From joubert@ext.jussieu.fr Tue May 6 04:41:11 1997 Received: from shiva.jussieu.fr for joubert@ext.jussieu.fr by www.ccl.net (8.8.3/950822.1) id EAA01378; Tue, 6 May 1997 04:22:40 -0400 (EDT) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.8.5/jtpda-5.2) with ESMTP id KAA21325 for ; Tue, 6 May 1997 10:22:16 +0200 (METDST) Received: from [134.157.11.17] by idf.ext.jussieu.fr (8.8.5/jtpda-4.0) with SMTP; Tue, 6 May 1997 10:22:14 +0200 (METDST) X-Sender: joubert@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 6 May 1997 10:24:22 +0200 To: chemistry@www.ccl.net From: joubert@ext.jussieu.fr (Laurent Joubert) Subject: Looking for good "all-electrons" basis sets (Ca and Zr) Dear Netters, I'm actually looking for "all-electrons" basis sets (better than STO-3G !) for the atoms Ca and Zr. Thanks in advance. Laurent Joubert ******************************************************** * Laurent JOUBERT (PhD student) * * * * Ecole Nationale Superieure de Chimie de Paris * * Laboratoire d'Electrochimie et de Chimie Analytique * * 11, rue Pierre et Marie Curie * * 75231 PARIS CEDEX 05- FRANCE * * * * Tel : (33) 01-44-27-66-94 * * Fax : (33) 01-44-27-67-50 * * * * E-Mail : joubert@ext.jussieu.fr * * http://www.enscp.jussieu.fr * ******************************************************** From roberson@kemibm.kemi.aau.dk Tue May 6 08:41:14 1997 Received: from kemibm.kemi.aau.dk for roberson@kemibm.kemi.aau.dk by www.ccl.net (8.8.3/950822.1) id IAA07146; Tue, 6 May 1997 08:15:52 -0400 (EDT) From: Received: by kemibm.kemi.aau.dk (AIX 3.2/UCB 5.64/4.03) id AA16591; Tue, 6 May 1997 13:44:51 +0200 Date: Tue, 6 May 1997 13:44:51 +0200 Message-Id: <9705061144.AA16591@kemibm.kemi.aau.dk> To: CHEMISTRY@www.ccl.net Subject: Small MD programs? Hi, A prof here is interested in having his students get some experience with MD simulations on PCs. He wants to know if there are any free or cheap programs that will handle 125 to 1000 water molecules. Any advice? Mark From chrmiri@techunix.technion.ac.il Tue May 6 09:03:33 1997 Received: from techunix.technion.ac.il for chrmiri@techunix.technion.ac.il by www.ccl.net (8.8.3/950822.1) id HAA05917; Tue, 6 May 1997 07:49:11 -0400 (EDT) Received: from localhost (chrmiri@localhost) by techunix.technion.ac.il (8.8.5/8.6.10) with SMTP id OAA27294 for ; Tue, 6 May 1997 14:48:56 +0300 (IDT) Date: Tue, 6 May 1997 14:48:56 +0300 (IDT) From: Miri Karni To: chemistry@www.ccl.net Subject: Archiving and browsing computational results from G94 and other computational software Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Is there a good software available for archiving and browsing computational results received from G94 and other computational software? Miri ****************************************************************************** Dr. Miri Karni Department of Chemistry Technion - Israel Institute of Technology Haifa 32000 Israel e-mail: chrmiri@tx.technion.ac.il FAX:972-4-8233735 PHONE:972-4-8292699 ****************************************************************************** From redime@azur.incm.u-nancy.fr Tue May 6 09:41:14 1997 Received: from brown.incm.u-nancy.fr for redime@azur.incm.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id JAA08794; Tue, 6 May 1997 09:38:30 -0400 (EDT) Received: from azur.incm.u-nancy.fr by brown.incm.u-nancy.fr via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for <@brown.incm.u-nancy.fr:chemistry@www.ccl.net> id PAA09054; Tue, 6 May 1997 15:38:07 +0100 Received: (from redime@localhost) by azur.incm.u-nancy.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) id PAA24145; Tue, 6 May 1997 15:32:01 +0100 From: "Redime HADJI" Message-Id: <9705061532.ZM24143@azur.incm.u-nancy.fr> Date: Tue, 6 May 1997 15:32:01 -0400 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: CCL: Micelles Cc: redime@azur.incm.u-nancy.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, I am looking for any information (references, reviews, methodology, etc.) about molecular dynamics simulations of MICELLE(S), conformational behaviour of peptides in micelles (in paticular in SDS micelles). Any hints would be grately appreciated. I will summarize your answers. Thank you very much in advance. Redime HADJI-PFEFFER -- ooooooooooooooooooooooooooooooooooooooooooooooooooooo Redime HADJI-PFEFFER redime@incm.u-nancy.fr Lab. Chimie theorique Univer. NancyI, France tel:+33-(0)3.83.91.20.00 poste : 32.70 fax:+33-(0)3.83.91.25.30 La vie est belle et c'est tant mieux J.-J. Vanier oooooooooooooooooooooooooooooooooooooooooooooooooooooo From 94970459@tolka.dcu.ie Tue May 6 09:48:14 1997 Received: from tolka.dcu.ie for 94970459@tolka.dcu.ie by www.ccl.net (8.8.3/950822.1) id JAA08654; Tue, 6 May 1997 09:34:29 -0400 (EDT) Received: by tolka.dcu.ie; (5.65v3.2/1.1.8.2/14Feb96-0535PM) id AA16470; Tue, 6 May 1997 14:33:07 +0100 Date: Tue, 6 May 1997 14:33:07 +0100 (BST) From: patrick kane <94970459@tolka.dcu.ie> To: CCL Every Subject: Advice on New Hardware and Software Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE Hi, My research group are about to purchase a workstation. We have ca. IR=A320= =20 K (=3D US$ 30 K) to spend and we do not wish to buy second hand equipment. We are interested in carrying out molecular dynamics simulations of solvated calixarene:metal complexes to estimate Gibb's free energy of complexation of these complexes. The calixarenes have ca. 120 heavy atoms and we are mostly interested in Group 1 and Group 2 metals. We have limited experience of programming and for the forseeable future, it is unlikely that we will be coding such programs.=20 I was hoping that someone could advise us on what are the best=20 combinations of software and hardware available. Rgds, Paddy. ************************************************************************* *=09=09=09=09=09=09=09=09=09* *=09Paddy Kane =09=09=09email: 94970459@tolka.dcu.ie *=20 * =09School of Chemical Sciences =09 =09=09=09=09* *=09Dublin City University =09=09 Tel: 00-353-1-7045641=09=09* *=09Dublin 9=09=09=09 =09=09=09=09* *=09Ireland.