From chemistry-request@ccl.net Tue Mar 22 07:04:39 2005 Received: from mb1i1.ns.pitt.edu (mb1i1.ns.pitt.edu [136.142.11.139]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2MC4ZSt015318 for ; Tue, 22 Mar 2005 07:04:35 -0500 Received: from [127.0.0.1] ([136.142.109.16]) by pitt.edu (PMDF V6.2-X27 #30902) with ESMTP id <01LM60I651Y200IE9A$at$mb1i1.ns.pitt.edu> for chemistry$at$ccl.net; Mon, 21 Mar 2005 21:04:34 -0500 (EST) Date: Mon, 21 Mar 2005 21:04:25 -0500 From: Kadir Diri Subject: Re: CCL:Cpu time in Gaussian output In-reply-to: <20050321193629.58541.qmail$at$web50403.mail.yahoo.com> To: Joseph Han Cc: Ian Hovell , "'chemistry'" Message-id: <423F7D29.10400$at$visual1.chem.pitt.edu> MIME-version: 1.0 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en-us, en, tr User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040803 References: <20050321193629.58541.qmail$at$web50403.mail.yahoo.com> X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Also, there is another strong possibility if you are running the program on some cluster and the nodes are writing back to the server. We had such a situation where the wall clock time was an order of magnitude larger compared to the CPU time even for a DFT calculation (which means it was not IO bound) and the only thing the program was writing back to the server was a log file! We spotted the problem, it was the slow communication between the gigabit switch and the nodes. The "auto negotiatiation" was not working properly. The problem was fixed as soon as the switch and the nodes were set to full duplex. Such a problem would be easy to spot looking at the network statistics and the CPU and disk usage. kadir Joseph Han wrote: >IO wait time is a valid explanation especially if there are large files that >are written and read such as during frequency or correlated wavefunction >techniques. > >Another possibility is if you are running in parallel (SMP or Linda), depending >upon the particular operating system, the CPU time reported can be different. >If might be the launching thread, one computation thread, or the total CPU >time. Also, if you are running in parallel, and one thread is delayed, then >there can be a difference in the total Wall time versus CPU time. > >Joseph > >--- Ian Hovell wrote: > > >>Dear CCLers, >>I was asked the other day about the meaning of the cpu time that Gaussian >>reports at the end of a job. The value does not match with the actual time >>of the calculation which can be worked out from the date stamps at the >>beginning and end of the output file.. >>The explanation I gave was that it was the time taken for the calculation on >>the cpu and the difference between that and the reported date stamps was the >>time the computer was waiting to write to the hard disk, transfer data etc. >>Would this be a reasonable explanation for the difference in values? >> >>TIA >> >> >>Ian Hovell - Ph.D. >>NUCLEO DE MODELAGEM MOLECULAR-NMM >>Centro de Tecnologia Mineral - CETEM >>Ministerio da Cincia e da Tecnologia- MCT >>Avenida Ip, No 900 - Cidade Universitaria >>Ilha do Fundo Rio de Janeiro RJ Brasil >>CEP 21941-590 >>tel 00 55 (xx) 3865 7344 ou 3865 - 7216 >>Fax 00 55 (xx) 22602837 ou 2290-4286 >>e-mail hovell$at$cetem.gov.br >> >> >> >> >> > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY$at$ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST$at$ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your is mail bouncing from ccl.net domain due to spam filters, please >use the Web based form from CCL Home Page >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Mon Mar 21 16:15:48 2005 Received: from hotmail.com (bay4-dav24.bay4.hotmail.com [65.54.171.54]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2LLFioK015148 for ; Mon, 21 Mar 2005 16:15:45 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 21 Mar 2005 12:13:40 -0800 Message-ID: Received: from 70.57.95.248 by BAY4-DAV24.phx.gbl with DAV; Mon, 21 Mar 2005 20:13:39 +0000 X-Originating-IP: [70.57.95.248] X-Originating-Email: [rwoodphd^at^msn.com] X-Sender: rwoodphd^at^msn.com From: "Richard Wood" To: Subject: Tinker help needed Date: Mon, 21 Mar 2005 13:13:39 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_04E5_01C52E17.CC06A440" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 Disposition-Notification-To: "Richard Wood" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-OriginalArrivalTime: 21 Mar 2005 20:13:40.0413 (UTC) FILETIME=[791DF6D0:01C52E52] X-Spam-Status: No, score=4.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,FORGED_MUA_OUTLOOK,HTML_50_60,HTML_MESSAGE, MSGID_FROM_MTA_HEADER autolearn=no version=3.0.1 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_04E5_01C52E17.CC06A440 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I am trying to load a monolayer of phospholipids into Tinker and I have = encountered some problems. The file was converted to a pdb file from a = HyperChem hin file and now I am trying to convert it to a Tinker xyz = file. The problem I am having is that the conversion is having a = problem with the nitrogen in the first phospholipid, as it tells me to = check the atom type of the first atom. Does anybody have any = suggestions for me? Thanks in advance, Richard =20 Richard L. Wood, Ph. D. Computational Chemist Hyrum, UT 84319 ------=_NextPart_000_04E5_01C52E17.CC06A440 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
 
