From chemistry-request@ccl.net Fri Jun 13 05:30:35 2003 Received: from mail.szote.u-szeged.hu (mail.szote.u-szeged.hu [160.114.96.63]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5D9UYkr030455 for >ccl.net>; Fri, 13 Jun 2003 05:30:35 -0400 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr<>ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id LAA01744 for >ccl.net>; Fri, 13 Jun 2003 11:30:32 +0200 Received: (qmail 9091 invoked by uid 525); 13 Jun 2003 09:30:32 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 13 Jun 2003 09:30:32 -0000 Date: Fri, 13 Jun 2003 11:30:32 +0200 (CEST) From: "Dr. Csaba Hetenyi" >ovrisc.mdche.u-szeged.hu> To: Nelson Fonseca >dq.ua.pt> cc: chemistry<>ccl.net Subject: Re: CCL:Mapping Intermolecular Interactions In-Reply-To: >backend-2.cgpmail.ua.pt> Message-ID: >ovrisc.mdche.u-szeged.hu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Try AUTODOCK. http://www.scripps.edu/pub/olson-web/doc/autodock/ "If you interfere with nature you will suffer for it." Best, Csaba On Thu, 12 Jun 2003, Nelson Fonseca wrote: > Experience is what you get when you don't get what you > want. > > -- Dan Stanford-- > > Dear cclers: > > Is there any free software than can calculate the best > docking conformation between 2 molecules based on > intermolecular interactions given by any Force Field? > > Thanks in advance > > > --------------------- > --------------------- > Nelson Fonseca > Dep. of Chemistry > University of Aveiro > Portugal > --------------------- > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY<>ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST<>ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl<>ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > ------ Csaba Hetenyi, MSc, PhD Dept. of Medical Chemistry, University of Szeged, 8 Dom ter, Szeged 6720, Hungary From chemistry-request@ccl.net Fri Jun 13 05:11:52 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5D9Bakr029206 for ; Fri, 13 Jun 2003 05:11:44 -0400 Received: from mail.ustc.edu.cn (mail.ustc.edu.cn [202.38.64.10]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with SMTP id RAA02556 for ; Fri, 13 Jun 2003 17:07:44 +0800 Received: (qmail 13015 invoked by uid 8812); 13 Jun 2003 09:07:44 -0000 Date: Fri, 13 Jun 2003 17:07:44 +0800 (CST) From: Dai Bing X-X-Sender: To: Subject: CCL:the ground state calculation with g98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, A simple Opt calculation with g98, HOMO and LUMO are the same symmetry, such as PI. But the energy of LUMO is lower than the one of HOMO, what's the problem? and how to resolve? The following two methods don't work. :( 1. Stable=opt. 2. change the symmetry of the molecule, HOMO and LUMO change to A1 and B1, then use guess=alter. Can someone help me? Thanks. = = = = = = = = = = = = = = = = = = = = =============== Bing Dai, Ph.D. Candidate, Laboratory of Bond Selective Chemistry, University of Science and Technology of China, Chinese Academy of Sciences. Hefei, Anhui, 230026, People's Republic of China, Tel.: 86-551-3603418,3603748,3601084 Fax.: 86-551-3602969 Http://www.bsc.ustc.edu.cn/~bdai E-mail: bdai..at..mail.ustc.edu.cn =============== From chemistry-request@ccl.net Fri Jun 13 04:48:35 2003 Received: from mail-nord.nord.univ-mrs.fr (mail-nord.nord.univ-mrs.fr [194.214.97.