=09=09=09 Fax: 00-353-1-7045503=09=09* *=09=09=09=09=09=09=09=09=09* ************************************************************************* From stephen_andruski@fmc.com Tue May 6 09:53:45 1997 Received: from igw.fmc.com for stephen_andruski@fmc.com by www.ccl.net (8.8.3/950822.1) id JAA08526; Tue, 6 May 1997 09:25:43 -0400 (EDT) Received: by igw.fmc.com id AA07906 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Tue, 6 May 1997 08:25:38 -0500 Message-Id: <199705061325.AA07906@igw.fmc.com> Received: by igw.fmc.com (Internal Mail Agent-1); Tue, 6 May 1997 08:25:38 -0500 Mime-Version: 1.0 Date: Tue, 6 May 1997 09:13:51 -0500 From: stephen_andruski@fmc.com (STEPHEN ANDRUSKI) Subject: Re:Substructure Searching in FileMaker Pro To: janet.cicariello-cook@roche.com Cc: chemistry@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part Janet, You do not mention what platform you're running on. I also do not know much about the specific capabilities of FileMaker Pro, but here is something to look into. The Windows 95 version of ChemWindow (V5 is out or will be out very soon) is a fully OLE 2.0 compliant application. As such, programs that support this will allow you to embed ChemWindow drawings into the files for other programs. SoftShell has taken this a step further. There are chemical functions available to the OLE client which can be used to do things like calculate the molecular weight of a compound in a drawing or do substructure searching. ChemWindow comes with several example Microsoft Access databases which illustrate these OLE automation features. If you are on Windows 95 and FileMaker Pro can act as an OLE client and access the OLE automation functions in ChemWindow then that is an option. If you're on Windows 95 and you're willing to switch to MS Access then this is even easier. If you're not on Windows 95 then I'm afraid that this information is useless :) If you're interested in more information about ChemWindow e-mail Rebecca Roseberry at SoftShell (now a division of BioRad). Her e-mail address is: Rebecca_Roseberry@bio-rad.com. Steve Andruski FMC Corporation stephen_andruski@fmc.com From buyong@ibmnla.chem.uga.edu Tue May 6 10:41:15 1997 Received: from dns1.uga.edu for buyong@ibmnla.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id KAA10089; Tue, 6 May 1997 10:24:38 -0400 (EDT) From: Received: from ibmnla.chem.uga.edu (ibmnla.chem.uga.edu [128.192.5.8]) by dns1.uga.edu (8.8.5/8.8.3) with SMTP id KAA09372; Tue, 6 May 1997 10:24:36 -0400 Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA12028; Tue, 6 May 1997 10:24:29 -0400 Date: Tue, 6 May 1997 10:24:27 -0400 (EDT) To: Laurent Joubert Cc: chemistry@www.ccl.net Subject: Re: CCL:Looking for good "all-electrons" basis sets (Ca and Zr) In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII For Ca: see Pettersson and Siegbahn, Chemical Physics, 82 (1983) 355. ================================================================= Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 ================================================================= On Tue, 6 May 1997, Laurent Joubert wrote: > Dear Netters, > > I'm actually looking for "all-electrons" basis sets (better than STO-3G !) > for the atoms Ca and Zr. > > Thanks in advance. > > Laurent Joubert > > > ******************************************************** > * Laurent JOUBERT (PhD student) * > * * > * Ecole Nationale Superieure de Chimie de Paris * > * Laboratoire d'Electrochimie et de Chimie Analytique * > * 11, rue Pierre et Marie Curie * > * 75231 PARIS CEDEX 05- FRANCE * > * * > * Tel : (33) 01-44-27-66-94 * > * Fax : (33) 01-44-27-67-50 * > * * > * E-Mail : joubert@ext.jussieu.fr * > * http://www.enscp.jussieu.fr * > ******************************************************** > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: joubert@ext.jussieu.fr > -- Original Sender From: Address: joubert@ext.jussieu.fr > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From kneth@chem.ruc.dk Tue May 6 12:41:28 1997 Received: from koala.ruc.dk for kneth@chem.ruc.dk by www.ccl.net (8.8.3/950822.1) id LAA11580; Tue, 6 May 1997 11:52:50 -0400 (EDT) Received: from localhost (kneth@localhost) by koala.ruc.dk (8.8.5/8.8.5) with SMTP id QAA29168; Tue, 6 May 1997 16:56:20 +0200 Date: Tue, 6 May 1997 16:56:20 +0200 (MET DST) From: Kenneth Geisshirt X-Sender: kneth@koala.ruc.dk To: roberson@kemibm.kemi.aau.dk cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Small MD programs? In-Reply-To: <9705061144.AA16591@kemibm.kemi.aau.dk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > A prof here is interested in having his students get some experience with > MD simulations on PCs. He wants to know if there are any free or cheap > programs that will handle 125 to 1000 water molecules. Try to write to Jiri Kolafa (kolafa@beba.cesnet.cz). He has written a program called cook which is a general-purpose MD program. DL_poly is another possibility (write to W. Smith - W.Smith@dl.ac.uk). Best regards Kenneth +-------------------------------------------------------------+ | Kenneth Geisshirt Ph.D.-student | | Dept. of Life Sciences and Chemistry Roskilde University | +-------------------------------------------------------------+ | E-mail: kneth@chem.ruc.dk Phone: +45 4675 7711, ext 2785 | +-------------------------------------------------------------+ From duanx@Picard.ml.wpafb.af.mil Tue May 6 12:51:05 1997 Received: from nsrhost.ml.wpafb.af.mil for duanx@Picard.ml.wpafb.af.mil by www.ccl.net (8.8.3/950822.1) id LAA11577; Tue, 6 May 1997 11:52:53 -0400 (EDT) Received: from Picard.ml.wpafb.af.mil by nsrhost.ml.wpafb.af.mil with SMTP (1.39.111.2/16.2) id AA068503777; Tue, 6 May 1997 11:49:37 -0400 Received: by Picard.ml.wpafb.af.mil (4.1/version) id AA11685; Tue, 6 May 97 11:52:47 EDT Date: Tue, 6 May 1997 11:52:46 -0400 (EDT) From: Xiaofeng Duan To: chemistry@www.ccl.net Subject: [Q]TCGMSG on SGI Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, everyone! I am running paralleled GAMESS on SGI machines. I found there is a problem that the TCGMSG which is used to parallel GAMESS only allows me to use maximum 8 processors although the machines has 16 and 32 processors respectively. Following is the error message I got when I tried running TCGMSG for testing program "hello" with 16 processors on the machine which is Origin 2000 having 32 processors: ----------------------------------------- hpc03-1:/fs31/duanx/tcgmsg/ipcv4.0/ parallel hello Creating: host=hpc03-1, user=duanx, file=/fs31/duanx/tcgmsg/ipcv4.0/hello.x, port=2376 0: SemSetCreate: n_sem has invalid value 48 (0x30). system error message: Permission denied 16: interrupt ----------------------------------------- I don't know what caused the above problem. Could somebody give me a help with it? Thanks! **************************************** Xiaofeng Duan, Ph.D WL/MLBP, Bldg. 654 2941 P St. Ste. 1 Wright-Patterson AFB, OH 45433 (513)255-9164 duanx@Picard.ml.wpafb.af.mil **************************************** From iiv@mmlds1.pha.unc.edu Tue May 6 12:53:16 1997 Received: from mmlds1.pha.unc.edu for iiv@mmlds1.pha.unc.edu by www.ccl.net (8.8.3/950822.1) id LAA11507; Tue, 6 May 1997 11:49:54 -0400 (EDT) Received: by mmlds1.pha.unc.edu (5.57/TAS/11-16-88) id AA19840; Tue, 6 May 97 12:04:06 -0400 Date: Tue, 6 May 1997 12:04:03 -0400 (EDT) From: Iosif Vaisman To: CHEMISTRY@www.ccl.net Subject: ACS Course in Molecular Modeling Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The American Chemical Society Short Course Molecular Modeling, Computational/Combinatorial Chemistry, and Chemical Diversity : Methods and