I am trying to load a monolayer of phospholipids = into=20 Tinker and I have encountered some problems.  The file was = converted to a=20 pdb file from a HyperChem hin file and now I am trying to convert it to = a Tinker=20 xyz file.  The problem I am having is that the conversion is having = a=20 problem with the nitrogen in the first phospholipid, as it tells me = to=20 check the atom type of the first atom.  Does anybody have any = suggestions=20 for me?
 
Thanks in advance,
Richard
 
 
 
Richard L. Wood, Ph. D.
Computational = Chemist
Hyrum,=20 UT 84319
------=_NextPart_000_04E5_01C52E17.CC06A440-- From chemistry-request@ccl.net Mon Mar 21 17:58:48 2005 Received: from mtaout-c.tc.umn.edu (mtaout-c.tc.umn.edu [160.94.128.21]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2LMwhJQ021703 for ; Mon, 21 Mar 2005 17:58:44 -0500 Received: from qix.software.umn.edu (qix.software.umn.edu [128.101.65.36]) by mtaout-c.tc.umn.edu with ESMTP; Mon, 21 Mar 2005 15:58:41 -0600 (CST) X-Umn-Remote-Mta: [N] qix.software.umn.edu [128.101.65.36] #+LO Received: (from nobody@localhost) by qix.software.umn.edu (8.12.11/8.12.8) id j2LLwfoE001758; Mon, 21 Mar 2005 15:58:41 -0600 Message-Id: <200503212158.j2LLwfoE001758^at^qix.software.umn.edu> Date: Mon, 21 Mar 2005 15:58:40 CST From: Yan Zhao Subject: Re: CCL:W:Activation barrier accuracy with B3LYP To: "Andreas, , Heyden" cc: CHEMISTRY^at^ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; CHARSET=US-ASCII X-Tick-Nemesis: American Maid X-remote-user-ip: 160.94.96.143 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net See : Tests of Second-Generation and Third-Generation Density Functionals for Thermochemical Kinetics Y. Zhao, J. Pu, B. J. Lynch, and D. G. Truhlar, Phys. Chem. Chem. Phys. 6, 673 (2004). Development and Assessment of a New Hybrid Density Functional Model for Thermochemical Kinetics Y. Zhao, B. J. Lynch, and D. G. Truhlar, J. Phys. Chem. A. 108, 2715 (2004). "Hybrid Meta Density Functional Theory Methods for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions: The MPW1B95 and MPWB1K Models and Comparative Assessments for Hydrogen Bonding and van der Waals Interactions," Y. Zhao and D. G. Truhlar, J. Phys. Chem. A 108, 6908 (2004). Benchmark Database of Barrier Heights for Heavy Atom Transfer, Nucleophilic Substitution, Association, and Unimolecular Reactions and its Use to Test Theoretical Methods, Y. Zhao and D. G. Truhlar, J. Phys. Chem. A. 109, 2012 (2005). Yan On 21 Mar 2005, Andreas, , Heyden wrote: > Hi, > > I have heard that DFT in general underestimates activation barriers for > chemical reactions. Does anyone know if this is also the case for hybrid > functionals like B3LYP? > If anyone knows good references please let me know. > > Regards, > Andreas > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line > and send your message to: CHEMISTRY^at^ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST^at^ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > *************************************** Yan Zhao yzhao^at^chem.umn.edu Smith Hall 232 (612)-625-5311 Department of Chemistry University of Minnesota 207 Pleasant St SE Minneapolis, MN 55455 *************************************** From chemistry-request@ccl.net Tue Mar 22 09:32:41 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2MEWfWi021211 for ; Tue, 22 Mar 2005 09:32:41 -0500 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j2MEWfFi021210 for chemistry^at^ccl.net; Tue, 22 Mar 2005 09:32:41 -0500 Date: Tue, 22 Mar 2005 09:32:41 -0500 Message-Id: <200503221432.j2MEWfFi021210^at^server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request^at^ccl.net using -f From: "Juan, , Elezgaray" To: chemistry^at^ccl.net X-Web-Message-Number: 050322092816-21009 Subject: W:Biomolecular Simulations Meeting Bordeaux, 2&3 Sept. 2005 X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net ===================== FIRST ANNOUNCEMENT ===================== BIOMOLECULAR SIMULATIONS - Satellite meeting to the International Biophysics Congress, Montpellier 2005 BORDEAUX-FRANCE: 2 & 3 SEPTEMBER 2003 