From yubofan@guomai.sh.cn Mon Sep 22 13:25:56 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id MAA21516; Mon, 22 Sep 1997 12:33:02 -0400 (EDT) Received: from ------ (others.guomai.sh.cn [202.96.206.112]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id AAA26595 for ; Tue, 23 Sep 1997 00:32:04 +0800 Message-ID: <34269DC7.A08CF41B@guomai.sh.cn> Date: Tue, 23 Sep 1997 00:33:11 +0800 From: Yubo Fan X-Mailer: Mozilla 4.01 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Which can get better performance, Windows 95/NT or LINUX X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, My lab will buy a copy of Gaussian 94. I have a question. For a same calculation, which OS will give better performance, Windows 95/NT or LINUX. With Best Regards Y. Fan -- ======================================================== FAN, Yubo Department of Chemistry E-Mail: yubofan@guomai.sh.cn Fudan University yubofan@fudan.edu.cn Shanghai, 200433 P. R. China Voice(86-21)65643978 ======================================================== From mckelvey@kodakr.kodak.com Mon Sep 22 15:25:58 1997 Received: from kodakr.kodak.com for mckelvey@kodakr.kodak.com by www.ccl.net (8.8.3/950822.1) id OAA22065; Mon, 22 Sep 1997 14:58:44 -0400 (EDT) Received: from mail.rl.kodak.com by kodakr.kodak.com with SMTP id AA23605 (5.67b/IDA-1.5 for ); Mon, 22 Sep 1997 14:56:08 -0400 Received: from mozart.rl.kodak.com by mail.rl.kodak.com (8.8.3/1.1.10.5/17Jan97-0515PM) id PAA03062; Mon, 22 Sep 1997 15:10:00 -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 OAA02828 for ; Mon, 22 Sep 1997 14:58:32 -0400 Message-Id: <3425D05E.7396@kodak.com> Date: Mon, 22 Sep 1997 02:56:46 +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: chemistry@www.ccl.net Subject: Dallas 1998 ACS Mar29-April2 Call for Posters and General Papers Content-Type: multipart/mixed; boundary="------------480B6F7E5A26" This is a multi-part message in MIME format. --------------480B6F7E5A26 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The dates of the 1998 Dallas ACS meeting are March 29-April 2. Below is the list of the Symposia. If you are interested in contributing a paper in a Symposia please contact the respective session chair. Please send all Poster abstracts, and General Oral (i.e., things that do not fit in a symposium for whatever reason) abstracts to me. All abstracts are due to the Symposia Chairs by October 20, 1997. Thanks!! John -- ************************************ * John McKelvey * * Imaging Research and Development * * Building 83 * * Research Laboratories * * Eastman Kodak Company * * Rochester, NY 14650-2216 * * (V)716-477-3335 * * (F)716-722-2327 * * (E)McKelvey@Kodak.COM * ************************************ --------------480B6F7E5A26 Content-Type: text/plain; charset=us-ascii; name="Dallas2.txt" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="Dallas2.txt" American Chemical Society Computers in Chemistry Division Dallas Meeting, March 29 - April 2, 1998 Program Chair: Dr. John McKelvey, B83 Research Labs, Eastman Kodak Company, Rochester, NY, 14650-2216; Voice: (716) 477-3335; Fax: (716) 722-2327; email: McKelvey@Kodak.com. If you are interested in presenting at Dallas, please contact one of the session chairs below. For all concerned four (4) copies of 150-word abstract (Original on ACS Abstract Form) are due by October 20, 1997 to respective session or symposium chairperson. . Computational Reaction Mechanisms - Dr. Timothy Clark, Chemie-Centrum des Institus fur Organische Chemie, Friedrich-Alesander-Universitaet, Erlhangen-Nuernberg, Naegelsbachstrasse 25, D-91052 Erlangen, GERMANY; voice: +49-9131-852948; fax: +49-9131-856565; email: clark@organik.uni-erlangen.de. . Compuational Chemisty on Organophosphorus Compounds - Dr. William E. White, U.S. Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, Aberdeen Proving Ground, MD 21010; voice: (410) 671-3058; fax: (410) 671-1912; email: wewhite@apgea.army.mil. . QSAR and Related Techniques - Dr. Curt Breneman, Department of Chemistry, Rensellaer Polytechnic University, Cogswell Lab, 110 8th St, Troy, NY; voice: (518) 276-2678; fax: (518)276-4045; email: brenec@rpi.edu. . Activity Prediction and Database Searching: A Synergistic Approach - Dr. Ajay Shah, Biosym Corporation, 9685 Scranton Road, San Diego, CA 92121-3752; fax: (619) 458-0136; email: avs@biosym.com. . Computational Methods in Catalysis - Dr. Donald Truhlar, Department of Chemistry, University of Minnesota, Minneapolis, MN 55455; voice: (612) 624-7555; fax: (612) 624-9390; email: mf12101@sc.msc.edu. . Diverse Perspectives in Chemical Diversity - Dr. Robert Pearlman, College of Pharmacy, University of Texas, Austin, Texas 78712; voice: (512) 471-3383; fax: (512) 471-7474; email: pearlman@vax.phr.utexas.edu. . Linear Scaling Quantum Mechnical Methods - Dr. Kenneth M. Merz Jr., Associate Professor of Chemistry, 152 Davey Laboratory, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802; voice: (814) 865-3623; fax: (814) 863-8403; email: merz@retina.chem.psu.edu . General Computational Chemistry - Poster and/or Oral Sessions - Dr. John McKelvey, Research Laboratories, Building 83, Eastman Kodak Company, Rochester, NY 14650-2216; voice: (716) 477-3335; fax: (716) 722-2327; email: McKelvey@Kodak.com. --------------480B6F7E5A26-- From chem101@ibm.net Tue Sep 23 02:26:02 1997 Received: from out1.ibm.net for chem101@ibm.net by www.ccl.net (8.8.3/950822.1) id CAA26210; Tue, 23 Sep 1997 02:06:32 -0400 (EDT) Received: from default (slip129-37-218-231.la.us.ibm.net [129.37.218.231]) by out1.ibm.net (8.8.5/8.6.9) with SMTP id GAA116874 for ; Tue, 23 Sep 1997 06:06:32 GMT Message-ID: <3428ADAC.3982@ibm.net> Date: Wed, 24 Sep 1997 01:05:32 -0500 From: chem10 X-Mailer: Mozilla 3.01Gold (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: DFT and Gaussian94 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Computational chemist: I would appreciate if someone will be describing the way (the command line), where I can run the exchange part only (but not the correlation) in DFT using G94. thanks in advance F. Awwad From Gerald.Loeffler@univie.ac.at Tue Sep 23 04:26:04 1997 Received: from mailbox.univie.ac.at for Gerald.Loeffler@univie.ac.at by www.ccl.net (8.8.3/950822.1) id EAA26851; Tue, 23 Sep 1997 04:23:02 -0400 (EDT) Received: from univie.ac.at (gerilap.imp.univie.ac.at [131.130.80.125]) by mailbox.univie.ac.at (8.8.4/8.8.4) with ESMTP id KAA30174 for ; Tue, 23 Sep 1997 10:23:00 +0200 Message-ID: <34277A3B.7BA089@univie.ac.at> Date: Tue, 23 Sep 1997 10:13:48 +0200 From: Gerald Loeffler Reply-To: Gerald.Loeffler@univie.ac.at Organization: I.M.P. X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: Computational Chemistry List Subject: Biotech Industry San Diego Area Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Comp Chemists! I would really be very grateful if someone familiar with the BIOTECH INDUSTRY in the SAN DIEGO AREA - and especially the COMPUTATIONAL CHEMISTRY or BIOINFORMATICS aspect of it - could contact me ASAP so that I can ask him just one simple question. thank you very much for your help, gerald -- Gerald Loeffler PostDoc in Theoretical Biophysics EMail: Gerald.Loeffler@univie.ac.at WWW: http://www.imp.univie.ac.at/Loeffler/ Phone: +43 1 79730 554 Fax: +43 1 7987153 SMail: I.M.P. - Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA From D.van.der.Spoel@chem.rug.nl Tue Sep 23 05:26:04 1997 Received: from mailhost.rug.nl for D.van.der.Spoel@chem.rug.nl by www.ccl.net (8.8.3/950822.1) id EAA26882; Tue, 23 Sep 1997 04:28:44 -0400 (EDT) From: Received: from rugch4.chem.rug.nl by mailhost with SMTP (XT-PP) with ESMTP; Tue, 23 Sep 1997 10:29:31 +0200 Received: from rugmd2 by rugch4.chem.rug.nl (KAA13106); Tue, 23 Sep 1997 10:28:26 +0200 (DST) Received: (from spoel@localhost) by rugmd2 (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA04508 for CHEMISTRY@www.ccl.net; Tue, 