Techniques Two Sessions: May 13-16, 1997 and August 19-22, 1997 Laboratory for Molecular Graphics and Theoretical Modeling College of Pharmacy, University of Texas at Austin The introductory course will be especially valuable for experimental chemists who design drugs or carry out syntheses, as well as other R&D scientists in the organic, medicinal, or biochemical fields. Each student will have their own Silicon Graphics workstation and access to desktop computers for the duration of the short course. There will be daily "hands-on" laboratory sessions so YOU can work with state-of-the-art hardware and software. Topics: Molecular Mechanics Calculations, Molecular Mechanics Parameterization, Quantum Mechanics Calculations, Conformational Searching, Drug Design, Pharmacophore Development, 3D Databases, 3D Searching Strategies, and Combinatorial Chemistry Concepts Who Should Attend? Anyone wanting to know more about molecular structure calculations, pharmacophore design, 3D database searching, and structure-function relationships. The course has been designed primarily for experimental scientists in industry or academics with a background in the chemical, biological, and/or biomedical sciences. Software: MM2/MM3, SYBYL, INSIGHT/DISCOVER, QUANTA/CHARMm, SPARTAN, ISIS, CONCORD, CAChe, and more Lecturers J. Phillip Bowen (University of Georgia) Norman L. Allinger (University of Georgia) Alex Tropsha (University of North Carolina) Warren Hehre (Wavefunction, Inc.) Bob Pearlman (University of Texas at Austin) Osman Guner (MSI) Call the ACS Education Services/Short Course Office at (800) 227-5558 or (202) 872-4508 or FAX (202) 872-6336 From raman@indigo1.biomol.uci.edu Tue May 6 13:41:28 1997 Received: from indigo1.biomol.uci.edu for raman@indigo1.biomol.uci.edu by www.ccl.net (8.8.3/950822.1) id NAA13855; Tue, 6 May 1997 13:27:34 -0400 (EDT) Received: by indigo1.biomol.uci.edu (8.8.5) id RAA24097; Tue, 6 May 1997 17:27:03 GMT From: CS Raman Message-Id: <199705061727.RAA24097@indigo1.biomol.uci.edu> Subject: Re: CCL:Micelles To: redime@azur.incm.u-nancy.fr (Redime HADJI) Date: Tue, 6 May 1997 10:27:03 -0700 (PDT) Cc: chemistry@www.ccl.net In-Reply-To: <9705061532.ZM24143@azur.incm.u-nancy.fr> from "Redime HADJI" at May 6, 97 03:32:01 pm X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Redime: {*} molecular dynamics simulations of MICELLE(S), conformational behaviour of {*} peptides in micelles (in paticular in SDS micelles). Please contact Dr. Sudha Veeraraghavan at Tufts U. She has done a lot of work in this area. Her email address is: sudha@biba.med.tufts.edu Cheers -raman ___________________________________________________________________ C.S.Raman Tel: (714) 824-4322 University of California Fax: (714) 824-8540 Dept. MB & B email: raman@indigo1.biomol.uci.edu 3205 Bio Sci II Irvine, CA 92697-3900 ------------------------------------------------------------------- In a time of drastic change it is the learners who inherit the future. The learned usually find themselves equipped to live in a world that no longer exists. --Eric Hoffer ___________________________________________________________________ From mg2@DEC3600.boa.uni.torun.pl Tue May 6 15:41:28 1997 Received: from DEC3600.boa.uni.torun.pl for mg2@DEC3600.boa.uni.torun.pl by www.ccl.net (8.8.3/950822.1) id PAA16254; Tue, 6 May 1997 15:01:41 -0400 (EDT) Received: by DEC3600.boa.uni.torun.pl; id AA29066; Tue, 6 May 1997 21:03:19 +0200 From: Turski Przemyslaw Message-Id: <9705061903.AA29066@DEC3600.boa.uni.torun.pl> Subject: GAUSSIAN-localization To: chemistry@www.ccl.net Date: Tue, 6 May 1997 21:03:16 +0200 (MET DST) X-Mailer: ELM [version 2.4 PL23] Content-Type: text HELLO EVERYBODY ! I have a small request for people who use Gaussian 94. I have problems with localization. For example in methane CH4 I expected to got 4 equivalent orbitals (hibridization sp3) localized on each bond C-H, but it just didn't work. If anybody could help me I would be very grateful ! mg2@dec3600.boa.uni.torun.pl From Keith.Refson@earth.ox.ac.uk Tue May 6 15:47:56 1997 Received: from earth.ox.ac.uk for Keith.Refson@earth.ox.ac.uk by www.ccl.net (8.8.3/950822.1) id PAA16787; Tue, 6 May 1997 15:10:50 -0400 (EDT) Received: from rahman.earth.ox.ac.uk (keith@max8.public.ox.ac.uk [192.76.27.8]) by earth.ox.ac.uk (8.8.5/8.8.5) with SMTP id UAA01446; Tue, 6 May 1997 20:10:38 +0100 (BST) Date: Tue, 6 May 97 20:08:39 BST Message-Id: <2477.9705061908@rahman.earth.ox.ac.uk> From: Keith Refson To: Cc: CHEMISTRY@www.ccl.net Subject: CCL:Small MD programs? In-Reply-To: <9705061144.AA16591@kemibm.kemi.aau.dk> References: <9705061144.AA16591@kemibm.kemi.aau.dk> X-Mailer: VM 6.30 under Emacs 19.34.1 Mime-Version: 1.0 (generated by tm-edit 7.92) Content-Type: text/plain; charset=US-ASCII roberson@kemibm.kemi.aau.dk writes: > A prof here is interested in having his students get some experience with > MD simulations on PCs. He wants to know if there are any free or cheap > programs that will handle 125 to 1000 water molecules. Hmm. You wrote "small" in the subject line... My program "Moldy" can not be described as "small" but it is free and it will handle 1000 water molecules. A quick, educated guess suggests that it will use about 5MB of memory to do that, and it will compile on a PC if you have an ANSI C compiler. See "http://www.earth.ox.ac.uk/~keith/moldy.html". Keith Refson -- ------------------------------------------------------------------------------ Email: Keith.Refson@ | Tel: +44 1865 272026 | Dr Keith Refson, | earth.ox.ac.uk | Fax: +44 1865 272072 | Dept of Earth Sciences | Spam: root@cyberpromo.com | Parks Road, Oxford OX1 3PR, UK| ------------------------------------------------------------------------------ From bruno@antas.agraria.uniss.it Tue May 6 15:50:09 1997 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id PAA17589; Tue, 6 May 1997 15:29:08 -0400 (EDT) Received: from antas.agraria.uniss.it by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA173866753; Tue, 6 May 1997 21:25:53 +0200 Date: Tue, 6 May 1997 21:26:03 +0100 (NFT) From: "Dr. Bruno Manunza" To: Redime HADJI Cc: chemistry@www.ccl.net, redime@azur.incm.u-nancy.fr Subject: Re: CCL:Micelles In-Reply-To: <9705061532.ZM24143@azur.incm.u-nancy.fr> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 6 May 1997, Redime HADJI wrote: > > > Hi, > > I am looking for any information (references, reviews, methodology, etc.) about > molecular dynamics simulations of MICELLE(S), conformational behaviour of > peptides in micelles (in paticular in SDS micelles). > > Any hints would be grately appreciated. I will summarize your answers. > > Thank you very much in advance. > > Redime HADJI-PFEFFER A search on the Beilstein gave these results: Author: Rusling, James F.; Kumosinski, Thomas F. Reference: Journal, JPCHAX, J.Phys.Chem., EN, 