From dixons%phvax.dnet@sb.com Thu Nov 18 00:27:35 1993 Received: from phinet.smithkline.com for dixons%phvax.dnet@sb.com by www.ccl.net (8.6.1/930601.1506) id XAA23862; Wed, 17 Nov 1993 23:49:11 -0500 From: Received: by phinet.smithkline.com (5.57/ULTRIX-az-040392); id AA05558; Wed, 17 Nov 93 23:40:12 -0500 Date: Wed, 17 Nov 93 23:40:12 -0500 Message-Id: <9311180440.AA05558@phinet.smithkline.com> To: "chemistry@ccl.net"%INET.dnet@sb.com Subject: Re: DGEOM questions for conf anal... Hi Joe- The issue of flat phenyl rings in DGEOM comes up from time to time. Generally, distance constraints alone are not enough to keep things from having some pucker. This is basically because it doesn't take a very big distance bounds violation to give noticable deviations from planarity. DGEOM will put chiral constraints on phenyl rings with a chiral volume of zero which tends to keep them much flatter. However, it will only do this if you have provided bond order information in the input PDB file. You need to indicate a Kekule (alternating single and double bond) structure for the phenyl rings. This is done with a non-standard extension to the PDB format (to indicate double bonds, you put the connected atoms numbers in twice in the CONECT record, ie, if atom 6 is doubly bonded to atom 5 the record would look like CONECT 6 5 5). If you are doing that and the phenyl rings are still noticably non-planar, then there is something wrong and you should give me more details. Hope this helps. Scott Dixon (dixons@sb.com) From ferenc@rchsg8.chemie.uni-regensburg.de Thu Nov 18 03:27:41 1993 Received: from rrzs1.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.1/930601.1506) id DAA24964; Thu, 18 Nov 1993 03:08:24 -0500 Received: from rchsg8.chemie.uni-regensburg.de by rrzs1.rz.uni-regensburg.de (4.1/URRZ-relay (1.4)) id AA03560; Thu, 18 Nov 93 09:08:16 +0100 Received: by rchsg8.chemie.uni-regensburg.de (920330.SGI/BelWue-1.0SG(subsidiary)) (for CHEMISTRY@ccl.net) id AA00718; Thu, 18 Nov 93 09:08:58 +0100 Date: Thu, 18 Nov 93 09:08:58 +0100 From: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9311180808.AA00718@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: constraints in molecular dynamics Dear Netters, a few days ago I wrote: >Now again I have a question and a request. >Can anybody tell me where I can get the GROMOS package referenced >in one of the letters? >Can someone send me a code of rattle and/or shake for arbitrarily >chosen molecules and constraints or tell me where I can find one? I got two very helpfull answers: From csoares@iris1.Fki.UU.SE Fri Nov 12 15:25:53 1993 Received: from iris1.FKI.UU.SE by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/BelWue-1.0SG(subsidiary)) (for ferenc) id AA19693; Fri, 12 Nov 93 15:25:53 +0100 Received: from [130.238.69.55] (Mac55.FKI.UU.SE) by iris1.Fki.UU.SE with SMTP id AA24428 (5.67a8/IDA-1.5 for ); Fri, 12 Nov 1993 15:00:45 GMT Date: Fri, 12 Nov 1993 15:00:45 GMT Message-Id: <199311121500.AA24428@iris1.Fki.UU.SE> To: ferenc (Ferenc Molnar) From: csoares@iris1.fki.uu.se Subject: Re: constraints in molecular dynamics Status: RO Hi again The GROMOS package can be obtained from Prof Wilfred van Gunsteren, Department of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Zentrum, 8092 Zurich, Switzerland. Regards, Claudio ----------------------------------------------------------------- I Claudio Soares I MOLECULAR MODELLING I I Uppsala University I GROUP I I Dep.Physical Chemistry I I I Box 532 I : I I S-751 21 Uppsala I l I I SWEDEN I C=O I I I l I I Pho: +46 18 183631 I H-N I I Fax: +46 18 508542 I l I I Email:CSOARES@IRIS1.FKI.UU.SE I : I ----------------------------------------------------------------- From @UICVM.UIC.EDU:carlos@pap.chem.uic.edu Fri Nov 12 21:51:33 1993 Received: from uicvm.uic.edu by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/BelWue-1.0SG(subsidiary)) (for ferenc) id AA20700; Fri, 12 Nov 93 21:51:33 +0100 Received: from pap.chem.uic.edu by UICVM.UIC.EDU (IBM VM SMTP V2R1) with TCP; Fri, 12 Nov 93 14:48:10 CST Received: by pap.chem.uic.edu (3.2/SMI-3.0DEV3) id AA01412; Fri, 12 Nov 93 14:49:44 CST Date: Fri, 12 Nov 93 14:49:44 CST From: Carlos Simmerling Message-Id: <9311122049.AA01412@pap.chem.uic.edu> To: ferenc Subject: Re: constraints in molecular dynamics Status: RO The public domain molecular dynamics code MOIL not only contains an implementation of RATTLE, but also another methos of constraints that is similar but involves inversion of matrices to get the Lagrange multipliers. It tends to converge much faster than RATTLE, especially for small sets of coupled constraints (like water). the program is available via ftp from 128.248.186.70 Carlos Simmerling Thanks a lot for this valuable help. Yours Sincerely, Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): ferenc@rchsg8.chemie.uni-regensburg.de c5071@rchs1.chemie.uni-regensburg.de ferenc@rchnw2.ngate.uni-regensburg.de --------------------------------------------------------------------------- :-) There is more to live than increasing its speed. -- Ghandi ;-) --------------------------------------------------------------------------- From H4870Ben@ELLA.HU Thu Nov 18 05:27:39 1993 Received: from phem3 for H4870Ben@ELLA.HU by www.ccl.net (8.6.1/930601.1506) id EAA25659; Thu, 18 Nov 1993 04:55:06 -0500 Received: from HUEARN.SZTAKI.HU (MAILER@HUEARN) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H5G5UWLBGG8X1XDZ@phem3.acs.ohio-state.edu>; Thu, 18 Nov 1993 04:55:00 EST Received: from HUGBOX.BITNET (NJE origin MAILER@HUGBOX) by HUEARN.SZTAKI.HU (LMail V1.1d/1.7f) with BSMTP id 8975; Thu, 18 Nov 1993 10:52:01 +0100 Received: by HUGBOX.SZTAKI.HU (MX V3.3 VAX) with SITE; Thu, 18 Nov 1993 10:50:27 gmt+1 Received: via VELLA (2.0) from: 4870 (Bencze Lajos) at 93-11-18 10:50:24 Date: Thu, 18 Nov 1993 10:45:02 +0100 From: H4870Ben@ella.hu Subject: ISOM-10 conference booklet To: CHMINF-L@IUBVM.UCS.INDIANA.EDU, LISTSERV%RPICICGE.BITNET@CUNYVM.CUNY.EDU, CHEMISTRY@ccl.net, szilagyi@miat0.vein.hu Message-id: <01H5G5UWLBGI8X1XDZ@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Ladies and Gentlemen, we would like to inform You about the offer limited number of copies of the Tenth International Symposium on Olefin Metathesis and Polymerization (ISOM-10) conference booklet. "If you missed the conference, do not miss the conference booklet." Topics of ISOM-10: o Metathesis Catalysts (homogeneous and heterogeneous) o New Application of Olefin Metathesis o Acyclic Olefin Metathesis o Ring-Opening Metathesis Polymerization o Polymer Degradation by Metathesis o Industrial Applications of Metathesis o Properties and Application of Metathesis Products o Olefin Polymerization o Metathesis Related Carbene Reactions o Theoretical Aspects of Olefin Metathesis o General >From the Contents of the booklet: o Abstracts of the Contributions (poster's abstracts included) o The complete scientific and social programme o Mailing list of the participants o List of Sponsors o 1st Computer Aided Polymer Modelling intensive hands-on course o and many more ... To obtain the booklet please contact: Professor Lajos Bencze Department of Organic Chemistry University of Veszprem H-8201 Veszprem, PO BOX 158 HUNGARY Telephone (36) 88 322022 Telex (36) 88 332397 Fax (36) 88 326016 EMAIL:h4870ben@ella.hu From TILBROOK@chem.surrey.ac.uk