http://www.iecb.u-bordeaux.fr/satellite2005/ ============================================================== Dear colleague, We are organizing a satellite meeting dedicated to Biomolecular Simulations in Bordeaux on September 2nd and 3rd 2005 The following speakers have already confirmed their participation: Paolo Carloni (Sissa, Italy) Christophe Chipot (Nancy, France) Jonathan Essex (Southampton, UK) Angel Garcia (Los Alamos, USA) Helmut Grubmller (Gttingen, Germany) Siewert-Jan Marrink (Groningen, The Netherlands) We kindly invite you to log on to our website for further information: http://www.iecb.u-bordeaux.fr/satellite2005/ You can also download a flyer describing this Summer School by following this link: http://www.iecb.u-bordeaux.fr/satellite2005/biomolsim.pdf Yours sincerely, The organisers Marc Baaden (IBPC, Paris) Juan Elezgaray (IECB, Bordeaux) Michel Laguerre (IECB, Bordeaux) Mark Sansom (LMB, Oxford) From chemistry-request@ccl.net Tue Mar 22 07:04:41 2005 Received: from mb1i1.ns.pitt.edu (mb1i1.ns.pitt.edu [136.142.11.139]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2MC4ZSv015318 for ; Tue, 22 Mar 2005 07:04:39 -0500 Received: from [127.0.0.1] ([136.142.109.16]) by pitt.edu (PMDF V6.2-X27 #30902) with ESMTP id <01LM60ST0PO600H38J^at^mb1i1.ns.pitt.edu> for chemistry^at^ccl.net; Mon, 21 Mar 2005 21:13:09 -0500 (EST) Date: Mon, 21 Mar 2005 21:13:00 -0500 From: Kadir Diri Subject: Re: CCL:Getting hessian out of Gaussian jobs In-reply-to: <423F02D5.2090908^at^yahoo.it> To: Michele Lunelli Cc: chemistry^at^ccl.net Message-id: <423F7F2C.5010805^at^visual1.chem.pitt.edu> MIME-version: 1.0 Content-type: text/plain; format=flowed; charset=ISO-8859-1 Content-transfer-encoding: 7bit X-Accept-Language: en-us, en, tr User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040803 References: <423F02D5.2090908^at^yahoo.it> X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Gaussian usually prints extra stuff by just re-reading the checkpoint file and including the guess=only option. This should take only a few seconds to do, and I bet it will give the force constants, though I am not 100% sure. You may want to include the #P option too. kadir Michele Lunelli wrote: > Tom Sundius wrote: > >> The hessian stored in the checkpoint file. If you did not have the p >> option on your >> route card ("#p...") you will not get the force constants listed >> (except for >> the list in the archive part, which is obviously missing from your >> output). >> Unfortunately the NewZMat utility does not seem to have an option to >> output >> the force constants in the check point file, so I guess that you will >> have >> to run a simple freq calculation with freq=readfc and geom=check >> guess=check, but it should be rather fast. >> > > You can use the formchk utility to format the checkpoint file, so you > can read the hessian matrix stored inside. Take care, all units are > atomic units, and being a symmetric matrix only one half is printed. > > Regards, > Michele Lunelli > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY^at^ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST^at^ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > From chemistry-request@ccl.net Tue Mar 22 03:23:45 2005 Received: from atlas.pnl.gov (atlas.pnl.gov [130.20.248.194]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2M8Nd7g006178 for ; Tue, 22 Mar 2005 03:23:39 -0500 Received: from emailfilter2.pnl.gov (emailfilter2.pnl.gov [130.20.248.24]) by pnl.gov (PMDF V6.2-1 #31042) with ESMTP id <0IDQ001TC3IA0M^at^pnl.gov> for chemistry^at^ccl.net; Mon, 21 Mar 2005 14:22:58 -0800 (PST) Received: from pnlmse21.pnl.gov (Not Verified[130.20.128.55]) by emailfilter2.pnl.gov with NetIQ MailMarshal (v5.5.6.6) id ; Mon, 21 Mar 2005 14:22:36 -0800 Received: from pnlmse27.pnl.gov ([130.20.128.36]) by pnlmse21.pnl.gov with Microsoft SMTPSVC(6.0.3790.211); Mon, 21 Mar 2005 14:22:35 -0800 Date: Mon, 21 Mar 2005 14:22:35 -0800 From: "DeJong, Wibe A" Subject: ACS symposium in Washington, DC: Chemistry in the Large -- Teraflop Computing and beyond To: chemistry^at^ccl.net