99, 22, 1995, 9241-9247 Title: An Approximation to Hydrophobic Attraction for Molecular Dynamics of Self-Assembled Surfactant Aggregates uthor: MacKerell, Alexander D. Reference: Journal, JPCHAX, J.Phys.Chem., EN, 99, 7, 1995, 1846-1855 Title: Molecular Dynamics Simulation Analysis of a Sodium Dodecyl Sulfate Micelle in Aqueous Solution: Decreased Fluidity of the Micelle Hydrocarbon Interior Author: Guba, Wolfgang; Haessner, Rainer; Breipohl, Gerd; Henke, Stefan; Knolle, Johen; et al. Reference: Journal, JACSAT, J.Amer.Chem.Soc., EN, 116, 17, 1994, 7532-7540 Title: Combined Approach of NMR and Molecular Dynamics within a Biphasic Membrane Mimetic: Conformation and Orientation of the Bradykinin Antagonist Hoe 140 Author: Klein, Michael L. Reference: Journal, JCFTEV, J.Chem.Soc.Faraday Trans., EN, 88, 13, 1992, 1701-1706 Title: Conformations of Flexible Molecules in Fluid Phases Author: Karaborni, S.; O'Connell, J. P. Reference: Journal, JPCHAX, J.Phys.Chem., EN, 94, 6, 1990, 2624-2631 Title: Molecular Dynamics Simulations of Model Micelles. 4. Effects of Chain Length and Head Group Characteristics Author: Linse, Per Reference: Journal, JCPSA6, J.Chem.Phys., EN, 93, 2, 1990, 1376-1385 Title: Accurate solution of a highly asymmetric electrolyte: Molecular dynamics simulation and integral equation Author: Watanabe, Kyoko; Klein, Michael L. Reference: Journal, JPCHAX, J.Phys.Chem., EN, 93, 19, 1989, 6897-6901 Title: Shape Fluctuations in Ionic Micelles Author: Joensson, Bo; Edholm, Olle; Teleman, Olle Reference: Journal, JCPSA6, J.Chem.Phys., EN, 85, 4, 1986, 2259-2271 Title: Molecular dynamics simulations of a sodium octanoate micelle in aqueous solution Author: Szleifer, I.; Ben-Shaul, A.; Gelbart, W. M. Reference: Journal, JCPSA6, J.Chem.Phys., EN, 85, 9, 1986, 5345-5358 Title: Chain statistics in micelles and bilayers: Effects of surface roughness and internal energy Author: Woods, M. C.; Haile, J. M.; O'Conell, J.P. Reference: Journal, JPCHAX, J.Phys.Chem., EN, 90, 9, 1986, 1875-1885 Title: Internal Structure of a Model Micelle via Computer Simulation. 2. Spherically Confined Aggregates with Mobile Head Author: Gruen, David W. R. Reference: Journal, JPCHAX, J.Phys.Chem., EN, 89, l, 1985, 146-153 Title: A Model for the Chains in Amphiphilic Aggregates. 1. Comparison with a Molecular Dynamics Simulation of a Bilayer Hope it helps Regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From mn1@helix.nih.gov Tue May 6 15:51:57 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id PAA16360; Tue, 6 May 1997 15:05:04 -0400 (EDT) Received: (from mn1@localhost) by helix.nih.gov (8.8.4/8.8.4) id PAA17464 for CHEMISTRY@www.ccl.net; Tue, 6 May 1997 15:05:05 -0400 (EDT) Date: Tue, 6 May 1997 15:05:05 -0400 (EDT) From: "M. Nicklaus" Message-Id: <199705061905.PAA17464@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: Re: G:Search for Benchmarks Gaussian94 Hi, On Tue, 29 Apr 1997, Vansweevelt Hans wrote: > does anyone has benchmark results for Gaussian94 running on different > platforms ? Or can someone tell me where I can find relevant information ? I'm > especially interested in DEC alphaserver, SGI powerchallenge and SUN > HPC-systems. Comments on problems (or benefits) with Gaussian on those > platforms are also welcome. We are in the process of performing extensive benchmarking using Gaussian 94 (among other programs) for the LoBoS project (see, e.g., Rick Venable's remarks in gopher://www.ccl.net/0R4056-18210-/archived-messages/97/04/15-rej). We are mostly concentrating on the P6 (Pentium Pro) platform, comparing different motherboards, cache sizes, compilers, compiler options etc., but we've also included a few other platforms for comparison purposes. Below I am listing one of those results for the P6 (among the better ones we found), along with three other platforms. More benchmark data will be made available in the near future. We are using the subset of the test jobs provided with G94 that is recommended by Gaussian, Inc.; these jobs "cover a range a Gaussian 94 capabilities" (G94 User's Manual p. 193). I also want to point out Joe Durant's G94 Benchmarks page, for which he used the same set of test jobs, so his numbers are directly comparable with ours (http://mephisto.ca.sandia.gov/benchmarks.html). As a bottom line, it is quite astonishing what performance one can get from inexpensive machines such as P6 based systems. Given the fact that a Dual P6 200 MHz system can now be bought for about $3,000 if one foregoes fancy graphics and expensive monitors, this means that Cray YM-P type preformance can now be had for about $1,500. (We've seen typically 10-15% performance hits if you run two G94 jobs on a Dual P6 simultaneously.) Note that the P6 results were achieved with 'cheap' hardware options, i.e. the 256 kB cache version of the processor, and a 3.1 GB E-IDE (not SCSI!) hard drive. Of course, for certain types of jobs a supercomputer will still be much faster. Test job 194 seems to be such a case. However, since, for QCISD(T) and related methods, "more memory reduces the number of passes, improves elapsed time" (Gaussian 92 Workshop Notes), this might simply be a RAM amount effect. I'd be interested to hear comments on this point from the CCL community and/or Gaussian, Inc. System/Motherboard/RAM | Test Job # OS/Compiler/Options | 001 028 094 155 194 296 302 | Total Gaussian 94 Revision | ("Job cpu time" in seconds) | ---------------------------------------------------------------------------------------------- Cray Y-MP/8128, 128 MW 7.6 21.6 74.3 353.6 4.1 1228.1 49.5 1738.8 UNICOS 8.0.4 G94 Rev. C.3 IBM RS/6000-590 4.0 13.8 55.4 201.5 53.1 749.5 66.7 1144.0 "Gaussian, Inc. reference system" G94 Rev. D.3 DEC AlphaServer 2100 4/275, 256 MB 12.6 28.3 32.7 321.5 108.7 1147.4 128.2 1839.4 4 x 21064 chip 275 MHz (1 CPU) OSF/1 (Digital Unix) v. 3.2 f77 (Gaussian, Inc. scripts) G94 Rev. C.3 Dual P6 200 MHz ASUS (1 CPU) 128 MB 5.9 15.7 57.0 298.3 178.3 969.9 75.1 1600.2 Debian Linux 2.0.27; f2c --> cc (optimizing compilation) G94 Rev. E.1 Notes ----- All results are the summed up "Job cpu time[s]" as reported by the G94 jobs at the end of the output files. The IBM RS/6000-590 results are from the output files provided with G94 in the subdirectory $g94root/g94/tests/rs6k. All jobs on Cray, DEC, P6 were run with the 'default' default memory use (i.e., no Default.Route file), which should be 2,000,000 words (Gaussian 94 User's Reference, p. 10). All jobs were submitted from interactive sessions as background jobs. Exceptions: Job 155 and 296 on Cray, which had to be submitted via qsub, with %Mem=9MW and 16MW for test155 and test296, respectively. NQS output reported "User CPU Time" of 324.9 sec and 1063.6 sec for test155 and test296, respectively. "(1 CPU)" for DEC, P6 means that, although these