From chemistry-request@server.ccl.net Tue Apr 4 04:10:01 2000 Received: from o200.cemes.fr (o200.cemes.fr [192.93.13.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA21025 for ; Tue, 4 Apr 2000 04:09:40 -0400 Received: from cemes.fr (o200.cemes.fr [192.93.13.4]) by o200.cemes.fr (8.9.3/8.9.3) with ESMTP id KAA683587 for ; Tue, 4 Apr 2000 10:09:24 +0200 (MET) Sender: bonvoisi@o200.cemes.fr Message-ID: <38E9A32B.11380313@cemes.fr> Date: Tue, 04 Apr 2000 10:09:15 +0200 From: Bonvoisin Jacques Organization: CNRS-CEMES X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP27) MIME-Version: 1.0 To: chemistry@ccl.net Subject: ZINDO/S parameter Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL members, I am looking for ZINDO/S parameters for I, Cl, Si and eventually Ru. Could you please help to find them in the literature ? I would appreciate if you answer directly to me at jbonvoisin@cemes.fr Thank you -- CEMES/CNRS - Groupe EM 29 rue Jeanne Marvig - BP 4347 F-31055 Toulouse cedex 4 tel: 33 (0)5 62 25 78 52 - fax: 33 (0)5 62 25 79 99 email: jbonvoisin@cemes.fr - URL: http://www.cemes.fr WEB page: http://www.cemes.fr/Personnel/bonvoisin.html From chemistry-request@server.ccl.net Tue Apr 4 05:27:31 2000 Received: from dogo.bq.ub.es (dogo.bq.ub.es [161.116.154.57]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA21372 for ; Tue, 4 Apr 2000 05:27:23 -0400 Received: from dogo.bq.ub.es (localhost [127.0.0.1]) by dogo.bq.ub.es (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA16324 for ; Tue, 4 Apr 2000 11:24:22 -0700 (PDT) Sender: bego@dogo.bq.ub.es Message-ID: <38EA3356.EA0DB1AE@dogo.bq.ub.es> Date: Tue, 04 Apr 2000 11:24:22 -0700 From: Bego Hernandez Organization: Universitat de Barcelona X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX 6.5 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: parameters of n-octanol Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everydody! Could anybody give me information about force field parameters for liquid n-octanol simulations? thanks in advance, bego From chemistry-request@server.ccl.net Tue Apr 4 13:37:03 2000 Received: from dns2.seanet.com (dns2.seanet.com [199.181.164.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA24271 for ; Tue, 4 Apr 2000 13:37:03 -0400 Received: from biggeek (dialup-209.245.175.134.Seattle1.Level3.net [209.245.175.134]) by dns2.seanet.com (8.9.3/8.9.0) with SMTP id KAA15647; Tue, 4 Apr 2000 10:36:29 -0700 (PDT) Message-ID: <001001bf9ec0$ba801990$01808080@biggeek> From: "Mark A. Thompson" To: "Bonvoisin Jacques" , References: <38E9A32B.11380313@cemes.fr> Subject: Re: CCL:ZINDO/S parameter Date: Tue, 4 Apr 2000 22:35:17 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Ru: Int. Journal of Quantum Chemistry vol 39, 1991, p 31-45. Mark ----- Original Message ----- From: Bonvoisin Jacques To: Sent: Tuesday, April 04, 2000 1:09 AM Subject: CCL:ZINDO/S parameter > Dear CCL members, > > I am looking for ZINDO/S parameters for I, Cl, Si and > eventually Ru. Could you please help to find them in > the literature ? > > I would appreciate if you answer directly to me at > jbonvoisin@cemes.fr > > Thank you > > -- > CEMES/CNRS - Groupe EM > 29 rue Jeanne Marvig - BP 4347 > F-31055 Toulouse cedex 4 > > tel: 33 (0)5 62 25 78 52 - fax: 33 (0)5 62 25 79 99 > > email: jbonvoisin@cemes.fr - URL: http://www.cemes.fr > WEB page: http://www.cemes.fr/Personnel/bonvoisin.html > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Tue Apr 4 03:37:02 2000 Received: from imc01.ex.nus.edu.sg (imc01.ex.nus.edu.sg [137.132.14.60]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA20815 for ; Tue, 4 Apr 2000 03:37:01 -0400 Received: by imc01.ex.nus.edu.sg with Internet Mail Service (5.5.2650.21) id ; Tue, 4 Apr 2000 15:36:49 +0800 Message-ID: From: Novak Igor To: "'chemistry@ccl.net'" Subject: isomer software Date: Tue, 4 Apr 2000 15:36:47 +0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="ISO-8859-1" Dear Netters, could someone please tell me what software (preferably freeware) is available for drawing structures of isomers upon entering a given bruto molecular formula!? Many thanks!! Yours sincerely I.Novak Dept.of Chemistry National University of Singapore Singapore 117543 chmigorn@nus.edu.sg From chemistry-request@server.ccl.net Tue Apr 4 04:24:35 2000 Received: from mjco-s2.ice.mpg.de (mjco-s2.ice.mpg.de [195.37.47.