Message-id: <0DF798CBF125BF4AA1227F26431C29BDEBE1A8^at^pnlmse27.pnl.gov> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-type: text/plain; charset=us-ascii Thread-Topic: ACS symposium in Washington, DC: Chemistry in the Large -- Teraflop Computing and beyond Thread-Index: AcUuZHuTRmhvdlu5Q6C6DsQYLtlKGg== Content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-OriginalArrivalTime: 21 Mar 2005 22:22:35.0732 (UTC) FILETIME=[7BB9F940:01C52E64] X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j2M8Nj7g006182 ANNOUNCEMENT OF ACS SYMPOSIUM: Chemistry in the Large -- Teraflop Computing and beyond Organizers: Theresa L. Windus, Wibe A. de Jong (EMSL/PNNL) You are cordially invited to submit papers for the symposium "Chemistry in the Large - Teraflop Computing and beyond". This symposium will take place as part of the COMP section symposia at the 230th American Chemical Society National Meeting, August 28-September 1 in Washington, DC. The goal of this symposium is to discuss current and future applications and challenges for computational chemistry research on large teraflop computer systems and beyond. What are the large scientific challenges that are being solved today? What will the science be that can be done on tera- and petascale computers? Do we need to change the algorithms and/or paradigms in computational chemistry? Sessions will include topics such as: * Searching for chemical accuracy: terascale computing with high accuracy ab inito methodologies * Simulating biological processes on thousands of processors * Teraflop computing in geochemistry, nanoscience and catalysis * Making computational chemistry codes efficient beyond the terascale In addition a general session on future scientific challenges in computational chemistry on petaflop computing platforms is available. The deadline for submittal of abstracts for the symposium is April 25, 2005. So, please submit soon! 123456789012345678901234567890123456789012345678901234567890123456789012 34567890 Note: This symposium is incorrectly listed with "Invited papers only" in the ACS OASYS abstract system (http://oasys.acs.org/oasys.htm). The organizers strongly encourage and welcome the submission of CONTRIBUTED papers. In addition, the title currently listed in OASYS is "Chemistry in the Large -- Multiple Processor Computing". More information about this symposium can be obtained from the organizers (Theresa.Windus^at^pnl.gov, bert.dejong^at^pnl.gov). From chemistry-request@ccl.net Tue Mar 22 14:13:13 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2MJDA6o000584 for ; Tue, 22 Mar 2005 14:13:10 -0500 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j2MJDACG000583 for chemistry)at(ccl.net; Tue, 22 Mar 2005 14:13:10 -0500 Date: Tue, 22 Mar 2005 14:13:10 -0500 Message-Id: <200503221913.j2MJDACG000583)at(server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request)at(ccl.net using -f From: "Archilles, , Tao" To: chemistry)at(ccl.net X-Web-Message-Number: 050322141234-542 Subject: W:The optimization of my molecule by PCM model failed. X-Spam-Status: No, score=-2.3 required=5.0 tests=ALL_TRUSTED, FROM_ENDS_IN_NUMS autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear all, I am currently using Gaussian 98 to optimize one molecule in water by PCM modle. Since in the previous optimization without any constraint, the molecule always changes between several very different structures, and the energies are very different: one is much higher than the other. The optimization process keeps the molecule back and forth between these structures until the maximum optimization steps exceeded. Therefore, I applied a geomitry constraint on the stucture to prevent the unwanted structure(with higher energy). unfortunately, the similar thing happend again: the structure keeps changing,and never converges. Why does this happen when I use PCM model? How can I prevent this? Any suggestions and help will be appreciated. Thanks a lot. Archilles. Here are my .com file: %nproc=2 B3LYP/6-31+G* opt=(Maxcycle=256,ModRedundant) freq SCRF=(PCM,Solvent=1) B3LYP6-31+GCAIR opt 0 1 C 0.089430 -0.342821 -0.022541 C -0.854579 0.702803 -0.005540 C 1.525406 -0.254975 -0.005510 N -0.746882 2.048119 -0.022172 N -2.063701 0.071033 0.018253 C -1.844040 -1.292458 0.011875 O 2.310191 -1.201398 0.005860 N -0.573857 -1.572363 -0.014770 O 1.972599 1.034613 0.007162 H 0.176006 2.475660 -0.028025 H -1.559141 2.647965 0.103511 H -2.982234 0.504484 -0.022494 H -2.661868 -2.003665 0.031258 H 2.958705 1.007028 0.072683 B 4 9 F 2.80 3.00 Since the log file is very long, you can get it from here: http://www.chemistry.ohio-state.edu/~ptao/log/pcmopt.log From chemistry-request@ccl.net Tue Mar 22 16:34:24 2005 Received: from mprelay.uc.edu (mprelay.uc.edu [129.137.3.48]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2MLYLRw007373 for ; Tue, 22 Mar 2005 16:34:21 -0500 Received: from mirapoint.uc.edu (webmail.uc.edu [10.23.4.254]) by mprelay.uc.edu (MOS 3.4.7-GR) with ESMTP id CRL82994; Tue, 22 Mar 2005 16:34:19 -0500 (EST) Received: from 10.52.7.99 by mirapoint.uc.edu (MOS 3.4.7-GR) with HTTP/1.1; Tue, 22 Mar 2005 16:34:19 -0500 Date: Tue, 22 Mar 2005 16:34:19 -0500 From: Chi-Yuan Chen Subject: Problem with ensembles in Gaussian03!! To: Computational Chemistry List X-Mailer: Webmail Mirapoint Direct 3.4.7-GR MIME-Version: 1.0 Message-Id: <9a3876ff.e137f79d.828d500)at(mirapoint.uc.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.8 required=5.0 tests=DEAR_SOMETHING autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear Sirs: Does anyone know how to set up ensembles, like NVT or NVE, for dynamics calculations(BOMD or ADMP) in Gaussian03? I very appreciate your help! Chi-Yuan Chen Graduate Student OBR Center for Computer-Aided Molecular Design Department of Chemical and Materials Engineering University of Cincinnati Cincinnati, Ohio 45221-0171 Email: chenca)at(email.uc.edu From chemistry-request@ccl.net Tue Mar 22 21:59:50 2005 Received: from hotmail.com (bay4-dav19.bay4.hotmail.com [65.54.170.123]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2N2xjWe017744 for ; Tue, 22 Mar 2005 21:59:46 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 22 Mar 2005 17:57:44 -0800 Message-ID: Received: from 70.57.95.248 by BAY4-DAV19.phx.gbl with DAV; Wed, 23 Mar 2005 01:57:44 +0000 X-Originating-IP: [70.57.95.248] X-Originating-Email: [rwoodphd :: msn.com] X-Sender: rwoodphd :: msn.com From: "Richard Wood" To: References: Subject: Re: CCL:Tinker help needed Date: Tue, 22 Mar 2005 18:57:44 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_05E5_01C52F11.07C57DE0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 Disposition-Notification-To: "Richard Wood" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-OriginalArrivalTime: 23 Mar 2005 01:57:44.0434 (UTC) FILETIME=[B4535520:01C52F4B] X-Spam-Status: No, score=4.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,FORGED_MUA_OUTLOOK,HTML_60_70,HTML_MESSAGE, MSGID_FROM_MTA_HEADER autolearn=no version=3.0.1 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_05E5_01C52F11.07C57DE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, Thanks to Geoff Hutchison, I was able to solve the conversion problem. = Now the question I have is what force field that works with Tinker is = good to use for phospholipids? TIA, Richard Richard L. Wood, Ph. D. Computational Chemist Hyrum, UT 84319 ----- Original Message -----=20 From: Richard Wood=20 To: CHEMISTRY :: ccl.net=20 Sent: Monday, March 21, 2005 1:13 PM Subject: CCL:Tinker help needed Hi all, I am trying to load a monolayer of phospholipids into Tinker and I = have encountered some problems. The file was converted to a pdb file = > from a HyperChem hin file and now I am trying to convert it to a Tinker = xyz file. The problem I am having is that the conversion is having a = problem with the nitrogen in the first phospholipid, as it tells me to = check the atom type of the first atom. Does anybody have any = suggestions for me? Thanks in advance, Richard Richard L. Wood, Ph. D. Computational Chemist Hyrum, UT 84319 ------=_NextPart_000_05E5_01C52F11.07C57DE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
 
