From burt@sandwich.pfizer.com Mon Dec 16 06:09:58 1996 Received: from pfizer.com for burt@sandwich.pfizer.com by www.ccl.net (8.8.3/950822.1) id FAA14668; Mon, 16 Dec 1996 05:31:30 -0500 (EST) Received: from sdu003.sandwich.pfizer.com by pfizer.com (SMI-8.6/3.1.090690-Pfizer Inc) id KAA19922; Mon, 16 Dec 1996 10:33:55 GMT Received: from siris13 by sdu003.sandwich.pfizer.com (5.65/Ultrix3.0-C) id AA04508; Mon, 16 Dec 1996 10:31:00 GMT Received: by siris13.sandwich.pfizer.com (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id KAA04124; Mon, 16 Dec 1996 10:27:53 GMT From: burt@sandwich.pfizer.com (Catherine Burt) Message-Id: <199612161027.KAA04124@siris13.sandwich.pfizer.com> Subject: Molecular Graphics and Modelling Society To: chemistry@www.ccl.net Date: Mon, 16 Dec 1996 10:27:53 +0000 (GMT) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit Dear informeister, My name is Kate Burt and I am the publicity officer of the Molecular Graphics and Modelling Society (MGMS) in the UK. I am about to send you a text file (mgms_diary.txt) which contains our diary of events for 1997. Please would you distribute it to all interested parties on your Computational Chemistry e-mail list? Your help here will be greatly appreciated. Best regards, Kate Burt From HILAL2@FRCU.EUN.EG Mon Dec 16 06:26:00 1996 Received: from FRCU.EUN.EG for HILAL2@FRCU.EUN.EG by www.ccl.net (8.8.3/950822.1) id GAA14753; Mon, 16 Dec 1996 06:00:03 -0500 (EST) From: Received: from FRCU.EUN.EG by FRCU.EUN.EG (PMDF V4.2-11 #3805) id <01ID2UD30K280013FQ@FRCU.EUN.EG>; Mon, 16 Dec 1996 13:00:03 O Date: Mon, 16 Dec 1996 13:00:02 +0000 (O) Subject: CI in Mopac7 To: chemistry@www.ccl.net Message-id: <01ID2UD325XU0013FQ@FRCU.EUN.EG> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT > Dear CCL > I am very interesting with configuration interaction to calculate the > electronic transitions of some organic compounds and compare calculated results > with experemintal values which measured at range 190-900 nm. > In deed I am very happy to modified CI in Mopac, but when I do CI=6 or CI=7 > the singlet state is disappeared and the same time all our spectra which are > measured contain only the singlet state. My questions > 1- Why when CI=6 or CI=7 the output file does not contain singlet state, but > when CI=4 or CI=5 the singlet is contained and so triplet state. Although the > singlet keyword is only limited in data file and with that output file contains > the singlet and triplet together. > 2- I would like to express my deep thanks if you give me further information > about CI in MOPAC7 and how I interpret triplet state that appears together with > singlet state when the singlet state is only required and limited in file.dat > > From burt@sandwich.pfizer.com Mon Dec 16 06:29:11 1996 Received: from pfizer.com for burt@sandwich.pfizer.com by www.ccl.net (8.8.3/950822.1) id FAA14674; Mon, 16 Dec 1996 05:32:20 -0500 (EST) Received: from sdu003.sandwich.pfizer.com by pfizer.com (SMI-8.6/3.1.090690-Pfizer Inc) id KAA20005; Mon, 16 Dec 1996 10:34:55 GMT Received: from siris13 by sdu003.sandwich.pfizer.com (5.65/Ultrix3.0-C) id AA04513; Mon, 16 Dec 1996 10:31:47 GMT Received: by siris13.sandwich.pfizer.com (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id KAA04131; Mon, 16 Dec 1996 10:28:40 GMT From: burt@sandwich.pfizer.com (Catherine Burt) Message-Id: <199612161028.KAA04131@siris13.sandwich.pfizer.com> Subject: mgms_diary.txt To: chemistry@www.ccl.net Date: Mon, 16 Dec 1996 10:28:40 +0000 (GMT) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit A Diary of Events of the Molecular Graphics and Modelling Society is given below. For more detailed information, please visit our Society Web Page on the following URL: http://www.yorvic.york.ac/~mgms Bioinformatics and Drug Discovery April 2nd - 4th, 1997 University of Manchester, UK Contact: Dr. J. W. Essex, Dept. of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ E-mail: jwe1@soton.ac.uk Conference Web site: http://mbisg2.sbc.man.ac.uk/hssp/mgms.html Joint