Thu Nov 18 06:27:41 1993 Received: from sun2.nsfnet-relay.ac.uk for TILBROOK@chem.surrey.ac.uk by www.ccl.net (8.6.1/930601.1506) id FAA25831; Thu, 18 Nov 1993 05:35:05 -0500 Via: uk.ac.surrey; Thu, 18 Nov 1993 10:07:08 +0000 Via: central.surrey.ac.uk; Thu, 18 Nov 93 10:06:56 GMT Received: from chemcharon.chem.surrey.ac.uk by central.surrey.ac.uk with SMTP (16.6/16.2) id AA00781; Thu, 18 Nov 93 10:06:46 GMT Received: From CHEMISTRY-1/WORKQUEUE by chemcharon.chem.surrey.ac.uk via Charon-4.0-VROOM with IPX id 100.931118100627.384; 18 Nov 93 10:07:16 +500 Message-Id: To: POLYMERP@HEARN.EARN From: Dave Organization: Chemistry Department, Uni of Surrey Date: Thu, 18 Nov 1993 10:06:23 GMT Subject: Simulation of infra-red spectra. Cc: chemistry@ccl.net Priority: normal X-Mailer: WinPMail v1.0 (R1) I am currently involved in a project which is trying to develop polymers with very specific infra-red characteristics. We will be attempting to speed up the development of the materials by using spectral simulation methods to 'test-out' proposed monomer units or 'model systems' to see if they meet the specifications that we have been given by our sponsors. We have an SG Indy on which we will be running POLYGRAF by MSI. As far as I am aware this software uses MM methods for the simulation of the spectra. I am however, doubtful of whether or not the vibrational analysis routines on this program will give sufficiently accurate IR spectra. Obviously Semi-emprical or ab-initio MO calculations (which it is conceivable that we may run on a Cray) will be more accurate but this is at the expense of being much more computationally intensive. It is also not clear to me just how much more useful, spectra calculated by Semi-empirical or ab-initio methods would be. Has anybody any experience in such work? If so I would be very interested to receive any advice regarding the pro's and cons of the various methods which are available. I look forward to hearing from you in the near future. Kind regards in advance Dave Tilbrook Has anybody ********************************************************** David Tilbrook * Tel: 44 483 300 800 x 2632 Polymer Group, * x 2617 Chemistry Department, * University of Surrey, * Fax: 44 483 300 803 Guildford, Surrey, GU2 5XH * U.K. * ********************************************************** From thmasson@ulb.ac.be Thu Nov 18 10:27:42 1993 Received: from cc1.kuleuven.ac.be for thmasson@ulb.ac.be by www.ccl.net (8.6.1/930601.1506) id JAA26973; Thu, 18 Nov 1993 09:49:31 -0500 Received: from rc1.vub.ac.be by cc1.kuleuven.ac.be (IBM VM SMTP V2R2) with TCP; Thu, 18 Nov 93 15:48:16 +0100 Received: from is2e.vub.ac.be by rc1.vub.ac.be (4.1/RC1-930922) id AA10222; Thu, 18 Nov 93 15:50:51 +0100 Received: by is2e.vub.ac.be (5.61/BFUCC-920211) id AA18276; Thu, 18 Nov 93 15:51:54 +0100 Date: Thu, 18 Nov 93 15:51:54 +0100 From: thmasson@ulb.ac.be (Masson Thierry) Message-Id: <9311181451.AA18276@is2e.vub.ac.be> To: CHEMISTRY@ccl.net Subject: HONDO on SGI Status: R Hello, A collegue is using HONDO an a IBM RS6000. He asks me if a Silicon Graphics version is available. Where can I find this version ? Thanks. Best Regards. ----------------------------------------------------------------------------- SOLVAY SA Thierry Masson DIRECTION CENTRALE TECHNIQUE Direct Phone Line : 32-2-264 29 06 Rue de Ransbeek, 310 Direct Fax Line : 32-2-264 32 75 B-1120 BRUSSELS (BELGIUM) E-Mail : thmasson@ulb.ac.be ----------------------------------------------------------------------------- From jxh@ibm12.biosym.com Thu Nov 18 12:27:52 1993 Received: from ibm12.biosym.com for jxh@ibm12.biosym.com by www.ccl.net (8.6.1/930601.1506) id MAA28542; Thu, 18 Nov 1993 12:16:44 -0500 Received: by ibm12.biosym.com (AIX 3.2/UCB 5.64/4.03) id AA01756; Thu, 18 Nov 1993 09:16:10 -0800 Date: Thu, 18 Nov 1993 09:16:10 -0800 From: jxh@ibm12.biosym.com (Joerg Hill) Message-Id: <9311181716.AA01756@ibm12.biosym.com> To: CHEMISTRY@ccl.net Subject: Re: Infrared Spectra Status: R There was a question concerning the calculation of infrared spectra: In principle the infrared spectra obtained with a molecular mechanics programme should be better than the spectra obtained with the common ab initio methods. But this requires parameters in your molecular mechanics programme which are fitted with the aim to reproduce infrared spectra. Most of the common force fields are designed for giving reasonable structures and energies, not wave numbers. Only in the so-called Class II force fields (MM3, CFF91) the wave numbers should be reproduced better. If you don't have a force field for your molecules which was determined for getting wave numbers right, I would prefer of course the ab initio methods. If you are running ab initio calculations (SCF) with a sufficiently good basis set (DZP or better) you can expect wave numbers which are approximately 10 % to high (systematically), so people often scale them with 0.9 or so (a factor which should be determined from experiment). If you want to improve your ab initio calculations you have to consider electron correlation. With MP2 the error in the wave numbers decreases to < 5 %, but such calculations are very demanding. It depends on the size of your molecules and on the required precision with method you can use (even on a Cray - besides in my experience I did the larger calculations on workstations than on a Cray, because the Cray you normally have to share with other people). I hope this will help you a little bit, if you have further questions feel free to contact me. Joerg-R. Hill From wipke@SECS.UCSC.EDU Thu Nov 18 18:27:47 1993 Received: from MOLENG.UCSC.EDU for wipke@SECS.UCSC.EDU by www.ccl.net (8.6.1/930601.1506) id RAA02898; Thu, 18 Nov 1993 17:57:21 -0500 Received: by SECS.UCSC.EDU (MX V3.1C) id 6617; Thu, 18 Nov 1993 14:59:10 PST Date: Thu, 18 Nov 1993 14:59:07 PST From: "W. Todd Wipke" To: chemistry@ccl.net Message-ID: <00975BAB.EE162357.6617@SECS.UCSC.EDU> Subject: Summer Undergraduate Research Fellowships Status: R Eleven NSF Summer Undergraduate Research Fellowships are available for study at UC Santa Cruz Department of Chemistry and Biochemistry. Stipends are $2,500 plus housing allowance. Applications are especially encouraged from women, minorities, and handicapped students. Students majoring in chemistry or biochemistry that are now juniors are elgible to apply. SURF students will be able to participate in the set of seminars on Molecular Design and Engineering. Many of the available projects involve computational chemistry. Application forms may be obtained by sending a message to fileserv@secs.ucsc.edu and in the BODY of the message put two words: SEND SURF Address questions and completed forms to surf@chemistry.ucsc.edu. or paper can be sent to: W. Todd Wipke (SURF) Department of Chemistry University of California Santa Cruz CA 95064 (408) 459-4002 Deadline for appl 15 Feb 94 Notificaiton by 15 Mar 94 W. Todd Wipke wipke@secs.ucsc.edu Molecular Engineering Laboratory wipke@chemistry.ucsc.edu Department of Chemistry wipke@cats.bitnet University of California tel 408 459-2397 Santa Cruz, CA 95064 FAX 408 459-2935 ============= where innovation is a tradition =================== Banana Slug Chosen "Best College Mascot" in 1992 by National Directory of College Athletics -Todd Wipke wipke@chemistry.ucsc.edu