are multiprocessor machines, G94 was run on one CPU only. It was made sure that the G94 job had >99% of this one processor. On Cray: Parallelized version of G94 was used. Dual P6: 256 kB cache Pentium Pro, 3.1 GB E-IDE hard drive. Compiler (optimization) options: -O3 -funroll-loops -fomit-frame-pointer -malign-double -m486 -malign-loops=2 -malign-jumps=2 -malign-functions=2. Route cards and comments: test001 #P TEST STO-3G COMPLEX pop=full scf=conventional SINGLET DELTA STO-3G//STO-3G DIOXYGEN test028 #p rhf/3-21g freq=anal water freq//hf/3-21g freq=anal explicit (compare test 27) test094 #p rmp2/sto-3g opt=calcfc test geom=modela Water MP2 Opt=CalcFC test155 #p 6-31+G* freq rcis(full,mo) test 1-B3u Ethene D2h test194 #p uqcisd(tq)/gen test guess(mix) symm=noscf iop1=synch UQCISD(TQ) water at 1.5 Re with [4s2p1d|2s1p] Dunning basis test296 #p G1 geom=modela test Water G1 from standard model test302 #p hf/3-21g opt=qst2 test reactant SiH2 +H2 -> SiH4 ts with constrained transition vector ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA mn1@helix.nih.gov http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM Laboratory of Medicinal Chemistry, National Cancer Institute, & Lab. of Structural Biology, Div. of Computer Research and Technology ------------------------------------------------------------------------ From chem8@york.ac.uk Tue May 6 16:41:31 1997 Received: from lendal.york.ac.uk for chem8@york.ac.uk by www.ccl.net (8.8.3/950822.1) id PAA17823; Tue, 6 May 1997 15:44:15 -0400 (EDT) Received: from ebor.york.ac.uk by lendal.york.ac.uk with SMTP (PP); Tue, 6 May 1997 20:43:03 +0100 Received: from localhost by ebor.york.ac.uk via SMTP (950511.SGI.8.6.12.PATCH526/951211.SGI) id UAA14578; Tue, 6 May 1997 20:43:54 +0100 Date: Tue, 6 May 1997 20:43:54 +0100 (BST) From: John Waite To: Laurent Joubert cc: chemistry@www.ccl.net Subject: Re: CCL:Looking for good "all-electrons" basis sets (Ca and Zr) In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Try the below bases: CONTRACTED GTO BASIS FOR Ca STATE: 1S J.WAITE, THE NATIONAL HELLENIC RESEARCH FOUNDATION, ORGANIC CHEMISTRY INSTITUTE, VAS. KONSTANTINOU 48, ATHENS 116-35, GREECE SCF OPTIMISED EXPONENTS CONTRACTION COEFFICIENTS S 9 1.0 3.397307381409616D+05 1.075546934217709D-04 5.089488380029188D+04 8.337775409597456D-04 1.158509950101352D+04 4.367199412989600D-03 3.281609379956390D+03 1.800566033117016D-02 1.068692471146671D+03 6.209707637522766D-02 3.844593276419919D+02 1.710473512456315D-01 1.491283856925592D+02 3.472568943508807D-01 6.151590402656595D+01 3.840860368566705D-01 2.656056432802532D+01 1.604991815536684D-01 S 2 1.0 9.316281947956541D+00 3.945780475230828D-01 3.837729749425772D+00 6.384180965642398D-01 S 2 1.0 1.022299706138474D+00 4.290327095856378D-01 4.202187518064820D-01 6.051022099402708D-01 S 1 1.0 4.434341262667522D-02 -1.000000000000000D+00 P 8 1.0 2.766926488866536D+03 3.879098125370103D-04 6.558542309544509D+02 3.351830521697240D-03 2.121991252320799D+02 1.791599055031762D-02 8.024076473609608D+01 6.870926698396888D-02 3.338917954581414D+01 1.893035161271595D-01 1.466780273656772D+01 3.522510123517987D-01 6.659117891605640D+00 3.875933496157682D-01 3.074566560994426D+00 1.724138501888948D-01 P 3 1.0 1.325180298075105D+00 4.964695369862341D-01 5.602792406696313D-01 4.224894152806844D-01 2.242846310542125D-01 1.905994850558602D-01 MP2 OPTIMISED D 1 1.0 7.602038315511520D-02 1.0 ============================================================== CONTRACTED GTO BASIS FOR Zr STATE: 5F J.WAITE, THE NATIONAL HELLENIC RESEARCH FOUNDATION, ORGANIC CHEMISTRY INSTITUTE, VAS. KONSTANTINOU 48, ATHENS 116-35, GREECE SCF OPTIMISED EXPONENTS CONTRACTION COEFFICIENTS S 9 1.0 2.486573181843873D+06 5.287880482325203D-05 3.688028951464521D+05 3.972377441079611D-04 8.365989713397903D+04 2.224541816378750D-03 2.378777707543828D+04 8.424589040006151D-03 7.751039705647294D+03 3.365684950664571D-02 2.784569521103022D+03 8.649241715095159D-02 1.094721257403145D+03 2.468349466741692D-01 4.655241751421860D+02 2.958701207484140D-01 2.075218288793711D+02 4.570859595172356D-01 S 3 1.0 8.537983711232660D+01 2.173125014664076D+00 9.518074011555653D+01 -2.008840045233817D+00 2.391648071232482D+01 8.021983870583334D-01 S 2 1.0 5.161206888047965D+00 5.183762125701647D-01 3.001554914489136D+00 4.951287363277170D-01 S 2 1.0 8.658102214545685D-01 5.218291753691155D-01 3.549535773084693D-01 5.135759459066868D-01 S 2 1.0 7.575145375597150D-02 4.154354024049967D-01 2.867337835403934D-02 6.244143438586058D-01 P 7 1.0 1.067977823804192D+04 5.331486607832325D-04 2.537932133325427D+03 4.592843765465807D-03 8.259313417488809D+02 2.452680297416170D-02 3.165056529398030D+02 9.259284612141781D-02 1.346713145477666D+02 2.443068522652222D-01 6.125525292891226D+01 4.158511813960783D-01 2.908566075814123D+01 3.692270326841297D-01 P 3 1.0 1.388963071345811D+01 -1.857763165481554D-01 6.550032882474525D+00 -5.292949662390513D-01 3.120900035779753D+00 -3.586454659067721D-01 P 3 1.0 1.311524870558885D+00 -3.431542628804351D-01 5.728324473390884D-01 -5.586966721200058D-01 2.275540275937311D-01 -1.921155692892563D-01 D 5 1.0 1.780973194461847D+02 1.655049056403397D-02 5.233055433092361D+01 1.070673283695154D-01 1.894870690377078D+01 3.263821183092809D-01 7.296428762559821D+00 4.919377003984310D-01 2.792308602127212D+00 3.040363239140685D-01 D 2 1.0 7.285743236599017D-01 5.219605117128163D-01 1.807892333525192D-01 6.481655696633243D-01 MP2 OPTIMISED F 1 1.0 3.935428089604293D-01 1.0 Good luck, John Dr. John Waite, e-mail: chem8@york.ac.uk * or The National Hellenic Research Foundation,* Organic and Pharaceutical Institute, phone: ++30-1-7238958 (direct) Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6513112-5 X219 * c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece On Tue, 6 May 1997, Laurent Joubert wrote: > Dear Netters, > > I'm actually looking for "all-electrons" basis sets (better than STO-3G !) > for the atoms Ca and Zr. > > Thanks in advance. > > Laurent Joubert > > > ******************************************************** > * Laurent JOUBERT (PhD student) * > * * > * Ecole Nationale Superieure de Chimie de Paris * > * Laboratoire d'Electrochimie et de Chimie Analytique * > * 11, rue Pierre et Marie Curie * > * 75231 PARIS CEDEX 05- FRANCE * > * * > * Tel : (33) 01-44-27-66-94 * > * Fax : (33) 01-44-27-67-50 * > * * > * E-Mail : joubert@ext.jussieu.fr * > * http://www.enscp.jussieu.fr * > ******************************************************** > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: joubert@ext.jussieu.fr > -- Original Sender From: Address: joubert@ext.jussieu.fr > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From Vladislav.Vassiliev@BRI.NRC.CA Tue May 6 18:41:31 1997 Received: from bravais.BRI.NRC.CA for Vladislav.Vassiliev@BRI.NRC.CA by www.ccl.net (8.8.3/950822.1) id RAA24500; Tue, 6 May 1997 17:41:58 -0400 (EDT) Received: from localhost by bravais.BRI.NRC.CA with SMTP id RAA27334; Tue, 6 May 1997 17:43:39 -0400 Date: Tue, 6 May 1997 17:43:38 -0400 (EDT) From: Vladislav Vassiliev To: CHEMISTRY@www.ccl.net Subject: How to calculate pKa values in large proteins?... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: Let's imagine I have coordinates of a real protein (for example, from PDB) and now I would like to know the pKa values of all the residues (Asp's, Glu's, Lys's, Arg's, His's) at a given pH. What kind of programs could predict these pKa values? I would also be interested in any references concerning the approaches of this kind of prediction. Thanks in advance, Dr. V.Vassiliev From klangevin@ibcusa.com Tue May 6 18:46:20 1997 Received: from lucius.ultra.net for klangevin@ibcusa.com by www.ccl.net (8.8.3/950822.1) id RAA25374; Tue, 6 May 1997 17:53:04 -0400 (EDT) Received: from cleopatra.ultra.net (cleopatra.ultra.net [199.232.56.35]) by lucius.ultra.net (8.8.5/ult1.05) with ESMTP id RAA26750 for ; Tue, 6 May 1997 17:53:36 -0400 (EDT) Received: from ultra-gw.ibcusa.com (ultra-gw.ibcusa.com [204.249.176.245]) by cleopatra.ultra.net (8.8.5/ult1.05) with SMTP id RAA18922 for ; Tue, 6 May 1997 17:53:01 -0400 (EDT) Received: from ccMail by ultra-gw.ibcusa.com (SMTPLINK V2.11 PreRelease 4) id AA862966260; Tue, 06 May 97 17:48:09 EST Date: Tue, 06 May 97 17:48:09 EST From: "Kristen Langevin" Message-Id: <9704068629.AA862966260@ultra-gw.ibcusa.com> To: CHEMISTRY@www.ccl.net Subject: Data Management Hello, I am writing to inform you of a conference entitled, "Data Management for Drug Discovery and Design", June 23-24, 1997 in San Francisco, CA. Please take a moment to view our brochure on-line at: http://www.ibcusa.com/conf/datamanagement. You may register here as well. In addition, if you have a website that you would be interested in linking to our conference page, please contact me to arrange. You may also contact me if you have questions. I can be reached directly at (508) 481-6400, ext. 257. My e-mail address is klangevin@ibcusa.com. Kristen P. Langevin Marketing Manager From ctarg@lv.levels.unisa.edu.au Tue May 6 19:41:31 1997 Received: from Ladyhawk.Levels.UniSA.Edu.Au for ctarg@lv.levels.unisa.edu.au by www.ccl.net (8.8.3/950822.1) id TAA00521; Tue, 6 May 1997 19:30:00 -0400 (EDT) Received: from itu204576 ("port 1240"@IWK204576.Levels.UniSA.Edu.Au) by Levels.UniSA.Edu.Au (PMDF V5.0-7 #20435) id <01IIKZCRE0OG8WWJ0D@Levels.UniSA.Edu.Au> for chemistry@www.ccl.net; Wed, 07 May 1997 08:59:54 +0930 Date: Wed, 07 May 1997 10:02:59 +0900 From: Andrea Gerson Subject: dynamics - part force field, part qunatum mechanics X-Sender: ctarg@lv.levels.unisa.edu.au To: chemistry@www.ccl.net Message-id: <3.0.1.32.19970507100259.006ef954@lv.levels.unisa.edu.au> MIME-version: 1.0 X-Mailer: Windows Eudora Light Version 3.0.1 (32) Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Hi all, I am interested in finding out about molecular dynamics codes that contain part force field and part qunatum mechanics, that is so the molecule/atoms of specific interest can be looked at qunatum mechanically. Does anybody know of/about these codes? Do they have a proven track record? Availablility? Many thanks Andy From Anthony.Scott@anugpo.anu.edu.au Tue May 6 19:44:09 1997 Received: from anugpo.anu.edu.au for Anthony.Scott@anugpo.anu.edu.au by www.ccl.net (8.8.3/950822.1) id SAA29050; Tue, 6 May 1997 18:59:37 -0400 (EDT) Received: from leonard.anu.edu.au (aps501@leonard.anu.edu.au [150.203.2.15]) by anugpo.anu.edu.au (8.8.5/8.8.5) with ESMTP id IAA03913 for ; Wed, 7 May 1997 08:59:32 +1000 (EST) From: Anthony P Scott Received: (aps501@localhost) by leonard.anu.edu.au (8.8.4/8.6.12) id IAA27368; Wed, 7 May 1997 08:59:31 +1000 (EST) Date: Wed, 7 May 1997 08:59:30 +1000 (EST) To: chemistry@www.ccl.net Subject: CCL:Raman intensities Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, A member of our group needs to calculate Raman intensities for a closed-shell molecule and wants to know if any of the current programs can do this beyond HF (e.g. MP2, B3-LYP). Does anyone by chance know (or can straightforwardly find out) the answer to this question? Thanks in advance, Tony Scott ______________________________________________________________________________ Dr. Anthony P. Scott, Computational Chemistry Group, Office Ph.: 61-6-249-3573 Research School of Chemistry, Dept. Ph.: 61-6-249-3637 Australian National University, Fax: 61-6-249-0750 Canberra, ACT 0200, Email: Anthony.Scott@anu.edu.au AUSTRALIA. ______________________________________________________________________________ From buyong@ibmnla.chem.uga.edu Tue May 6 21:41:34 1997 Received: from dns1.uga.edu for buyong@ibmnla.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id VAA03701; Tue, 6 May 1997 21:32:18 -0400 (EDT) From: Received: from ibmnla.chem.uga.edu (ibmnla.chem.uga.edu [128.192.5.8]) by dns1.uga.edu (8.8.5/8.8.3) with SMTP id VAA13790; Tue, 6 May 1997 21:32:18 -0400 Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA20435; Tue, 6 May 1997 21:32:11 -0400 Date: Tue, 6 May 1997 21:32:07 -0400 (EDT) To: Anthony P Scott Cc: chemistry@www.ccl.net Subject: Re: CCL:Raman intensities In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In principle, Gaussian can do that by performing numerical third derivative calculation. But I have not tried this myself. ================================================================= Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 ================================================================= On Wed, 7 May 1997, Anthony P Scott wrote: > > Dear CCL members, > > A member of our group needs to calculate Raman intensities for a closed-shell > molecule and wants to know if any of the current programs can do this > beyond HF (e.g. MP2, B3-LYP). > > Does anyone by chance know (or can straightforwardly find out) the answer > to this question? > > Thanks in advance, > > Tony Scott > > ______________________________________________________________________________ > Dr. Anthony P. Scott, > Computational Chemistry Group, Office Ph.: 61-6-249-3573 > Research School of Chemistry, Dept. Ph.: 61-6-249-3637 > Australian National University, Fax: 61-6-249-0750 > Canberra, ACT 0200, Email: Anthony.Scott@anu.edu.au > AUSTRALIA. > ______________________________________________________________________________ > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: Anthony.Scott@anugpo.anu.edu.au > -- Original Sender From: Address: Anthony.Scott@anu.edu.au > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From ccl@www.ccl.net Wed Apr 30 11:39:47 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA07223; Wed, 30 Apr 1997 10:59:19 -0400 (EDT) Received: from gatekeeper.roche.com for JANET.CICARIELLO-COOK@roche.com by bedrock.ccl.net (8.8.3/950822.1) id KAA26689; Wed, 30 Apr 1997 10:59:16 -0400 (EDT) Received: by gatekeeper.roche.com (5.65v3.2/fma-120691); id AA14433; Wed, 30 Apr 1997 10:57:47 -0400 Received: from rnudnb.nut.roche.com by mailgate.roche.com; (5.65v3.2/1.1.8.2/20Mar96-0227PM) id AA05891; Wed, 30 Apr 1997 10:59:17 -0400 Received: from mr.nut.roche.com by rnuc01.nut.roche.com (PMDF V5.0-6 #9043) id <01IIBBFGISCW8WWXAF@rnuc01.nut.roche.com> for chemistry@ccl.net; Wed, 30 Apr 1997 10:57:47 -0500 (EST) Received: with PMDF-MR; Wed, 30 Apr 1997 10:53:45 -0500 (EST) Mr-Received: by mta RNIS08; Relayed; Wed, 30 Apr 1997 10:53:45 -0500 Mr-Received: by mta RNUC01; Relayed; Wed, 30 Apr 1997 10:57:45 -0500 Alternate-Recipient: prohibited Date: Wed, 30 Apr 1997 10:53:43 -0500 (EST) From: JANET CICARIELLO-COOK 57165 Subject: Substructure Searching in FileMaker Pro To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Posting-Date: Wed, 30 Apr 1997 10:53:45 -0500 (EST) Importance: normal Priority: normal Ua-Content-Id: E1363IUY2CPNE X400-Mts-Identifier: [;54350103407991/570099@RNISD0] A1-Type: MAIL Hi everyone, We use FileMaker Pro extensively, for example, storing structures and data related to a specific project. The one thing that our Chemists would like to be able to do is a substructure search of the molecules in the FileMaker Pro database. I know this cannot be done the same way as using the "Find" option to search for something in a data field. Does anyone have a workaround? Using other software (such as ChemFinder, etc)? Or via a script (FMPro and/or AppleScript)? I have thought about trying to write something (maybe an AppleScript???) to do the searches based on SMILES strings, but since SMILES strings are not unique I don't know if this would work. I should mention that the moleculess in the FileMaker Pro databases are all ChemDraw structures. Thanks in advance for your help. I will summarize the responses to the list if anyone is interested. Janet ********************************************* * Janet Cicariello-Cook, Ph.D. * * Hoffmann-LaRoche, Inc. * * 340 Kingsland St. * * Nutley, NJ 07110 * * ph: (201) 235-7165 * * fax: (201) 235-7292 * * e-mail: janet.cicariello-cook@roche.com * **************************************************** From Eugene.Leitl@lrz.uni-muenchen.de Sun May 4 12:40:45 1997 Received: from sunsrv5.lrz-muenchen.de for Eugene.Leitl@lrz.uni-muenchen.de by www.ccl.net (8.8.3/950822.1) id MAA22955; Sun, 4 May 1997 12:30:15 -0400 (EDT) Received: from sun6.lrz-muenchen.de by sunsrv5.lrz-muenchen.de; Sun, 4 May 97 18:30:15 +0200 Received: by sun6.lrz-muenchen.de (5.x/SMI-SVR4) id AA24073; Sun, 4 May 1997 18:30:15 +0200 Date: Sun, 4 May 1997 18:30:14 +0200 (MET DST) From: Eugene Leitl X-Sender: ui22204@sun6 To: chemistry Subject: FYI:File molecular-dynamics-news introduction (fwd) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This is one list devoted to molecular dynamics I have been pointed to by a friendly CCL subscriber. Thanks! -- Eugene Leitl ---------- Forwarded message ---------- Date: Sun, 4 May 1997 17:24:34 +0100 (BST) From: mailbase-admin@mailbase.ac.uk To: Eugene.Leitl@lrz.uni-muenchen.de Subject: File molecular-dynamics-news introduction Welcome to the mailing list molecular-dynamics-news @ mailbase.ac.uk. This mailing list exists to facilitate communication among those interested in experimental and theoretical molecular dynamics (in the sense of dynamical studies of molecules, rather than classical dynamical simulations of ensembles). The topics covered will include molecular collisions, photodissociation processes, clusters and complexes, etc. etc. The email list is coordinated by Jeremy Hutson, J.M.Hutson @ durham.ac.uk It is associated with the (paper) newsletter Molecular Dynamics News, edited by Enzo Aquilanti and Roger Anderson. However, you do not have to subscribe to the paper version to be a member of the email list. The list may be used for announcements of general interest to the community: conference announcements, faculty and postdoctoral positions vacant, new computer programs available etc. It is not intended that the email list should replace the paper version of MDN for announcements of papers in the field. If you have views on how the list should or should not be used, by all means send them to the list, and we can have a discussion on the topic. None of us wants to be swamped by "junk mail", but different people will certainly have different views on just what constitutes "junk mail". If your registered email address fails to work at any time, I get error messages. I like to keep such messages to a minimum, and they usually indicate that the account no longer exists, so I remove any addresses that fail repeatedly. Rather by definition, I can't notify you under these circumstances! If your account keeps getting removed, this may be the reason: you can send me a message at the address molecular-dynamics-news-request @ mailbase.ac.uk to enquire. If your email address changes, please remember to remove your old registration (by sending a "leave" message from your old account, as described below) and add your new address (by sending a "join" message from your new account). Although I CAN add and remove registrations by hand, I shouldn't normally have to, and will only do so if the usual mechanisms fail for some reason. Please also remember that lots of people use the molecular-dynamics-news list as an "address book" of email addresses, so that it is to your advantage for it to contain your correct address. The list is at present unmoderated: that is, anything you send will be circulated to the list without being checked by a real person. This policy will be reviewed from time to time. To circulate an item to the list, just send it to the (Internet) email address: molecular-dynamics-news @ mailbase.ac.uk Please AVOID sending mailbase commands to this address, as they will be circulated to all the list members rather than acted upon. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MAILBASE COMMANDS Anyone may join this list, and membership of the list is completely independent of a subscription to the Molecular Dynamics News newsletter on paper. To join the list, send a message to mailbase @ mailbase.ac.uk containing a line (in the message text) that says something like join molecular-dynamics-news Bill Clinton Similarly, you can remove your name from the list with a line that says: leave molecular-dynamics-news To get a complete listing of the current membership, use the command review molecular-dynamics-news To get more information about the mailbase system itself, and all the useful information it contains, send one of the two lines: send mailbase user-guide send mailbase user-card The user-card file is essentially a short version of the full user-guide. Please note that all the above commands must be sent to mailbase @ mailbase.ac.uk and NOT to molecular-dynamics-news @ mailbase.ac.uk If you send them to the latter, they will be forwarded to everyone on the list! ...Jeremy Hutson updated 14 December 1994 From ccl@www.ccl.net Mon May 5 15:55:00 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA21501; Mon, 5 May 1997 15:05:40 -0400 (EDT) Received: from kodakr.kodak.com for mckelvey@kodakr.kodak.com by bedrock.ccl.net (8.8.3/950822.1) id PAA00226; Mon, 5 May 1997 15:05:37 -0400 (EDT) Received: from mail.rl.kodak.com by kodakr.kodak.com with SMTP id AA13474 (5.67b/IDA-1.5 for ); Mon, 5 May 1997 15:03:21 -0400 Received: from mozart.rl.kodak.com by mail.rl.kodak.com (8.8.3/1.1.10.5/17Jan97-0515PM) id PAA01505; Mon, 5 May 1997 15:13:43 -0400 (EDT) Received: from stomper (stomper.rl.kodak.com [150.220.76.39]) by mozart.rl.kodak.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id PAA04968; Mon, 5 May 1997 15:05:07 -0400 Message-Id: <336DE99A.7E25@kodak.com> Date: Mon, 05 May 1997 15:07:22 +0100 From: John McKelvey Reply-To: mckelvey@kodakr.kodak.com Organization: Eastman Kodak Company X-Mailer: Mozilla 3.0 (WinNT; I) Mime-Version: 1.0 To: Joe M Leonard Cc: chemistry@ccl.net Subject: Re: CCL:G77 - looking for intrinsic random number fn References: <199605242116.AA11129@world.std.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Joe M Leonard wrote: > > Folks, > > If you don't use g77, please skip the rest of this message. > > Is there an intrinsic random number function in g77? I have > tried ran() and rand(), but nothing works. It's picked up the rest > of the Fortran intrinsics I have in the code, which is why I'm > hoping it's there but under a different name. If there isn't > one, has anybody figured out how to call the gcc library functions - > and could give me some pointers? > > Why ask this on the CCL? Because chemists are probably > the largest target community for g77! Well, maybe not chemists > alone, maybe scientists (and dinosaurs :-) in general... > > No, this isn't for new stuff, but there's this large pile of > VAX code that I have lying about and I want to use some of it... > > Thanks in advance, > > Joe Leonard > jle@world.std.com > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: owner-chemistry@ccl.net > -- Original Sender From: Address: jle@world.std.com > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html Joe: Is there any reason not to use PC-SPARTAN to do rendering from G94 running on an SGI box? or how hard is it to do? Is the issue just a file format? Regards... John See you in LV? -- ************************************ * John McKelvey * * Imaging Research Advanced Design * * Building 83 * * Research Laboratories * * Eastman Kodak Company * * Rochester, NY 14650-2216 * * (V)716-477-3335 * * (F)716-722-2327 * * (E)McKelvey@Kodak.COM * ************************************ From Gjlinker@aol.com Mon May 5 18:41:05 1997 Received: from emout19.mail.aol.com for Gjlinker@aol.com by www.ccl.net (8.8.3/950822.1) id RAA23938; Mon, 5 May 1997 17:45:23 -0400 (EDT) From: Received: (from root@localhost) by emout19.mail.aol.com (8.7.6/8.7.3/AOL-2.0.0) id RAA02072 for chemistry@www.ccl.net; Mon, 5 May 1997 17:44:52 -0400 (EDT) Date: Mon, 5 May 1997 17:44:52 -0400 (EDT) Message-ID: <970505174205_-1031076348@emout19.mail.aol.com> To: chemistry@www.ccl.net Subject: Software announcement: Extended Huckel calculator for Windows95 I want to announce Huckel 3.0, a shareware program I developed. With the program you can perform the Huckel analysis on any molecule you wish. The number of atoms is unlimited, the number of kinds of atoms is unlimited and you have full control of the parameters involved. I tried to make this program for students as well as for researchers. Extensive help is available online for all the options available. A short tutorial can be taken as a quick guide through the program. A theory section is available for students that get interested in the theory behind the calculations. As input to the program you draw a structure formula. The results of a calculations can be viewed as a level diagram and as a MO diagram. At any stage the bare numbers can be viewed: the Huckel matrix, the diagonal Hamiltonian, the eigenvectors and the eigenfunctions. To preview of the software, turn to the Huckel project pages on my web site. Go to the downloads section to download the program (about 4.3 MB). http://members.aol.com/gjlinker/ Key program characteristics: -windows 95 version only. -draw a structure formula to define the molecule you want to calculate. -output is presented in MO diagrams, a level diagram and in bare numbers. -full control of all alpha and beta parameters. -define your own atoms in the atoms database. -save molecules to files for later use. -extensive help file. -calculation of pi charges and bond orders. -size: about 4.3 MB download -no specific memory/hardware required There is more information available on my web site. Please send your comments and feedback to linker@ilovechocolate.com drs Gerrit-Jan Linker Analyst programmer @ SCT international Ltd. Manchester UK email: linker@ilovechocolate.com web: http://members.aol.com/gjlinker/index.htm >From perera@qtp.ufl.edu Tue May 6 10:53 EDT 1997 Received: from qtp.ufl.edu for perera@qtp.ufl.edu by bedrock.ccl.net (8.8.3/950822.1) id KAA19973; Tue, 6 May 1997 10:52:59 -0400 (EDT) Received: from visi4 by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id KAA14444; Tue, 6 May 1997 10:47:30 -0400 Date: Tue, 6 May 1997 10:53:04 -0400 (EDT) From: Ajith Perera Reply-To: Ajith Perera Subject: 97.06.15 50 Years of the Correlation Problem To: chemistry@www.ccl.net Message-ID: "FIFTY YEARS OF THE CORRELATION PROBLEM" A WORKSHOP ON COUPLED-CLUSTER THEORY AND OTHER CORRELATED METHODS (Cedar Key, Fl., june 15-19, 1997) This is the final notice for the above, one-of-a-kind meeting on Electron Correlation. This meeting will bring together the pioneers and the current principal practitioners of correlated methods in molecular electronic structure and spectra, plus applications to polymers and crystals, and related atomic and field theory applications (schedule can be found in the postscript file at ftp://www.ccl.net/pub/chemistry/info/50yrs.ps). Cedar Key, Fl, an island on the Gulf of Mexico, 60 miles from Gainesville, is the unique, rustic location for the meeting. There is still room for several more attendees. If interested, please consult our web site at http://www.qtp.ufl.edu/cct.html, and please contact zeynep@qtp.ufl.edu as soon as possible for a reservation. Thank you. Rod Bartlett, Graduate Research Professor, Quantum Theory Project, University Florida, Gainesville, FL, 32611; bartlett@qtp.ufl.edu; phone 352-392-6974.