with the SCI Young Chemists "Virtual Molecules - the use of computers in drug design" April 22nd, 1997 Glaxo Wellcome, Stevenage, UK Contact:Dr. Mike Hann. Glaxo Wellcome R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY Telephone:+44 1438 745745 Fax:+44 1438 764918 Email:mmh1203@ggr.co.uk 16th Annual Meeting - "Computer Modelling of Biological Systems" September 2nd- 5th 1997 Erlangen,Germany Contact:Dr. Tim Clark, Computer Chemie Centrum Universitat Erlangen Nurnberg, Nagelsbachstrasse 25, D-91052, Erlangen. Telephone:+49 0131 852948 Fax:+49 9131 856565 E-mail:clark@organik.uni-erlangen.de Meeting on Combinatorial Chemistry (provisional) December 1997 Location to be announced Contact:Dr. Mike Hann. Glaxo Wellcome R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY Telephone:+44 1438 745745 Fax: +44 1438 764918 Email:mmh1203@ggr.co.uk From inge.muszynski@uni-tuebingen.de Mon Dec 16 11:10:03 1996 Received: from outmail.zdv.uni-tuebingen.de for inge.muszynski@uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id KAA16833; Mon, 16 Dec 1996 10:18:12 -0500 (EST) Received: from by outmail.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AB25029; Mon, 16 Dec 96 16:17:55 +0100 Received: from commlink.zdv.uni-tuebingen.de by mailserv.uni-tuebingen.de with SMTP (PP); Mon, 16 Dec 1996 16:08:51 +0100 Received: (from cpcmu01@localhost) by commlink.zdv.uni-tuebingen.de (8.6.12/8.6.12) id QAA03263; Mon, 16 Dec 1996 16:08:45 +0100 Date: Mon, 16 Dec 1996 16:08:45 +0100 (MEZ) From: Inge Muszynski To: chemistry@www.ccl.net Subject: SEAL Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL's, I recently asked to get some information on the program SEAL. Here is a short summary of the answers I received. SEAL stands for "steric and electrostatic alignment". It is used to automatically align one molecule to another while maximizing the similarity in steric and electrostatic fields. Such an alignment can be used for pharmacophore development, ligand docking, CoMFA-analyses.... SEAL is a Fortran program (QCPE#634_sgrw) that can be ordered directly from the QCPE (qcpe@ucs.indiana.edu.). Furthermore some references: Ref.: Kearsley, S.K.; Smith, G.M.: "An alternative method for the alignment of molecular structures maximizing electrostatic overlap" Tetrahedron Computer Methodology 1990; 3; (p. 615-633) For Sybyl-users, a SPL script that calls SEAL form SYBYL is available in the WWW: http://www.tripos.com/services/spl_archive/seal.spl A GA programm called PADRE doing the same sort of alignment is available from the CCL archives. Thank you to everybody who has sent me a mail. Regards Inge Muszynski Inge Muszynski Pharmazeutisches Institut Auf der Morgenstelle 8 71126 Tuebingen Tel.: 07071/ 2975278 Fax: 07071/ 292470 From jerickson@dowelanco.com Mon Dec 16 12:10:06 1996 Received: from elinet1.dowelanco.com for jerickson@dowelanco.com by www.ccl.net (8.8.3/950822.1) id LAA17571; Mon, 16 Dec 1996 11:31:58 -0500 (EST) Received: by elinet1.dowelanco.com id AA14301 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Mon, 16 Dec 1996 11:31:56 -0500 Received: by elinet1.dowelanco.com (Internal Mail Agent-1); Mon, 16 Dec 1996 11:31:56 -0500 Message-Id: From: "Erickson, Jon" To: "'CCL'" Subject: RE: C-H...O hydrogen bond Date: Mon, 16 Dec 1996 11:32:07 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Lara, We did some theoretical and experimental work in this area, see: Erickson and McLoughlin, JOC, 1995, 60, 1626 and refs therein. Jon Erickson DowElanco CAMD jerickson@dowelanco.com From wagenert@uni-marburg.de Mon Dec 16 12:40:06 1996 Received: from Mailer.Uni-Marburg.DE for wagenert@uni-marburg.de by www.ccl.net (8.8.3/950822.1) id LAA17577; Mon, 16 Dec 1996 11:34:41 -0500 (EST) Received: from localhost by Mailer.Uni-Marburg.DE (AIX 4.1/UCB 5.64/25.11.96) id AA42576; Mon, 16 Dec 1996 14:29:32 +0100 Date: Mon, 16 Dec 1996 14:29:32 +0100 (CET) From: Thomas Wagener X-Sender: wagenert@pprz03.HRZ.Uni-Marburg.DE To: Computational Chemistry List Subject: Compiling Gaussian 94 under Linux