23 Sep 1997 10:28:25 +0200 Message-Id: <199709230828.KAA04508@rugmd2> Subject: Perf. of Alpha vs. R10k To: CHEMISTRY@www.ccl.net Date: Tue, 23 Sep 1997 10:28:24 +0200 (DST) Reply-To: D.van.der.Spoel@chem.rug.nl X-Mailer: ELM [version 2.4 PL25] Content-Type: text More on performance. My Alpha has 2 Mb of Cache, My Indigo has 1 Mb of cache. Still my R10k is considerably faster. Maybe the use of cahce is not very intelligent on DEC machines (no wonder they are now advertising machines with 8 Mb of Cache memory...) I have just a single loop that is important. For those of you that are interested I add just a single fortran file that I have used for benchmarking. In this case all the data should fit in cache, nevertheless the difference remains in favour of the SGI. Groeten, David. ________________________________________________________________________ Dr. Ir. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ C C @(#) in_loopf.f 1.17 18 Aug 1996 C C This source-code is part of C C G R O M A C S C C GROningen MAchine for Chemical Simulations C C Copyright (c) 1990-1995, C BIOSON Research Institute, Dept. of Biophysical Chemistry, C University of Groningen, The Netherlands C C Please refer to: C GROMACS: A Message Passing Parallel Molecular Dynamics Implementation C H.J.C. Berendsen, D. van der Spoel and R. van Drunen C Comp. Phys. Comm. 1995 C C Also check out our WWW page: C http://rugmd0.chem.rug.nl/~gmx C or e-mail to: C gromacs@chem.rug.nl C C And Hey: C Gyas ROwers Mature At Cryogenic Speed C C C This code is meant to be called from C routines. C Therefore all indices start at 0, although the arrays C start at 1, if an array contains an index we must add 1 to it. C EG: jjnr points to particles starting at 0 C type is indexed from 1 to ... C subroutine FORLJC(ix,iy,iz,qi, $ pos,nj,type,jjnr,charge,nbfp, $ faction,fip, $ Vc,Vnb) implicit none real ix,iy,iz,qi real pos(*),charge(*),faction(*),fip(3) integer*4 nj,jjnr(*),type(*) real Vc,Vnb,nbfp(*) integer k,jnr,j3,tj real twelve,six real fX,fY,fZ real rijX,rijY,rijZ real fijscal,vijcoul real vctot,vnbtot real rinv1,rinv2,rinv6 real fjx,fjy,fjz real tx,ty,tz,vnb6,vnb12 parameter(twelve=12.0,six=6.0) fX = 0 fY = 0 fZ = 0 vctot = 0 vnbtot = 0 cray compiler directive ignore vector dependencies c$dir ivdep do k=1,nj jnr = jjnr(k)+1 j3 = 3*jnr-2 rijX = ix - pos(j3) rijY = iy - pos(j3+1) rijZ = iz - pos(j3+2) rinv1 = 1.0/sqrt((rijX*rijX)+(rijY*rijY)+(rijZ*rijZ)) rinv2 = rinv1*rinv1 rinv6 = rinv2*rinv2*rinv2 tj = 2*type(jnr)+1 vnb6 = nbfp(tj)*rinv6 vnb12 = nbfp(tj+1)*rinv6*rinv6 vijcoul = qi*charge(jnr)*rinv1 vctot = vctot+vijcoul vnbtot = vnbtot+vnb12-vnb6 fijscal = (twelve*vnb12-six*vnb6+vijcoul)*rinv2 fjx = faction(j3) tx = rijX*fijscal fX = fX + tx faction(j3) = fjx - tx fjy = faction(j3+1) ty = rijY*fijscal fY = fY + ty faction(j3+1) = fjy - ty fjz = faction(j3+2) tz = rijZ*fijscal fZ = fZ + tz faction(j3+2) = fjz - tz end do fip(1) = fX fip(2) = fY fip(3) = fZ Vc = Vc + vctot Vnb = Vnb + vnbtot return end program main implicit none integer maxatom,maxx,maxlist,maxtype parameter(maxatom=1000,maxx=3*maxatom,maxlist=100) parameter(maxtype=19) real*4 ix,iy,iz,qi,pos(maxx),faction(maxx),fip(3) real*4 charge(maxatom),nbfp(2*maxtype),Vc,Vnb integer type(maxatom),jjnr(maxlist) integer i,i3,j c setup benchmark do i=1,maxtype nbfp(2*i-1) = 1e-3 nbfp(2*i) = 1e-6 end do type(1)=1 do i=2,maxatom type(i)=1+mod(type(i-1)+91,maxtype) end do do i=1,maxatom i3=3*(i-1) pos(i3+1) = i pos(i3+2) = i pos(i3+3) = 1 charge(i) = mod(i,2)-0.5 end do jjnr(1) = 13 do i=2,maxlist jjnr(i) = mod(jjnr(i-1)+13,maxatom) end do ix = 0.0 iy = 0.0 iz = 0.0 qi = 1.0 Vc = 0.0 Vnb= 0.0 c run it do j=1,100 do i=1,maxatom call FORLJC(ix,iy,iz,qi, $ pos,maxlist,type,jjnr,charge,nbfp, $ faction,fip, $ Vc,Vnb) end do end do print *,Vc, Vnb stop end From HMARQUES@AURUM.CHEM.WITS.AC.ZA Tue Sep 23 07:26:19 1997 Received: from caesar.wits.ac.za for HMARQUES@AURUM.CHEM.WITS.AC.ZA by www.ccl.net (8.8.3/950822.1) id GAA27592; Tue, 23 Sep 1997 06:27:32 -0400 (EDT) Received: from aurum.chem.wits.ac.za (aurum.chem.wits.ac.za [146.141.18.2]) by caesar.wits.ac.za (8.8.5/8.8.5) with ESMTP id MAA04690 for ; Tue, 23 Sep 1997 12:29:09 +0200 (GMT) Received: from CHEMISTRY/SpoolDir by aurum.chem.wits.ac.za (Mercury 1.20); 23 Sep 97 12:27:52 GMT +2:00 Received: from SpoolDir by CHEMISTRY (Mercury 1.20); 23 Sep 97 12:27:31 GMT +2:00 From: "Helder Marques" Organization: CHEMISTRY - WITS UNIVERSITY To: CHEMISTRY@www.ccl.net Date: Tue, 23 Sep 1997 12:27:26 GMT + 2:00 Subject: Virtual orbital energies Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <1FBAB8D72F7@aurum.chem.wits.ac.za> I would appreciate your views on the following. We have been doing some semi-empirical (PM3) and ab initio calculations (6-31G* basis set) on a series of ligands (pyridines and imidazoles) to try to find correlations between the properties of the ligands themselves and the stability constants for their binding to an iron(III) porphyrin. Our question is the following. In addition to being sigma donors, the ligands are potential pi-acceptors from, and pi-donors to Fe(III). Hence we are interested in the energies of the frontier orbitals. Of the occupied orbitals, two have pi symmetry and one sigma symmetry. The two virtual orbitals (LUMO and LUMO+1) both have pi symmetry. Now the energies of the filled orbitals presumably have some physical meaning. But do the computed energies of the virtual orbitals? Are we justified in using these energies in multivariate correlations with the experimental stability constants? Thanks for your time Helder Marques _________________________________________________ | Prof. Helder M. Marques, Department of Chemistry| | University of the Witwatersrand, P.O. Wits | | 2050 Johannesburg, | | South Africa | | Fax: +27+11+339-7967; Tel: +27+11+716-2303 | _________________________________________________ From kruger@eng.und.ac.za Tue Sep 23 08:26:05 1997 Received: from Raven.und.ac.za for kruger@eng.und.ac.za by www.ccl.net (8.8.3/950822.1) id IAA28063; Tue, 23 Sep 1997 08:00:16 -0400 (EDT) Received: from eng.und.ac.za (engfs1.ee.und.ac.za [146.230.192.3]) by Raven.und.ac.za (8.8.3/8.7.3) with ESMTP id NAA21055 for ; Tue, 23 Sep 1997 13:59:59 +0200 (SAT) Received: from ENGFS1/SpoolDir by eng.und.ac.za (Mercury 1.31); 23 Sep 97 14:02:38 +0200 Received: from SpoolDir by ENGFS1 (Mercury 1.31); 23 Sep 97 14:02:11 +0200 From: "Mr HG Kruger" Organization: University of Natal To: Computational Chemistry List Date: Tue, 23 Sep 1997 14:02:08 +0200 (SAST) Subject: calibration of semiempirical MO calculations X-Confirm-Reading-To: "Mr HG Kruger" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.54) Message-ID: <55622597BDB@eng.und.ac.za> CCL list I am looking for any references to the callibration of MO calculations using the known X-ray structure of molecule. I will summarise the responces if more people are interested. Thanks for your time Gert Kruger __________________________________________________________ Dr HG Kruger, Dept Chemistry, University of Natal, PO Box 18091, Dalbridge 4014, Durban, South Afica Tel +27-31-2602181 Fax +27-31-2603091 Email kruger@che.und.ac.za __________________________________________________________ From kim@traj.chem.wayne.edu Tue Sep 23 08:29:02 1997 Received: from traj.chem.wayne.edu for kim@traj.chem.wayne.edu by www.ccl.net (8.8.3/950822.1) id HAA27988; Tue, 23 Sep 1997 07:38:26 -0400 (EDT) Received: by traj.chem.wayne.edu (AIX 3.2/UCB 5.64/4.03) id AA14511; Tue, 23 Sep 1997 07:38:27 -0400 Date: Tue, 23 Sep 1997 07:38:27 -0400 From: kim@traj.chem.wayne.edu (Kim Bolton) Message-Id: <9709231138.AA14511@traj.chem.wayne.edu> To: chemistry@www.ccl.net Subject: Ab initio and MD calculations on Pentiums Dear colleagues, We are planning to buy a Pentium PC that will be used for number crunching only (i.e., it will *not* be used as a terminal). We plan to incorporate the LINUX operating system. Molecular dynamics code (VENUS96), semiemprical codes (e.g., MOPAC) and ab initio code (Gaussian) will be run on the machine. Does anyone have experience with these machines, so that they can comment on i) The model of Pentium PC that we need, or would prefer, to run the above packages, especially Gaussian (e.g., Pentium II, Pentium Pro). ii) Is there is a distinct advantage in having the dual CPU machine, or is it better to stick with a single precessor PC. iii) The amount of RAM and hard disk that is required. iv) Problems with fortran compilation on these PCs, and what fortran compiler is preferred. v) Any other machines that may be better suited for our applications. I will summarise the responses, Many thanks Kim Kim Bolton --- kim@traj.chem.wayne.edu Chemistry Department Wayne State University Detroit USA From desingh@syr.edu Tue Sep 23 11:26:08 1997 Received: from mailbox.syr.edu for desingh@syr.edu by www.ccl.net (8.8.3/950822.1) id LAA29400; Tue, 23 Sep 1997 11:01:34 -0400 (EDT) Received: from fermi.cat.syr.edu (fermi.cat.syr.edu [128.230.59.16]) by mailbox.syr.edu (8.8.7/8.8.7) with SMTP id LAA29797 for ; Tue, 23 Sep 1997 11:01:34 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <3427D9B2.31DF@syr.edu> Date: Tue, 23 Sep 1997 11:01:06 -0400 From: Deepak Singh Organization: Dept. of Chemistry and W. M. Keck Center for Molecular Electronics X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: ccl Subject: Software Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLer's. I have a DEC-alpha 500(running unix), which I am using to run simulations on proteins. Can you suggest some software which I can use to visualise these proteins and simulations. I do not think Sculpt works, and I am not sure if there is a version of Midas for this platform. Thanks -- Deepak. -------------------------------------------------------------------- Deepak Singh 1-014 Scitech, Graduate Student Syracuse, NY 13244 Department of Chemistry Syracuse Univ. TEL:(315) 443 1739 FAX:(315) 443 4070 email : desingh@syr.edu URL: http://web.syr.edu/~desingh ...the time has gone. the dream is over. thought I had something more to say. Roger Waters in "TIME" --------------------------------------------------------------------- From larrydeb@infocom.net Thu Sep 18 12:25:04 1997 Received: from login1.infocom.net for larrydeb@infocom.net by www.ccl.net (8.8.3/950822.1) id LAA25525; Thu, 18 Sep 1997 11:56:42 -0400 (EDT) Received: from [207.170.89.112] (ip112.infocom.net [207.170.89.112]) by login1.infocom.net (8.8.5/8.6.9) with ESMTP id LAA03777 for ; Thu, 18 Sep 1997 11:20:11 -0500 X-Sender: larrydeb@infocom.net (Unverified) Message-Id: Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Date: Thu, 18 Sep 1997 10:57:02 -0600 To: chemistry@www.ccl.net From: Lawrence DeBolt Subject: Call for Papers - Polymer Modeling CCL Members, TimesKevin Squire and I are organizing a symposium entitled "Computer Modeling of Polymers" for the March 29 - April 2, 1998 ACS meeting in Dallas, TX for the PMSE Division(cosponsored by the Polymer Division). The aim of this symposium is the application of molecular modeling approaches to the prediction and understanding of polymer properties. Representative modeling areas are: - Conformation Properties, such as RIS, dynamic RIS, etc. - Thermodynamic Properties from simulations: calculations of Tg, phase diagrams and morphologies - Interfacial properties: surface tension, surface migration of additives and chains, compatibilizers, adhesion, etc. - Rheologica/Dynamic properties: viscosities, diffusion constants, compliance and other mechanical properties Of particular interest to us are modeling applications on systems of commercial application, and those which compare calculated results to experimental data. ACS abstract and preprint forms will be sent immediately to anyone who shows an interest in participating in this symposium. Deadline for submission of the abstract and preprint is Friday, November 7, 1997. If you have any questions, please contact either Kevin or myself directly at the numbers/addresses listed below. Dr. Kevin Squire Exxon Chemical Company Baytown Polymers Center 5200 Bayway Drive Baytown, TX 77522 (281) 834-5211 (Office) FAX: (281) 834-2395 or Dr. Lawrence DeBolt Exxon Chemical Company Baytown Polymers Center 5200 Bayway Drive Baytown, TX 77522 (281) 834-1343 (Office) FAX: (281) 834-2480 larrydeb@infocom.net From chipot@host7.lctn.u-nancy.fr Tue Sep 23 13:26:08 1997 Received: from host7.lctn.u-nancy.fr for chipot@host7.lctn.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id MAA00448; Tue, 23 Sep 1997 12:26:09 -0400 (EDT) From: Received: (from chipot@localhost) by host7.lctn.u-nancy.fr (AIX4.2/UCB 8.7/8.7) id SAA23122 for chemistry@www.ccl.net; Tue, 23 Sep 1997 18:18:47 +0200 (DFT) Message-Id: <199709231618.SAA23122@host7.lctn.u-nancy.fr> Subject: Chambery Meeting - April 1998 To: chemistry@www.ccl.net Date: Tue, 23 Sep 1997 18:18:47 +0200 (DFT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text _______________________________________________________________________ European Conference on COMPUTATIONAL CHEMISTRY AND THE LIVING WORLD: FROM SEQUENCE TO FUNCTION. Chambery (French Alps), 20-24 April, 1998 Organised by the Physical Chemistry Division, French Chemical Society Bunsen-Gesellschafft fur Physikalische-Chemie, Faraday Division of the Royal Society of Chemistry, Division di Chimica Fisica (SCI), French Biophysical Society. International Scientific Committee: J.C. Smith (CEA-Saclay, Chairman); R. Botter (DCP Paris), secretary; J. Brickmann (TH Darmstadt); J.E. Dubois (U Paris VII); J. Garnier (INRA-Jouy); M. Karplus (U. Strasbourg); R. Lavery (IBPC, Paris); B. Maigret (U. Nancy); C. Chipot (U Nancy); G. Richards (U. Oxford); E. Soulie (CEA-Saclay); J. Tomasi (U. Pisa); C. Troyanowsky (DCP Paris). _______________________________________________________________________ THIS PAGE CONTAINS THE FOLLOWING INFORMATION: A) DESCRIPTION OF THE SCOPE OF THE MEETING B) PROGRAMME C) APPLICATION FORM A) DESCRIPTION OF THE SCOPE OF THE MEETING. _______________________________________ The results of the genome projects are expected to lead to a scientific revolution in the beginning of the next century. The complete gene se- quences of organisms of several different levels of development, in- cluding Homo sapiens, will be available. This enormous amount of gene- tic information will be in the form of nucleotide sequences. The infor- mation present in a gene sequence is translated in the cell into a protein sequence. This sequence determines the way the protein folds into a three-dimensional architecture which confers biological function (catalysis, recognition etc). The question arises as to how to exploit the genetic information as ef- fectively as possible. To do this will require an understanding of the processes of translation of the genetic information from sequence to structure and function. Both theory and experiment are expected to play major roles in obtaining this understanding. The meeting in Chambery will focus on the role of computational chemistry= in the activity that will be sparked by the genome results. How can numerical calculation help us to understand and exploit genome sequences? How can modelling and simulation help in understanding how amino-acid sequence is trans- lated into three-dimensional biological structure, the functional interactions of these structures and the effect of engineered modifica- tions? The meeting will be treating the following topics organised into three themes: Sequence analysis, Biomolecular structure and folding, and Biomolecular function. In the first theme the impact of genome sequencing projects will be as- sessed, genome organisation discussed and the access and direct exploi- tation of sequence data reviewed. Evolutionary analysis of sequences will be examined, together with the classification of sequences in terms of structure. The second theme concerns biomolecular folding and structure. On the experimental side X-ray crystallography and nuclear magnetic resonance spectroscopy are the major techniques capable of solving macromolecular structures at atomic resolution. However, for technical reasons, the rate at which new structures are being solved far lags behind the rate at which new gene sequences are being produced. Thus, there is a need for reliable theoretical/computational techniques capable of predicting protein structures from sequences. To do this requires an understanding of the principles by which proteins fold: the factors determining their thermodynamic stability and kinetic folding pathways. We will examine modelling of protein structure by homology and with energy functions, the "inverse folding " methods (from structure to sequence), and tech- niques for global energy optimization. Prion protein conformational flexibility will be addressed with reference to prion diseases as diseases of protein conformation. Nucleic acid sequence-structure rela- tionships will also be discussed, with special reference to the fine structure, bending and supercoiling of DNA, and the prediction of the structure and activity of tRNA. The third theme will be the functional interactions of biomolecules. The calculation of binding modes and reaction mechanisms will be exami- ned and methods for calculating free energy changes associated with bi- ological processes assessed. The modelling and simulation of ordered molecular systems such as protein-protein and protein-nucleic acid com- plexes, oligosaccharides and glycoproteins and membrane-based systems will be reviewed. Finally, dynamic processes in biological function will be examined, from fast, picosecond events to slower, domain motions and allosteric phenomena. The meeting will be over five days and will consist of long lectures (45 mins), short lectures (15 mins), poster sessions and informal dis- cussion. Research into the chemistry of biological macromolecules requires close cooperation between theorists and experimentalists. In the present meeting we hope to attract scientists from both fields. We will invite a number of leading experimentalists to give lectures, and hope to emphasize the broad complementarity between theory and experi- ment in the lectures rather than specialized discussion of theoretical methodology. The meeting is expected to be of interest to researchers in all bran- ches of computational chemistry, as well as structural and molecular biologists and biochemists. The consequences for industry of success in the endeavours discussed above are enormous, and this has been rea- lised in several drug companies that have set up integrated computa- tional/experimental groups on sequence-structure-function relation- ships. A famous example of 'rational' structure-based drug design is the very-recent successful development of HIV Protease inhibitors for the treatment of AIDS. Industrial researchers working on this and other problems will also be invited to speak. B) PROVISIONAL PROGRAMME _____________________ MONDAY APRIL 20th _________________ 8.45-9.15 Welcome. THEME 1: SEQUENCES. 9.15-10.00 Jean-Michel Claverie 10.00-10.30 Pause+Exhibition. 10.30-11.15 A. Danchin. 11.00-12.15 Three short talks 14.00-14.45 Cyrus Chothia (Cambridge) 14.45-15.45 Three short talks. 15.45-16.15 Break. 16.15-17.15 Oral Poster presentations. 17.15-18.15 Poster session. TUESDAY 21 APRIL ________________ THEME 2: FOLDING AND STRUCTURE. 9.00- 9.45 Mannfred Sippl(Graz) 9.45-10.45 Three short talks 10.45-11.30 Pause+Exhibition. 11.30-12.15 Michael Hecht (Princeton) 14.00-14.45 Eugene Shakhnovitch (Harvard) 14.45-15.45 Three short talks. 15.45-16.15 Break. 16.15-17.15 Oral poster presentations. 17.15-18.15 Poster session. WEDNESDAY 22 APRIL __________________ 9.00- 9.45 Wilfred van Gunsteren (Zurich) 9.45-10.30 Pause+Exhibition. 10.30-11.15 Three short talks. Afternoon free * SKI TRIP * WINE TRIP THURSDAY 23 APRIL _________________ 9.00- 9.45 Chris Dobson (Oxford) 9.45-10.30 Pause+Exhibition. 10.30-11.30 Three short talks. 11.15-12.15 Eric Westhof (Strasbourg) THEME 3: BIOMOLECULAR INTERACTIONS AND FUNCTION. 14.00-14.45 David Chandler (Berkeley) 14.45-16.00 Pause+Exhibition. 15.30-16.30 Three short talks. FRIDAY 24 APRIL _______________ 9.00- 9.45 Harel Weinstein (New York) 9.45-10.30 Pause+Exhibition. 10.30-11.30 Three short talks. 11.30-12.15 Klaus Schulten (Illinois) Afternoon - To be announced. C) PRELIMINARY REGISTRATION FORM _____________________________ Please send this form by REGULAR MAIL to the following address: M. Rene Botter, Computational Chemistry and the Living World, Laboratoire de Chimie Physique, 11 rue P. et M. Curie, 75005 PARIS France. ..................................................................>8... Name: ______________________________________________________________ Address: ___________________________________________________________ ____________________________________________________________________ ____________________________________________________________________ Telephone: _________________________________________________________ Fax: _______________________________________________________________ E-mail: _____________________________________________________________ _____ I WISH/DO NOT WISH TO PRESENT A POSTER. _____ I WISH/DO NOT WISH TO MAKE AN ORAL PRESENTATION. ..................................................................>8... _______________________________________________________________________ Chris Chipot Laboratoire de Chimie Theorique Phone: (33) 3-83-91-25-96 U.R.A. C.N.R.S. No 510 Fax: (33) 3-83-91-25-30 Universite Henri Poincare - Nancy I B.P. 239 54506 Vandoeuvre-les-Nancy Cedex E-mail: chipot@lctn.u-nancy.fr `Veritas est index sui et falsi' _______________________________________________________________________ From netsci@awod.com Tue Sep 23 17:26:10 1997 Received: from sumter.awod.com for netsci@awod.com by www.ccl.net (8.8.3/950822.1) id QAA03105; Tue, 23 Sep 1997 16:35:32 -0400 (EDT) Received: from [208.140.97.42] (chs0282.awod.com [208.140.97.42]) by sumter.awod.com (8.8.7/8.8.5) with SMTP id QAA04352; Tue, 23 Sep 1997 16:35:30 -0400 (EDT) X-Sender: arichon@awod.com Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 23 Sep 1997 16:33:22 +0100 To: chemistry@www.ccl.net From: netsci@awod.com (Network Science) Subject: New Issue of NetSci The current issue of NetSci featuring "An Introduction to Job Searching Strategies" is available at: http://www.netsci.org From philfen@dabulls.chem.wisc.edu Tue Sep 23 20:26:23 1997 Received: from dabulls.chem.wisc.edu for philfen@dabulls.chem.wisc.edu by www.ccl.net (8.8.3/950822.1) id TAA03915; Tue, 23 Sep 1997 19:55:10 -0400 (EDT) Received: by dabulls.chem.wisc.edu (950215.SGI.8.6.10/940406.SGI.AUTO) for chemistry@www.ccl.net id SAA01201; Tue, 23 Sep 1997 18:55:00 -0500 From: "Peter Hilfenhaus" Message-Id: <9709231854.ZM1199@dabulls.chem.wisc.edu> Date: Tue, 23 Sep 1997 18:54:54 -0500 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Rh basis set Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi CCL-people, I performed a study (geometry optimization) of Rh complexes using B3LYP/LANL2DZ in Gaussian 94. Now I want to verify my results using a larger basis set at the Rh center. Since simple uncontraction of (341/321/31) in LANL2DZ might not be an appropriated way to get a larger basis set I would like to ask for suggestions, experiences and references about larger basis sets for Rh!! Please respond directly to: philfen@chem.wisc.edu I 'll post a summary. Peter -- ---------------------------------------------------- Peter Hilfenhaus University of Wisconsin 1101 W. University Avenue Madison, WI 53706, U.S.A. ----------------------------------------------------