cooper.edu/engineering/chemechem/ ***************************************************************************** From chemistry-request@server.ccl.net Mon Nov 11 14:06:49 2002 Received: from fulcrum.physbio.mssm.edu ([146.203.4.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gABJ6nQ07163 for ; Mon, 11 Nov 2002 14:06:49 -0500 Received: from mezei (helo=localhost) by fulcrum.physbio.mssm.edu with local-esmtp (Exim 3.11 #1) id 18BJsz-006W8T-00; Mon, 11 Nov 2002 14:06:13 -0500 Date: Mon, 11 Nov 2002 14:06:13 -0500 From: Mihaly Mezei X-X-Sender: mezei@fulcrum.physbio.mssm.edu To: Stephen Bowlus cc: "'James Robinson'" , , "Dr. Daniel Glossman-Mitnik" Subject: Re: CCL:whom to teach what In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: Mihaly Mezei > of chemists, and so on. To a degree, I am plugged in to the experimental > program. "How to talk to the lab chemists" seems to be one of the weaker > points in the academic training of new computational chemists. As the field > becomes increasingly specialized ("a recognizable science"), I wonder how > this connection, important to the industrial side, will be maintained? Hmmm. What about teaching the lab chemists to talk to the computational chemists? Mihaly Mezei, Dept. of Physiology & Biophysics, Mount Sinai School of Medicine Voice: (212) 241-2186 Fax: (212) 860-3369| WWW (MSSM home): http:// adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei