From chemistry-request@server.ccl.net Wed Dec 19 08:12:55 2001 Received: from web15005.mail.bjs.yahoo.com ([61.135.128.8]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fBJDCsU18738 for ; Wed, 19 Dec 2001 08:12:54 -0500 Message-ID: <20011219131226.8144.qmail@web15005.mail.bjs.yahoo.com> Received: from [61.151.253.47] by web15005.mail.bjs.yahoo.com via HTTP; Wed, 19 Dec 2001 21:12:26 CST Date: Wed, 19 Dec 2001 21:12:26 +0800 (CST) From: =?gb2312?q?yong=20pei?= Subject: MD at constant temperature To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear sir I have some problems when I perform MD at constant temperature . I combine Nose-Hoover scheme with velocity-Verlet algorithm ,which is write as : a(I,J)=F(I,J)/ATOM_M-DELTA_T*(KINETIC-3*NATOM*1.38E-23* TARGET_TEMPERATURE)*V(I,J)/PISTON where a(I,J) the accelation of atom I ATOM_M the weight of atom I KINETIC the kinetic of the total atoms V(I,J) the velocity of the atom I DELTA_T the time step with value 1.0e-14 PISTON the parameter in the Nose-Hoover method TARGET_TEMPERATURE the disire temperature NATOM the number of atoms in the system But I can't get the correct temperature with above algorithm .Are there any errors in it? Anyway , are there any programs about constant NPT OR NVT ,NPH downlord from internet freely? Regards, Yong Pei _________________________________________________________ Do You Yahoo!? 登录免费雅虎电邮! http://mail.yahoo.com.cn 无聊？郁闷？高兴？没理由？都来聊天吧！—— 雅虎全新聊天室! http://cn.chat.yahoo.com/c/roomlist.html From chemistry-request@server.ccl.net Tue Dec 18 18:45:57 2001 Received: from web21210.mail.yahoo.com ([216.136.175.253]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fBINjvU09111 for ; Tue, 18 Dec 2001 18:45:57 -0500 Message-ID: <20011218234536.99392.qmail@web21210.mail.yahoo.com> Received: from [129.109.166.146] by web21210.mail.yahoo.com via HTTP; Tue, 18 Dec 2001 15:45:36 PST Date: Tue, 18 Dec 2001 15:45:36 -0800 (PST) From: Ovidiu Ivanciuc Subject: Special issue dedicated to Dr. Milan Randic To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii First Circular - Call for Papers Internet Electronic Journal of Molecular Design, http://www.biochempress.com Special Issue - dedicated to Professor Milan Randic on theoccasion of the 70th birtday You are invited to contribute a paper to the special issue of the Internet Electronic Journal of Molecular Design, http://www.biochempress.com, dedicated to Professor Milan Randic. The topic of the paper can be any original contribution regarding computer-assisted molecular design applications in chemistry, biochemistry, biology, chemical and pharmaceutical industry, including: - Computer-aided organic synthesis - Chemical structure and reactivity investigated with molecular mechanics, quantum chemistry, and molecular dynamics methods - Definition, calculation and evaluation of novel structural descriptors - Chemical database searching, clustering, similarity and diversity measure - Prediction of physico-chemical properties with Quantitative Structure-Property Relationships (QSPR) - Quantitative Structure-Activity Relationships (QSPR) models for biological activity, toxicity, mutagenicity, and carcinogenicity - Prediction of chromatographic retention parameters and design of stationary phases for chromatography - Modeling of bioorganic compounds, such as proteins, enzymes, and nucleic acids - New algorithms for modeling chemical and biochemical phenomena, such as global optimization methods, simulated annealing, neural networks, genetic algorithms, ant colony algorithm - Design of special materials, catalysts, high energy compounds, polymers, molecular machines If you have any questions regarding this special issue, please contact me by E-mail at: iejmd@yahoo.com For instructions for contributors send an Email to iejmd@yahoo.com or to editor@biochempress.com A Word file with the instructions for contributors is available at the following Web site: http://www.biochempress.com If you decide to contribute a paper, please note these important deadlines: Title of manuscript and authors submitted by Email to iejmd@yahoo.com : January 30, 2002 Manuscript submitted by Email to iejmd@yahoo.com : March 30, 2002 If you want to contribute a paper, but need more time for the submission, send an E-mail with an estimated time of submission. Best regards, Dr. Mircea V. Diudea __________________________________________________ Do You Yahoo!? Check out Yahoo! Shopping and Yahoo! Auctions for all of your unique holiday gifts! Buy at http://shopping.yahoo.com or bid at http://auctions.yahoo.com From chemistry-request@server.ccl.net Tue Dec 18 12:17:39 2001 Received: from bos-nt6.wkap.com ([204.164.87.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBIHHdU02108 for ; Tue, 18 Dec 2001 12:17:39 -0500 Received: from bos-nt5.wkap.com (bos-nt5.wkap.com [204.164.86.10]) by bos-nt6.wkap.com (Build 101 8.9.3/NT-8.9.3) with SMTP id MAA07433 for ; Tue, 18 Dec 2001 12:16:12 -0500 Received: by BOS-EXCH with Internet Mail Service (5.5.2653.19) id ; Tue, 18 Dec 2001 12:11:20 -0500 Message-ID: <725A164A2A84214DAAAA1CBDF7CEA098012370@nyc-exch1.wkap.com> From: Scott Starr To: "'chemistry@ccl.net'" Subject: New Book: Free Energy Calculations in Rational Drug Design Date: Tue, 18 Dec 2001 12:15:26 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Free Energy Calculations in Rational Drug Design Edited by M. Rami Reddy and Mark D. Erion Free energy calculations represents the most accurate computational method available for predicting enzyme inhibitor binding affinities. Advances in computer power in the 1990's enabled the practical application of these calculations in rational drug design. This book represents the first comprehensive review of this growing area of research and covers the basic theory underlying the method, numerous state-of-the art strategies designed to improve throughput, and dozens of examples wherein free energy calculations were used to design and evaluate potential drug candidates. For More Information, Visit: http://www.wkap.nl/prod/b/0-306-46676-7 Order online at www.wkap.nl or www.wkap.com From chemistry-request@server.ccl.net Wed Dec 19 05:22:11 2001 Received: from ms.cdtltd.co.uk ([193.128.61.145]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBJAMAU16499 for ; Wed, 19 Dec 2001 05:22:11 -0500 Received: from cdtpost.cdtltd.co.uk (unverified) by ms.cdtltd.co.uk (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Wed, 19 Dec 2001 10:21:49 +0000 Received: by ThisAddressDoesNotExist with Internet Mail Service (5.5.2653.19) id ; Wed, 19 Dec 2001 10:24:59 -0000 Message-ID: <06E726E44BB2D511A58A0090278A10FF1866CB@ThisAddressDoesNotExist> From: Ilaria Grizzi To: "'chemistry@ccl.net'" Subject: seeking software for copolymerisation statistics Date: Wed, 19 Dec 2001 10:24:53 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi, I am looking for a software to predict copolymer sequencing (given monomer reactivity) for a step-growth polymerisation process. Also is there a general softwarre to calculate average blocks lengths with measured triades distribution? Any help will be appreciated. Thanks in advance Have a happy X-mas Ilaria igrizzi@cdtltd.co.uk ilaria.grizzi@btinternet.com ********************************************************************** The information and materials contained in this e-mail and any attachment are confidential and solely for the use of the intended recipient. Any dissemination, distribution, copying or use of this communication without prior permission of CDT is strictly prohibited. ********************************************************************** From chemistry-request@server.ccl.net Wed Dec 19 10:01:19 2001 Received: from hamiltonian.chem.cornell.edu (IDENT:QW7z+2dKsq8ObLZvrcvkfDBunXwj6f2j@[128.253.229.83]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBJF1Jq01082 for ; Wed, 19 Dec 2001 10:01:19 -0500 Received: from localhost (marketa@localhost) by hamiltonian.chem.cornell.edu (8.11.6/8.11.2) with ESMTP id fBJF0TG02381 for ; Wed, 19 Dec 2001 10:00:29 -0500 Date: Wed, 19 Dec 2001 10:00:29 -0500 (GST) From: To: Subject: g98/linux: a disk usage problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, in order to use maximum of my disk capacity for a "large" MP2 calc., I have splitted the *rwf file in the following way: -- %RWF=a,1800MB,b,1800MB,c,1800MB,d,1800MB,e,1800MB,f,1800MB,g,1800MB #p mp2/6-311+G(2d,p) nmr guess=read maxdisk=12GB -- At the disk-space most demanding point of the calc (correlated calc of nmr) the calc crashes as it apparently requires more disk space than it was allowed to allocate: -- Reordered first order wavefunction length = 434653128 WUsed= 342120743 WInt= 4679168 WEnd= 752340992 Dk804= -331254506 Dk1111= 0 Dk1112= 538051750 MaxDsk= 1610612736 LAFull= 434653128 LimDsk= 1610612736 NUsed= 110526959 226931055 411771717 194624975 1170984046 1106062213 In DefCFB: NBatch= 1, ICI= 42, ICA=351, LFMax= 4 Large arrays: LIAPS= 1143323488, LIARS= 1812020608 words. No file to extend for IUnit= 1 -- out of disk space. Error termination in NtrErr: NtrErr called from NtrExt. -- At the same time, however, the "maxdisk" keyword ensures that _less_ space should be required than available in the 7 *rwf files (which is less than my disk capacity). Is there a stronger way of telling the code how much disk can be used, or can this be a compilation-related problem? Many thanks for any hint. Marketa From chemistry-request@server.ccl.net Wed Dec 19 11:40:46 2001 Received: from hschipaa.hsc.usf.edu ([131.247.16.97]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fBJGekq03131 for ; Wed, 19 Dec 2001 11:40:46 -0500 Received: from hschipaa.hsc.usf.edu ([131.247.16.105]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with SMTP id LAA05965 for ; Wed, 19 Dec 2001 11:40:23 -0500 (EST) Message-ID: <3C20C2F6.6D19AAC2@mindless.com> Date: Wed, 19 Dec 2001 11:40:22 -0500 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Viewing Auitodock runs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hey there CCL'ers, and Merry Christmas, I was wondering if anyone new of any software that aided in viewing docking results from autodock? I have been using the Autodock Tools (ADT) python package but this seems to run extremely slow on my linux i386. I also know that Gopenmol has capabilities for viewing docking jobs > from trajectory files however this is only applicable if you are using simulated annealing and will not work for genetic algorithm dockings. Thanks for all suggestions. David Smith From chemistry-request@server.ccl.net Wed Dec 19 11:49:16 2001 Received: from ingfi1.ing.unifi.it ([150.217.10.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBJGnCq03345 for ; Wed, 19 Dec 2001 11:49:16 -0500 Received: from dsi.unifi.it (glycine.dsi.unifi.it [150.217.15.192]) by ingfi1.ing.unifi.it (8.11.6/8.11.6) with ESMTP id fBJGmIF06569 for ; Wed, 19 Dec 2001 17:48:19 +0100 Message-ID: <3C20D3CD.4080907@dsi.unifi.it> Date: Wed, 19 Dec 2001 18:52:13 +0100 From: Addis User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.5) Gecko/20011023 X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: determine Amber ff coefficients for pdb file Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit We started to work on biomolecular docking by means of optimization algorithms. We take a configuration from the pdb database, with two molecules, we split the complex and try to recostruct the docking minimizing the potential energy. We have been using a ff ( Gromos), but the problem is that in our fragment database there aren't all we need and we aren't able to introduce new ones, in fact our knowledge in computational chemistry is very little. We would like to use Amber (in fact it is on of the most frequently used), so it's easy to make comparison between published and our results. The problem in using Amber is that we don't simply need the value of the ff for a certain configuration, but we need all the parameters involved for evaluating the potential by ourself: in fact in our algorithm we need to evaluate the ff function many times, and in some cases we consider modification of this function. Another problem is finding input data for the algorithm: we would like to use the pdb archive, but some time we find proteins in which there are fragment different from aminoacids. So we would to know whether it is possible to costruct rules for determine from a file in pdb format (or a large part of these) the coefficient needed for evaluate the Amber ff ( for example Van der Walls coefficients or dihedral angles and coefficients). Thank you very much, Addis Bernardetta addis@dsi.unifi.it From chemistry-request@server.ccl.net Wed Dec 19 15:20:33 2001 Received: from marconi.rtp.epa.gov ([134.67.208.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBJKKWq06642 for ; Wed, 19 Dec 2001 15:20:33 -0500 Received: from epahub11.rtp.epa.gov (epahub11.rtp.epa.gov [134.67.213.52]) by epamail.epa.gov (PMDF V5.2-33 #42056) with ESMTP id <0GOL007OYXQ8U3@epamail.epa.gov> for chemistry@ccl.net; Wed, 19 Dec 2001 15:18:09 -0500 (EST) Date: Wed, 19 Dec 2001 15:17:33 -0500 From: Moudgal.Chandrika@epamail.epa.gov Subject: RE: QSAR models for pathogens/microbes To: chemistry@ccl.net Message-id: MIME-version: 1.0 X-Mailer: Lotus Notes Release 5.0.6a January 17, 2001 Content-type: text/plain; charset=us-ascii X-MIMETrack: Serialize by Router on EPAHUB11/USEPA/US(Release 5.0.6a |January 17, 2001) at 12/19/2001 03:18:08 PM Hello, I would like to know if there has been any work done in terms of QSAR models for toxins released by pathogens/microbes. If there are any publications in this area, I would appreciate references and also some feed back on the feasibility of this task. Thank you in advance for your time and attention. Chandrika Chandrika J. Moudgal National Center for Environmental Assessment, US EPA 26 W. Martin Luther King Dr., ML 117 Cincinnati, OH 45268 Phone: 513-569-7078 Fax: 513-569-7475 e-mail: moudgal.chandrika@epa.gov From chemistry-request@server.ccl.net Wed Dec 19 15:29:18 2001 Received: from chem.wisc.edu ([128.104.68.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBJKTHq06829 for ; Wed, 19 Dec 2001 15:29:17 -0500 Received: from localhost (uddin@localhost) by chem.wisc.edu (8.11.2/8.11.2) with ESMTP id fBJKSur29559 for ; Wed, 19 Dec 2001 14:28:56 -0600 Date: Wed, 19 Dec 2001 14:28:51 -0600 (CST) From: Jamal Uddin To: Subject: solvent in ipcm Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Folks, I am trying to perform some solvation (SCRF) calculations using Gaussian 98. When I try to use isodensity PCM (IPCM) model with Benzene as the solvent, the calculation is done with Water instead of Benzene. I failed to change the solvent using all possible options including NonStd route card. Did anyone encounter this problem? This problem does not exist with other models such as SCIPCM, PCM or CPCM. I would appreciate of someone can help me with this. Thank you. Sincerely Yours, Jamal --------------------------------- Jamal Uddin Department of Chemistry University of Wisconsin-Madison From chemistry-request@server.ccl.net Wed Dec 19 14:33:38 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBJJXcq05941 for ; Wed, 19 Dec 2001 14:33:38 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id OAA16764; Wed, 19 Dec 2001 14:33:36 -0500 (EST) Date: Wed, 19 Dec 2001 14:33:36 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Happy Holidays and the much better New 2002 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, So, we have another holiday season... Some already started, some finished, some still waiting... So... All the best to you all and have a happy and prosperous New Year 2002. This year, I will not write my traditional long and boring thoughts which usually come to my head at this time of the year. I just somehow do not have a spirit... But I wish you all the best and have a really good one... It must be better next year -- we all believe in cycles, don't we? Yours Jan Labanowski jkl@ccl.net Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ ------------------------------------------------------------------------------- + ! XXX ! XXXXX ! XXXXXXX ! XXXXXXXXX ! "BOAS FESTAS" ! "JOYEUX NOEL" \ / * ! "VESELE VANOCE" --O-- XXX ! "MELE KALIKIMAKE" / \ "HOME" ! "NODLAG SONA DHUIT" "PEACE." ! "BLWYDDYN NEWYDD DDA" "BON NADAL." ! "GOD JUL" "BOLDOG UJ EVET" ! "BUON ANNO" \ / "CHANUKAH SAMEACH" ! \ / "FELIZ NATAL" --O-- "DOSIEGO!" ! --O-- "FELIZ NAVIDAD" / \ "HAPPY HANUKKAH" ! / \ "KALA CHRISTOUGENA" "PARI ARTSAGOURT" ! "VROLIJK KERSTFEEST" "KELLEMES UNNEPEKET" ! "FROEHLICHE WEIHNACHTEN" "NAYA VARSH SHUBH HO" ! "BUON NATALE-GODT NYTAR" "ATHBHLIAIN FAOI MHAISE ! "HUAN YING SHENG TAN CHIEH" "IYI YILLAR-HYVAEAE LOMAA ! "WESOLYCH SWIAT-SRETAN BOZIC" \ / "NA ZDOROVE" ! "MOADIM LESIMHA-LINKSMU KALEDU" --O-- "MERRY CHRISTMAS" ! "HAUSKAA JOULDA-AID SAID MOUBARK" / \ "FELICHAN JARFINON" ! "'N PRETTIG KERSTMIS" "#-SHUB NAYA BARAS-@" ! "ONNELLISTA UUTTA VUOTTA" ! "INPAKARAMAANA VIDUMURAI! "Z ROZHDESTVOM KHRYSTOVYM" >+< "STASTNY NOVY ROK-CHEERS!! "NADOLIG LLAWEN-GOTT NYTTSAR" ! "CHING CHI SHEN TAN-@@@@@!! "CRACIUN FERICIT-GOJAN KRISTNASKON" *** **!! ! "S NOVYM GODOM-FELIZ ANO NUEVO" .-'-. mmmmmm !!!! ! "GLEDILEG JOL-NOELINIZ KUTLU OLSUM" .-' .-. '-.! ! xxxx ! "EEN GELUKKIG NIEUWJAAR-SRETAN BOSIC" .-' .-' '-. '-.! . ! 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XXXXXX ! ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Dec 19 14:19:25 2001 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBJJJOq05757 for ; Wed, 19 Dec 2001 14:19:25 -0500 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id fBJJKqr22334 for chemistry@ccl.net; Wed, 19 Dec 2001 11:20:52 -0800 Received: from jnauss1-pc.accelrys.com (jnauss1-pc.sd.accelrys.com [172.30.51.68]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id fBJJKqK22289 for ; Wed, 19 Dec 2001 11:20:52 -0800 Message-Id: <5.1.0.14.0.20011219104724.00abada0@sparky2.sd.accelrys.com> X-Sender: jnauss@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Wed, 19 Dec 2001 10:48:09 -0500 To: chemistry@ccl.net From: Jeff Nauss Subject: Accelrys Workshops on Biomolecular NMR Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Accelrys Inc. will be holding a pair of workshops focusing on NMR techniques at the SGI facility in Mt. View, CA. These workshops are currently the only NMR workshops scheduled in North America for 2002. On January 22-23, the "Biomolecular NMR: Processing and Analysis Workshop" will be held. This is an introductory course that addresses processing, display, and analysis of NMR data, culminating in the generation of specific NMR-based restraints using FELIX. No prior experience with FELIX is necessary for this workshop. On January 24-25, the "Biomolecular NMR: Structure Determination Workshop" will be given. This course addresses the generation, refinement, and evaluation of structures based upon NMR data predominantly using NMR X-PLOR in Insight II and CNX. Different methods of structure generation using NMR restraints are discussed, as well as methods for evaluating the quality of structures. Knowledge of routine NMR data collection and analysis techniques is required. Attendees of the Structure Determination Workshop should have either completed the "Introduction to Life Science Modeling with Insight II Workshop" or have general experience with the Insight II interface. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for both courses and receive a 25% discount for the second workshop. Registration is on-line at URL http://www.accelrys.com/training/lifesci/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Please note that on 1 June, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Thank you very much. Jeffrey L. Nauss 858-799-5555 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Life Science Customer Training Fax: (858) 799-5100 Accelrys Inc. E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/lifesci/ San Diego, CA 92121-3752 From chemistry-request@server.ccl.net Wed Dec 19 14:19:25 2001 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBJJJOq05756 for ; Wed, 19 Dec 2001 14:19:25 -0500 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id fBJJKq522335 for chemistry@ccl.net; Wed, 19 Dec 2001 11:20:52 -0800 Received: from jnauss1-pc.accelrys.com (jnauss1-pc.sd.accelrys.com [172.30.51.68]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id fBJJKqK22298 for ; Wed, 19 Dec 2001 11:20:52 -0800 Message-Id: <5.1.0.14.0.20011219104412.00b00140@sparky2.sd.accelrys.com> X-Sender: jnauss@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Wed, 19 Dec 2001 10:45:10 -0500 To: chemistry@ccl.net From: Jeff Nauss Subject: Accelrys Life Science Training with Cerius2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Accelrys will be holding a pair of 2-day workshops at Rutgers University, New Brunswick, NJ. On January 15-16, the "Introduction to Cerius2 for Life Sciences Workshop" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications using Cerius2. The workshop will focus on basic skills for use of the interface and will explore various modules in the areas of rational-drug design, structure-based drug design, and combinatorial chemistry. Prior modeling experience is not assumed making this course a great place to learn molecular modeling with Cerius2. On January 17-18, the " Small Molecule and Drug Design with Cerius2" workshop will be offered. This workshop is aimed at our customers who are involved in drug design or the development of other bioactive compounds and who would like to make more effective use of modeling in their research. The course will focus on QSAR techniques and methodologies as well as structure-based ligand design. Attendees should possess knowledge of basic UNIX commands and have a basic understanding of QSAR theory. Familiarity with the Cerius2 environment is required for attendance to this workshop. Both suggested prerequisites can be met by attending the introductory workshop. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for both courses and receive a 25% discount for the second course. Registration is on-line at URL http://www.accelrys.com/training/lifesci/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Please note that on 1 June, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Thank you very much. Jeffrey L. Nauss 858-799-5555 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Life Science Customer Training Fax: (858) 799-5100 Accelrys Inc. E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/lifesci/ San Diego, CA 92121-3752 From chemistry-request@server.ccl.net Wed Dec 19 16:40:14 2001 Received: from mm01snlnto.sandia.gov ([132.175.109.20]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fBJLeDq08130 for ; Wed, 19 Dec 2001 16:40:13 -0500 Received: from 132.175.109.1 by mm01snlnto.sandia.gov with ESMTP ( Tumbleweed MMS SMTP Relay (MMS v4.7)); Wed, 19 Dec 2001 14:39:39 -0700 X-Server-Uuid: 95b8ca9b-fe4b-44f7-8977-a6cb2d3025ff Received: from valeria.mp.sandia.gov (valeria.mp.sandia.gov [134.253.242.90]) by sass165.sandia.gov (8.12.1/8.12.1) with ESMTP id fBJLdo0B016558 for ; Wed, 19 Dec 2001 14:39:51 -0700 (MST) Received: from mp.sandia.gov (singsing [134.253.242.62]) by valeria.mp.sandia.gov (8.9.3/8.9.3) with ESMTP id OAA183354 for ; Wed, 19 Dec 2001 14:37:07 -0700 (MST) Received: (from sjplimp@localhost) by mp.sandia.gov (8.9.3/8.9.3) id OAA84941; Wed, 19 Dec 2001 14:41:59 -0700 (MST) Date: Wed, 19 Dec 2001 14:41:59 -0700 (MST) Message-ID: <200112192141.OAA84941@mp.sandia.gov> From: "Steve Plimpton" To: chemistry@ccl.net Subject: new release of LAMMPS molecular dynamics software X-Filter-Version: 1.8 (sass165) MIME-Version: 1.0 X-WSS-ID: 103FD6912910774-01-01 Content-Type: text/plain Content-Transfer-Encoding: 7bit For those interested in classical molecular dynamics (MD) modeling, we recently released a new version of the LAMMPS code. LAMMPS can model atomic or molecular systems such as polymers and proteins. It was designed for parallel, and runs on any parallel machine that supports F90, C, and MPI (or on workstations and PCs). The source code is distributed freely under the terms of a simple license agreement. LAMMPS capabilities include a variety of polymer and bio force fields, including support for class 2 (cross-term) force fields, particle-mesh Ewald, rRESPA, a restricted form of SHAKE, an energy minimizer, and various ensemble and constraint choices. More details can be found on the LAMMPS WWW page: www.cs.sandia.gov/~sjplimp/lammps.html which includes HTML documentation, benchmark results, and the licensing info. Steve Plimpton Sandia National Labs sjplimp@sandia.gov www.cs.sandia.gov/~sjplimp From chemistry-request@server.ccl.net Wed Dec 19 19:45:01 2001 Received: from mail1.doit.wisc.edu ([144.92.9.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBK0ixq14384 for ; Wed, 19 Dec 2001 19:45:00 -0500 Received: from [128.104.71.140] by mail1.doit.wisc.edu id SAA75398 (8.9.1/50); Wed, 19 Dec 2001 18:44:36 -0600 From: To: chemistry@ccl.net Date: Wed, 19 Dec 2001 18:44:38 -0800 MIME-Version: 1.0 Content-type: text/enriched; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: SUMMARY: solvent in ipcm Message-ID: <3C20E016.5018.3B048F@localhost> X-Confirm-Reading-To: uddin@chem.wisc.edu X-pmrqc: 1 Priority: normal In-reply-to: <004801c188d1$b9211520$ad504a81@mahler> References: X-mailer: Pegasus Mail for Win32 (v3.12c) Dear Folks, I would like to thank the following persons who replied my question about choosing solvents in SCRF=IPCM calculations. Nicolas Saettel of University of Notre Dame 0100,0100,0100Professor Ronald R. Sauers, The State University of New Jersey 0100,0100,0100Hua-Jun Fan of Texas A&M University The Sovent=XXX (Benzene in my case) keyword is not recognized in the SCRF=IPCM calculations unlike PCM, or SCI-PCM models either in the route section or along with READ option. The trick is, one needs to put the dielectric constant (just the number) after a blank line of the molecular geometry specification. Sincerely, Jamal Uddin Department of Chemistry University of Wisconsin-Madison