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA21112 for ; Tue, 4 Apr 2000 04:24:34 -0400 Received: from ice.mpg.de (unverified [195.37.47.89]) by mjco-s2.ice.mpg.de (EMWAC SMTPRS 0.83) with SMTP id ; Tue, 04 Apr 2000 10:24:46 +0200 Message-ID: <38E9A69E.9441EE2E@ice.mpg.de> Date: Tue, 04 Apr 2000 10:23:58 +0200 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max-Planck-Institute of Chemical Ecology X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: destack@unomaha.edu, chemistry@ccl.net Subject: Re: Scaling of G98 on Clusters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Subject: Scaling of G98 on Clusters > > With the recent discussion of how G98 scales on Beowulf clusters, I have an > additional question (we are thinking of putting together a cluster for G98 > calculations and are deciding about specifics of configuration). > > If there seems to be little gain above 8 CPUs using 100MB ether net > communication, is it possible to put together a 32 CPU cluster, use Linda for > the G98 code, then have cluster management software give 8 CPUs per Gaussian > job? In other words, using the Link 0 command, %NProc=8, would a 32 CPU cluster > be able to run 4 jobs at 8 CPU each and still provide maximum usage to Gaussian > users. Or does a Beowulf cluster require all CPUs by used in tandem. > > This leads to other question about cluster management software. I've seen > several mentioned on different web sites. Any experience as to which offers the > best mix of ease and functionality? > > > > Douglas E. Stack > Assistant Professor > Department of Chemistry > University of Nebraska at Omaha > Omaha, NE 68182-0109 > (402) 554-3647 > (402) 554-3888 (fax) > destack@unomaha.edu Hi Douglas, this is exactly what I'm doing now as a reaction to the result of my performance evaluation and what was said in the discussion. So, if you have a Linda license for 32 nodes, all you need to do is setup the linda communication modules ntsnet on cluster node 1 (cn01), cn09, cn17 and cn25, such that each uses only the subsequent seven nodes as workers. This is simple done by listing the machines names in the tsnet.config. The tsnet.config of the first node contains a line "Tsnet.Appl.nodelist: cn01 cn02 cn03 cn04 cn05 cn06 cn07 cn08", the one of cn09 shows "Tsnet.Appl.nodelist: cn09 cn10 cn11 cn12 cn13 cn14 cn015 cn016", and so on. I then set-up a network queue on GNQS (http://www.gnqs.org) to be aware only of cn01, cn09, cn16 and cn25. The rest is done by linda. Hope this help. I'm not sure of this is the most elegant solution and I appreciate any comments. Greetings, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Tatzendpromenade 1a, 07745 Jena, Germany Tel: +49(0)3641 643644 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Tue Apr 4 11:23:02 2000 Received: from gatekeeper.tripos.com (firewall-user@gatekeeper.tripos.com [192.160.145.62]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA23694 for ; Tue, 4 Apr 2000 11:23:01 -0400 Received: (from uucp@localhost) by tripos.com (SMI-8.6) id KAA25514 for <@firewall.tripos.com:CHEMISTRY@ccl.net>; Tue, 4 Apr 2000 10:22:47 -0500 Received: from unknown(172.20.5.15) by gatekeeper.tripos.com via smap (V5.0) id xma025476; Tue, 4 Apr 00 10:22:42 -0500 Received: from tripos.com (thebe [172.20.6.145]) by tripos.com (980919.SGI.STAND) via ESMTP id KAA71602 for ; Tue, 4 Apr 2000 10:22:41 -0500 (CDT) Sender: dlarson@elara.tripos.com Message-ID: <38EA08C0.16E32A44@tripos.com> Date: Tue, 04 Apr 2000 10:22:40 -0500 From: David Larson Reply-To: bclark@tripos.com Organization: Tripos, Inc. http://www.tripos.com X-Mailer: Mozilla 4.6 [en] (X11; U; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: SYMPOSIUM ANNOUNCEMENT AND CALL FOR PAPERS Content-Type: multipart/mixed; boundary="------------87B52D3618599B5AEB63CD94" This is a multi-part message in MIME format. --------------87B52D3618599B5AEB63CD94 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit SYMPOSIUM ANNOUNCEMENT AND CALL FOR PAPERS QSAR in vivo to be held at the American Chemical Society Meeting in Washington, DC August 20-24, 2000 Sponsored by the Division of Computers in Chemistry Theoretical treatments of quantitative structure/activity relationship (QSAR) analysis methods are generally statistical in nature, and so focus on very "clean" cell-free assays, usually involving highly purified enzymes. Many of the day-to-day applications of such methods, however, involve individual living cells, tissue culture or intact higher organisms. Biological processes such as cytotoxicity, secondary inhibitions, changes in the levels of non-target metabolites, uptake and metabolism can influence the results one obtains in such situations, which often necessitates changes in validation, interpretation, or methodology. This symposium will focus on practical ways of getting useful and reliable results out of such work, with primary emphases on case studies, anecdotal insights, and "tricks of the trade" rather than on spectacular statistics per se. The deadline for filing a full abstract is 1 May 2000, but it would be useful for scheduling if you could notify me of your intent to do so sooner. Please use OASys ( http://www.acs.org/meetings/abstract/absdown.html ) for abstract submission if at all possible. Otherwise, you can fill out the MS Word template provided there and e-mail it to me. --------------87B52D3618599B5AEB63CD94 Content-Type: text/x-vcard; charset=us-ascii; name="dlarson.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for David Larson Content-Disposition: attachment; filename="dlarson.vcf" begin:vcard n:Larson;David A. tel;fax:314-647-9241 tel;work:314-647-1099 x-mozilla-html:FALSE org:Tripos, Inc. adr:;;1699 S. Hanley Road;St. Louis;MO;63144; version:2.1 email;internet:dlarson@tripos.com title:Customer Support Scientist note;quoted-printable:Please Send Requests For Technical=0D=0ASupport to 'support@tripos.com'=0D=0A=0D=0ASYBYL 6.6.1/UNITY 4.1.1 now available for download from www.tripos.com=0D=0A x-mozilla-cpt:;-14080 fn:David Larson end:vcard --------------87B52D3618599B5AEB63CD94-- From chemistry-request@server.ccl.net Tue Apr 4 11:24:00 2000 Received: from gatekeeper.tripos.com (firewall-user@gatekeeper.tripos.com [192.160.145.62]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA23706 for ; Tue, 4 Apr 2000 11:24:00 -0400 Received: (from uucp@localhost) by tripos.com (SMI-8.6) id KAA25656 for <@firewall.tripos.com:CHEMISTRY@ccl.net>; Tue, 4 Apr 2000 10:23:46 -0500 Received: from unknown(172.20.5.15) by gatekeeper.tripos.com via smap (V5.0) id xma025616; Tue, 4 Apr 00 10:23:35 -0500 Received: from tripos.com (thebe [172.20.6.145]) by tripos.com (980919.SGI.STAND) via ESMTP id KAA73814 for ; Tue, 4 Apr 2000 10:23:34 -0500 (CDT) Sender: dlarson@elara.tripos.com Message-ID: <38EA08F6.6D1D616C@tripos.com> Date: Tue, 04 Apr 2000 10:23:34 -0500 From: David Larson Reply-To: bclark@tripos.com Organization: Tripos, Inc. http://www.tripos.com X-Mailer: Mozilla 4.6 [en] (X11; U; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: ACS CALL FOR PAPERS: QSAR in vivo Content-Type: multipart/mixed; boundary="------------CDC3FE7784CB450EFEB5BA1D" This is a multi-part message in MIME format. --------------CDC3FE7784CB450EFEB5BA1D Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit SYMPOSIUM ANNOUNCEMENT AND CALL FOR PAPERS QSAR in vivo to be held at the American Chemical Society Meeting in Washington, DC August 20-24, 2000 Sponsored by the Division of Computers in Chemistry Theoretical treatments of quantitative structure/activity relationship (QSAR) analysis methods are