Thanks to Geoff Hutchison, I was able to solve = the=20 conversion problem.  Now the question I have is what force field = that works=20 with Tinker is good to use for phospholipids?
 
TIA,
Richard
 
 
Richard L. Wood, Ph. D.
Computational Chemist
Hyrum, UT=20 84319
----- Original Message -----
From:=20 Richard = Wood=20
Sent: Monday, March 21, 2005 = 1:13=20 PM
Subject: CCL:Tinker help = needed

Hi all,
 
I am trying to load a monolayer of = phospholipids into=20 Tinker and I have encountered some problems.  The file was = converted to a=20 pdb file from a HyperChem hin file and now I am trying to convert it = to a=20 Tinker xyz file.  The problem I am having is that the conversion = is=20 having a problem with the nitrogen in the first phospholipid, as = it tells=20 me to check the atom type of the first atom.  Does anybody have = any=20 suggestions for me?
 
Thanks in advance,
Richard
 
 
 
Richard L. Wood, Ph. D.
Computational=20 Chemist
Hyrum, UT 84319
------=_NextPart_000_05E5_01C52F11.07C57DE0-- From chemistry-request@ccl.net Tue Mar 22 19:48:32 2005 Received: from mx1.ustc.edu.cn (ns.ustc.edu.cn [202.38.64.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2N0mQAW013802 for ; Tue, 22 Mar 2005 19:48:27 -0500 Received: from image ([202.38.82.38]) by mx1.ustc.edu.cn (8.11.6/8.11.6) with SMTP id j2N0ZXR21652 for ; Wed, 23 Mar 2005 08:35:33 +0800 Message-ID: <001101c52f41$bea60c20$265226ca@image> From: To: "CCL" Subject: How to determine spin multiplicity for a given silver cluster Date: Wed, 23 Mar 2005 08:46:25 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000E_01C52F84.CBDFAF70" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, score=1.2 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_WHOIS,HTML_50_60,HTML_MESSAGE,MIME_BASE64_TEXT, NO_REAL_NAME autolearn=no version=3.0.1 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_000E_01C52F84.CBDFAF70 Content-Type: text/plain; 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Tue, 22 Mar 2005 20:18:55 -0500 Received: from exgw1-mel.nexus.csiro.au (138.194.3.56) by vic-ironport-ext-out3.csiro.au with ESMTP; 23 Mar 2005 10:48:26 +1100 X-BrightmailFiltered: true X-Brightmail-Tracker: AAAAAQAAA+k= X-IronPort-AV: i="3.91,112,1110114000"; d="scan'208,217"; a="31033165:sNHT52908260" Received: from [138.194.51.27] ([138.194.51.27]) by exgw1-mel.nexus.csiro.au with Microsoft SMTPSVC(5.0.2195.6713); Wed, 23 Mar 2005 10:48:03 +1100 Mime-Version: 1.0 Message-Id: Date: Wed, 23 Mar 2005 10:48:00 +1100 To: chminf-l :: listserv.indiana.edu, chemistry :: server.ccl.net, qsar_society :: accelrys.com From: Dave Winkler Subject: Pacifichem - abstracts closing on 13 April Content-Type: multipart/alternative; boundary="============_-1100587213==_ma============" X-OriginalArrivalTime: 22 Mar 2005 23:48:03.0932 (UTC) FILETIME=[96C8F1C0:01C52F39] X-Spam-Status: No, score=-3.5 required=5.0 tests=DNS_FROM_RFC_WHOIS, HTML_50_60,HTML_FONT_BIG,HTML_MESSAGE,RCVD_IN_BSP_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net --============_-1100587213==_ma============ Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: quoted-printable PACIFICHEM 2005 December 15-20 2005, Honolulu, Hawaii http://www.pacifichem.org Pacifichem is one of the world's largest chemical=20 congresses, presenting in excess of 5000 papers=20 in a diverse range of topics, and attracting top=20 researchers in many fields of chemistry. It is=20 held in the major hotels on Waikiki beach. The=20 congress is somewhat unusual as it is made up of=20 a large number of symposia that have been=20 proposed as hot areas by researchers. Although=20 it is very large, it is streamed to avoid clashes=20 between symposia who may have audiences with=20 overlapping interests. The deadline for receipt of abstracts is 13th=20 April 2005; late submissions will not be accepted. Symposium number 7 in the Medicinal Chemistry theme is Complexity and Related Computational Methods in Bioactive Discovery Many chemical and biological systems are 'complex=20 systems' that exhibit emergent properties and=20 behaviour often not well modelled by reductionist=20 approaches. Novel complex systems science tools=20 such as neural networks, and other agent-based=20 methods, genetic algorithms and genetic=20 programming, artificial ant colonies, particle=20 swarms, nonlinear methods, knot theory etc are=20 finding increased application in chemistry and=20 bioactive discovery and development (drugs and=20 ag/vet agents). This symposium will provide an=20 opportunity for participants to present their=20 work on these new methods, and to probe the=20 extent to which a complex systems science (CSS)=20 approach to bioactive discovery is useful for=20 developing new leads. It will challenge=20 participants to explore other CSS methods in=20 modelling chemical and biological systems and=20 developing novel bioactive agents. The symposium=20 will also probe the overlap between traditional=20 computational approaches to drug discovery and=20 development, ADMET modelling, and related fields=20 and methods of complexity. The symposium is very=20 broad based and will accept any papers relating=20 to computational approaches to bioactive design,=20 discovery and development, and complexity methods=20 applied to chemistry and bioactive discovery. Invited speaker Indicative topic Dimitris Agrafiotis (J&J) Self-organization and drug discovery Gerry Maggiora (Arizona) Rough sets,=20 multi-sets, information theory and mutual=20 information Bernard Testa (Lausanne)=20 Emergence-dissolvence, molecules as complex=20 adaptive systems Tim Clark (Erlangen) Non-linear mapping of physical property space John Finnigan (CSIRO) Overview of Complex Systems =46rank Burden (Scimetrics) Agent-based=20 modelling applications in chemistry and biology Prof. Yuzong Chen (NUS) Machine learning and data mining. Monty Kier (VCU) Cellular=20 automata modelling of ligand diffusion on proteins Val Gillett (Sheffield) Multiobjective optimization and genetic programmin= g Tudor Oprea Interface between=20 chemical and biological complex systems Martyn Ford (Portsmouth) Complexity in drug design John Gasteiger (Erlangen) Molecular evolution using genetic algorithms Jean-Fran=E7ois Truchon (Merck)Deterministic algorithms for reagent selectio= n Peter Stadler (Leipzig) Functional organization in molecular systems Nigel Richards (Florida) Genetic=20 algorithms in docking, computational enzymology Greg Dewey (Keck Inst) Complexity in biology Hideaki Suzuki Biologically-mimetic computing Contributed papers are very welcome. All=20 delegates wishing to present a paper (invited or=20 contributed, oral or poster) must submit an=20 abstract on-line. Please read the guidelines=20 first. The electronic abstract system can then be=20 accessed via the Online Abstract Login button on=20 the web site. I look forward to meeting you in Honolulu next December -- Cheers, Dave Prof. David A. Winkler FRACI CChem CPChem Email: dave.winkler :: csiro.au CSIRO Centre for Complexity in Drug Design Voice: 61-3-9545-2477 Senior Principal Research Scientist Fax: 61-3-9545-2561 CSIRO Molecular Science or 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au Join us at CONNECT2005=20 (http://www.pco.com.au/connect2005/) 3-7 July=20 2005, the Royal Australian Chemical Institute's=20 National Convention, the 11th Asian Chemical=20 Congress in Seoul, August 24-26 2005=20 (http://www.11acc.org/), and Pacifichem 2005 in=20 Honolulu December 15-20=20 (http://www.pacifichem.org). --============_-1100587213==_ma============ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Pacifichem - abstracts closing on 13 April
PACIFICHEM 2005
December 15-20 2005, Honolulu, Hawaii

http://www.pacifichem.org

Pacifichem is one of the world's largest chemical congresses, presenting in excess of 5000 papers in a diverse range of topics, and attracting top researchers in many fields of chemistry.  It is held in the major hotels on Waikiki beach.  The congress is somewhat unusual as it is made up of a large number of symposia that have been proposed as hot areas by researchers.  Although it is very large, it is streamed to avoid clashes between symposia who may have audiences with overlapping interests.

The deadline for receipt of abstracts is 13th April 2005; late submissions will not be accepted.

Symposium number 7 in the Medicinal Chemistry theme is

Complexity and Related Computational Methods in Bioactive Discovery

Many chemical and biological systems are 'complex systems' that exhibit emergent properties and behaviour often not well modelled by reductionist approaches. Novel complex systems science tools such as neural networks, and other agent-based methods, genetic algorithms and genetic programming, artificial ant colonies, particle swarms, nonlinear methods, knot theory etc are finding increased application in chemistry and bioactive discovery and development (drugs and ag/vet agents). This symposium will provide an opportunity for participants to present their work on these new methods, and to probe the extent to which a complex systems science (CSS) approach to bioactive discovery is useful for developing new leads. It will challenge participants to explore other CSS methods in modelling chemical and biological systems and developing novel bioactive agents. The symposium will also probe the overlap between traditional computational approaches to drug discovery and development, ADMET modelling, and related fields and methods of complexity. The symposium is very broad based and will accept any papers relating to computational approaches to bioactive design, discovery and development, and complexity methods applied to chemistry and bioactive discovery.