Kernel 2.xx Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi netters, I have two questions concerning the topic: The first one is probably a FAQ but I have no connection to the WWW at the moment and so I have not checked the CCL archives. I apologize for wasting the bandwidth. The problem occuring is that Gaussian needs a "UNIX make facility" and does not work with the GNU make. My question now is where I may get a standard Unix make for Linux. I have tried the BSD make with no success and all I have found browsing the standard ftp servers was the "normal" GNU make. The Linux distribution I installed on the PC comes with a "native" GNU fortran compiler. Is there any possibility and - above all - advantage in trying to compile Gaussian with this beast or is the general f2c approach preferrable? Many thanks in advance. If there is need I will summarize to the list. Sicerely, Thomas Wagener - "You are wrong! 2+2=5.8354! Please adjust your equipment accordingly." The Computer (your friend) ***************************************************************************** * Thomas Wagener * Tel: ++49-(0)6421-285561 * * FB Chemie * * * Phillips-Universitaet Marburg * Email: wagenert@mailer.uni-marburg.de * * * * * 35032 Marburg * * * Germany * * ***************************************************************************** From somsak@atc.atccu.chula.ac.th Mon Dec 16 21:10:07 1996 Received: from atc.atccu.chula.ac.th for somsak@atc.atccu.chula.ac.th by www.ccl.net (8.8.3/950822.1) id UAA26042; Mon, 16 Dec 1996 20:18:25 -0500 (EST) Received: by atc.atccu.chula.ac.th (5.57/CFTHAI-2e1.ULTRIX) id AA16431; Tue, 17 Dec 96 10:40:31 GMT From: somsak@atc.atccu.chula.ac.th (Somsak Tonmunphean) Message-Id: <9612171040.AA16431@atc.atccu.chula.ac.th> Subject: Summary of How to calculate Bond Orders. To: CHEMISTRY@www.ccl.net Date: Tue, 17 Dec 1996 10:40:31 +0000 (WET) X-Mailer: ELM [version 2.4 PL20] Content-Type: text Dear Netters, A few days ago, I asked the question "How to calculate bond order of molecule ?", I have received some good anwering mails and here is my summary. Thank you very much to the following persons who gave the great answers. Robert Ponec (RPONEC@icpf.cas.cz) Dr.Stephan Irle (stephan.irle@itc.uivie.ac.at) Dr. Jeff Gosper (Jeffrey.Gosper@brunel.ac.uk) John R. Nash (nash@chem.wisc.edu) Dr. Joel Polowin (polowin@hyper.com) Elmar Gerwalin (gerwalin@chemie.uni-kl.de) Alan Shuterman (Alan.Shusterman@directory.Reed.EDU) Dr. Tapas Kar (TAPASKAR@SIUCVMB.SIU.EDU) Dr. Damir Kovacek (dkovacek@spider.irb.hr) *************************************************************************** From: Robert Ponec (RPONEC@icpf.cas.cz) There is still some discussion about how to define bond order. The situation is clearer at SCF level where the generally accepted definition of bond order (sometimes called bon index) is that proposed some years ago by Wiberg. His bond indeces are sometimes referred to as Wiberg indices). What MOPAC calculates using BOND keyword is just this type of index. It has the advantage that his values for single bonds are close to 1, dor double bonds close to 2 etc and for nonbonded atoms they are usually negligible and so they correspond well to the classical understanding of bond multiplicity. The Wiberg indices were originally defined for orthogonal basis sets ( i.e. they are straightforwardly applicabl;e at semiempirical level) but the extension to ab initio level was proposed by Mayer. If you are satisfied with SCF level only, it is best to use Wiberg or Mayer indices. A bit more complex situation is for correlated wave functions where the definition od bond index is still the subject of discussion. Since I have been working in this field quite recently, I can send you a reprint of my recent study on this subject. You can find all the references to Wiberg and Mayer works there. Let me please know whether you are interested in it. ************************************************************************** From: stephan.irle@itc.univie.ac.at (Stephan Irle) You should have asked me. I've implemented Mayer's bond orders into G92, and you can have it, of course with the references. ************************************************************************** From: polowin@hyper.hyper.com (Joel Polowin) It is not possible to calculate bond orders automatically with HyperChem, but they can be calculated manually from the density matrices, which can be printed in a log file. The bond order between atoms A and B is the sum of the squares of the elements in the density matrix with rows for atom A's orbitals and columns for atom B's orbitals, or vice versa. If you are doing UHF calculations, you must add the elements of the alpha and beta matrices together before squaring. I tried this for C2H4 as model-built, with an AM1 single-point calculation, and got a C--C bond order of 2.0004. ************************************************************************** From: "John R. Nash" F. Weinhold's Natural Bond Order (NBO) calculation available with G92 (and G94) will calculate bond orders (and do decomposition of bonds into "ionic" and "covalent" parts if requested). Check the manual for details, but at its simplest, you just put "POP=NBO" in the route card and $NBO $END at the end of the input file. This gives the default NBO analysis, including bond orders. ************************************************************************** From: Jeffrey J Gosper MOPAC can calculate bond orders (using the BONDS keyword). We are currently working on an Windows program that will take XYZ files, run MOPAC, and produce an 'extended' XYZ file that contain bond connectivities and orders which can be viewed in Re_View2. Until this is finished you can look at the degrees of bonding table in the MOPAC output. ************************************************************************** From: Elmar Gerwalin In Gaussian you can calculate Bond orders very easily: Mulliken Overlap Populations are calculated by default. Better is the NBO-Program Package that mostly comes along with Gaussian (all Versions up to G94) Please refer to the Gaussian Homepage, your Software ADministrator or search the Web for NBO (Natural Bond Order Analysis). If I find a link to Gaussian/NBO in my own Bookmarks, I will tell you. ************************************************************************** From: "Tapas Kar, Ph.D, Asst. Scientist" Here is some important references for bond order calculations: J. Chem.Education 65(1988)674, J. Mol.Structure(Theochem)209(1990)45, Chem.Phys.lett.173(1990),569 and 192(1992)14. You have to modify l601.F of gaussian92 to add bond order calculation because it is not available as standard calculation in G92. It is a simple program and you can add few lines in l601.F. ************************************************************************** From Dr. Damir Kovacek GAMESS (US version) can calculate total bond orders and I have programs that can extract pi-bond orders from GAMESS and MOPAC output. If you are interested just send e-mail. ************************************************************************** From igshmu@gis.net Mon Dec 16 22:10:07 1996 Received: from home.gis.net for igshmu@gis.net by www.ccl.net (8.8.3/950822.1) id VAA26183; Mon, 16 Dec 1996 21:18:43 -0500 (EST) Received: from LOCALNAME (ppp34.gis.net [206.42.64.134]) by home.gis.net (8.8.0/8.6.11) with SMTP id VAA01651; Mon, 16 Dec 1996 21:18:22 -0500 (EST) Message-ID: <32B5A08E.ECC@gis.net> Date: Mon, 16 Dec 1996 11:18:38 -0800 From: Igor Shmuylovich X-Mailer: Mozilla 2.01 (Win16; U) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: igshmu@gis.net Subject: X-Ray Crystallography Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 7bit To Whom it may concern: I am a student currently participating an a contest. The subject I have chosen to write about is X-Ray Crystallography. I don't know much about this topic and any information will help me. I am especially interested in the possible future uses of X-Ray Crystallography. Coantact me at igshmu@gis.net. Sincerly, Leonid Shmuylovich