generally statistical in nature, and so focus on very "clean" cell-free assays, usually involving highly purified enzymes. Many of the day-to-day applications of such methods, however, involve individual living cells, tissue culture or intact higher organisms. Biological processes such as cytotoxicity, secondary inhibitions, changes in the levels of non-target metabolites, uptake and metabolism can influence the results one obtains in such situations, which often necessitates changes in validation, interpretation, or methodology. This symposium will focus on practical ways of getting useful and reliable results out of such work, with primary emphases on case studies, anecdotal insights, and "tricks of the trade" rather than on spectacular statistics per se. The deadline for filing a full abstract is 1 May 2000, but it would be useful for scheduling if you could notify me of your intent to do so sooner. Please use OASys ( http://www.acs.org/meetings/abstract/absdown.html ) for abstract submission if at all possible. Otherwise, you can fill out the MS Word template provided there and e-mail it to me. --------------CDC3FE7784CB450EFEB5BA1D Content-Type: text/x-vcard; charset=us-ascii; name="dlarson.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for David Larson Content-Disposition: attachment; filename="dlarson.vcf" begin:vcard n:Larson;David A. tel;fax:314-647-9241 tel;work:314-647-1099 x-mozilla-html:FALSE org:Tripos, Inc. adr:;;1699 S. Hanley Road;St. Louis;MO;63144; version:2.1 email;internet:dlarson@tripos.com title:Customer Support Scientist note;quoted-printable:Please Send Requests For Technical=0D=0ASupport to 'support@tripos.com'=0D=0A=0D=0ASYBYL 6.6.1/UNITY 4.1.1 now available for download from www.tripos.com=0D=0A x-mozilla-cpt:;-14080 fn:David Larson end:vcard --------------CDC3FE7784CB450EFEB5BA1D-- From chemistry-request@server.ccl.net Tue Apr 4 14:07:52 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA24458 for ; Tue, 4 Apr 2000 14:07:52 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id LAA03780; Tue, 4 Apr 2000 11:05:17 -0700 (PDT) Message-Id: <200004041805.LAA03780@mailhost.msi.com> Received: from osman-pc.msi.com(146.202.7.202) by mailhost via smap (V2.0) id xma003775; Tue, 4 Apr 00 11:05:16 -0700 X-Sender: osman@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Tue, 04 Apr 2000 11:05:33 -0700 To: CHEMISTRY@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, owner-qsar_society@unil.ch From: "Osman F. Guner" Subject: Second Call for Papers - Virtual-HTS Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id OAA24459 VIRTUAL HIGH-THROUGHPUT SCREENING To be held at the 220th National American Chemical Society Meeting in Washington, D.C., August 20-24, 2000. Sponsored by the Division of Chemical Information (CINF) Co-sponsored by the Medicinal Chemistry (MEDI) and Computational Chemistry (COMP) Divisions Ability to screen virtual libraries and large databases of compounds is at an increasing demand in today's pharmaceutical and biotech industry providing new, and sometimes audacious, challenges to the existing informatics environments. Many parameters can be used for such computational screening, including property-based screening (like ADME properties), structure-, similarity-, and/or pharmacophore-based screening (database searching), as well as rapid docking. In this symposium we will cover all aspects of in silico high-throughput screening technologies. If you have an opinion on this topic, or if you know success stories or failures in this area that you can share with your colleagues, you may want to consider giving a presentation in this symposium. Please use the On-line Abstract System (OASys) to submit your abstracts http://acs.confex.com/acs/220nm/cinf/papers/index.cgi. The deadline for submitting abstracts is April 17, 2000. Cheers...Osman --- Osman F. Güner, Ph.D. Director, Lead Identification & Optimization Molecular Simulations Inc. (858) 799-5341 osman@msi.com http://www.msi.com