    Invited speaker                     Indicative topic

Dimitris Agrafiotis (J&J)         Self-organization and drug discovery                         
Gerry Maggiora (Arizona)          Rough sets, multi-sets, information theory and mutual information
Bernard Testa (Lausanne)          Emergence-dissolvence, molecules as complex adaptive systems                         
Tim Clark (Erlangen)      Non-linear mapping of physical property space
John Finnigan (CSIRO)     Overview of Complex Systems                          
Frank Burden (Scimetrics)         Agent-based modelling applications in chemistry and biology                          
Prof. Yuzong Chen (NUS)   Machine learning and data mining.            
Monty Kier (VCU)                  Cellular automata modelling of ligand diffusion on proteins  
Val Gillett (Sheffield)   Multiobjective optimization and genetic programming          
Tudor Oprea               Interface between chemical and biological complex systems            
Martyn Ford (Portsmouth)          Complexity in drug design            
John Gasteiger (Erlangen)         Molecular evolution using genetic algorithms 
Jean-Fran=E7ois Truchon (Merck)Deterministic algorithms for reagent selection
Peter Stadler (Leipzig)   Functional organization in molecular  systems                
Nigel Richards (Florida)          Genetic algorithms in docking, computational enzymology              
Greg Dewey (Keck Inst)    Complexity in biology        
Hideaki Suzuki            Biologically-mimetic computing               

Contributed papers are very welcome.  All delegates wishing to present a paper (invited or contributed, oral or poster) must submit an abstract on-line. Please read the guidelines first. The electronic abstract system can then be accessed via the Online Abstract Login button on the web site.

I look forward to meeting you in Honolulu next December
--
Cheers,
Dave

Prof. David A. Winkler FRACI CChem CPChem    Email: dave.winkler :: csiro.au  
CSIRO Centre for Complexity in Drug Design      Voice: 61-3-9545-2477
Senior Principal Research Scientist                Fax:  61-3-9545-2561
CSIRO Molecular Science                               or 61-3-9545-2446
Private Bag 10,Clayton South MDC 3169        http://www.csiro.au
Australia                                    http://www.molsci.csiro.au

Join us at CONNECT2005 (http://www.pco.com.au/connect2005/) 3-7 July 2005, the Royal Australian Chemical Institute's National Convention, the 11th Asian Chemical Congress in Seoul, August 24-26 2005 (http://www.11acc.org/), and Pacifichem 2005 in Honolulu December 15-20 (http://www.pacifichem.org).
--============_-1100587213==_ma============-- From chemistry-request@ccl.net Tue Mar 22 21:26:07 2005 Received: from smtp.cnc.com (smtp.chemnavigator.com [12.22.207.36]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2N2Q1aa016889 for ; Tue, 22 Mar 2005 21:26:02 -0500 Received: by smtp.chemnavigator.com with Internet Mail Service (5.5.2653.19) id ; Tue, 22 Mar 2005 16:32:47 -0800 Message-ID: <2B0CF44FC7E8D3118B4900508BA599EF01ACF022 #%# smtp.chemnavigator.com> From: Duncan Beniston To: "'chemistry #%# ccl.net'" Subject: New structure analysis & virtual screening tools Date: Tue, 22 Mar 2005 16:32:38 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net ChemNavigator is pleased to announce the availability of new chemical structure management and analysis software tools and the release of 3DPL Version 3.4 for virtual screening. Please use the URL below to learn more. CncTranslate - Cheminformatics Utility Program provides a broad range of cheminformatics software utilities ranging from basic file conversions (SD, SLN, SMILES and more) to 2D structure searching to 3D coordinate generation. Use CncTranslate to build your own text file based cheminformatics system. CncMCS - New maximum common substructure analysis tool. CncDiverse - A software tool for the selection of diverse chemical libraries > from within a very large database of chemical structures. 3DPL(tm) Version 3.4 - Fast, Exhaustive, Flexible 3D Virtual Screening based on a combination of 3D flexible searching and molecular docking techniques. Now available for use within your organization. These tools are available under both commercial and academic license fee models. Contact us to learn more about our Academic Collaboration Program for Free Access to these tools. Learn more at: http://www.chemnavigator.com/cnc/products/products.asp or contact: Duncan Beniston Director, Sales & Business Development ChemNavigator + 858-450-9740, x1373 dbeniston #%# chemnavigator.com www.chemnavigator.com