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5D8mXkr028212 for ; Fri, 13 Jun 2003 04:48:34 -0400 Received: from localhost (localhost [127.0.0.1]) by mail-nord.nord.univ-mrs.fr (Postfix) with ESMTP id A4816B3AB3 for ; Fri, 13 Jun 2003 09:49:42 +0200 (CEST) Received: from [194.214.91.105] (unknown [194.214.91.105]) by mail-nord.nord.univ-mrs.fr (Postfix) with ESMTP id C8B9FB3AB1 for ; Fri, 13 Jun 2003 09:49:40 +0200 (CEST) X-Sender: sampieri..at..mail-nord.nord.univ-mrs.fr (Unverified) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 13 Jun 2003 10:46:39 +0200 To: chemistry..at..ccl.net From: Francois Sampieri Subject: Inter-residue contact matrix X-Virus-Scanned: by AMaViS perl-11 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h5D8mZkr028213 Hi all, Is there any free program (executable for SGI Irix 6.5, or Mac OS X) that could make a graphical representation of matrix of protein inter-residue contacts? Thank you and best regards! Frangois Sampieri ____________________________________________ UMR 6560 CNRS-Universite de la Mediterranee Laboratoire de Biochimie - IFR Jean Roche Faculte de Medecine Nord, Bd Pierre Dramard 13916 Marseille Cedex 20 E-mail: sampieri.f..at..jean-roche.univ-mrs.fr Tel: (33) 4 91 69 88 44 Fax: (33) 4 91 65 75 95 From chemistry-request@ccl.net Fri Jun 13 06:42:42 2003 Received: from apex.ibpc.fr (apex.ibpc.fr [193.49.234.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5DAggkr001567 for ; Fri, 13 Jun 2003 06:42:42 -0400 Received: from baaden.galaxy.ibpc.fr (baaden[at]serv-1B2A.galaxy.ibpc.fr [193.49.27.42]) by apex.ibpc.fr (8.9.3/jtpda-5.3.3) with ESMTP id MAA14954 for ; Fri, 13 Jun 2003 12:42:40 +0200 (MET DST) Message-Id: <200306131042.MAA14954[at]apex.ibpc.fr> X-Mailer: exmh version 2.5 07/13/2001 (debian 2.5-1) with nmh-1.0.4+dev To: chemistry[at]ccl.net Subject: Re: CCL:Inter-residue contact matrix In-reply-to: Your message of "Fri, 13 Jun 2003 10:46:39 +0200." X-image-url: http://crypt.u-strasbg.fr/marc/m-baaden.gif X-url: X-face: -Nz&SN]%I8g9WFR#/!fe9se!_G_OndNloj@t+6jrGsoZ"z)?an0n P!Nls~*o?u7fy:]1N|^^(KX*uE>Nk{bHaCJ)(hXF~E#5)j.k0n4hgfIzpmn,[VY'\7X:;VOZ\CItIq G!2f8,k2`VLrkXQ:<.3LxEQ'E-;d:A)V# Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii From: Marc Baaden Date: Fri, 13 Jun 2003 12:42:40 +0200 Sender: baaden[at]smplinux.de sampieri.f[at]jean-roche.univ-mrs.fr said: >> Is there any free program (executable for SGI Irix 6.5, or Mac OS X) >> that could make a graphical representation of matrix of protein >> inter-residue contacts? There are such tools in the gromacs package (www.gromacs.org), which is free and can be compiled on linux, SGI, MacosX and windows. I think there are even binaries for some of these platforms. The precise tool you are looking for is g_mdmat, I believe. Here goes its description: g_mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames these distance matrices can be stored as a function of time, to be able to see differences in tertiary structure as a funcion of time. If you choose your options unwise, this may generate a large output file. Default only an averaged matrix over the whole trajectory is output. Also a count of the number of different atomic contacts between residues over the whole trajectory can be made. The output can be processed with xpm2ps to make a PostScript (tm) plot. Best wishes, Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden[at]smplinux.de - http://www.marc-baaden.de FAX: +49 697912 39550 - Tel: +33 15841 5176 ou +33 609 843217 From chemistry-request@ccl.net Fri Jun 13 08:26:02 2003 Received: from august.V-LO.krakow.pl (august.V-LO.krakow.pl [62.121.131.17]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5DCQ1kr005514 for >ccl.net>; Fri, 13 Jun 2003 08:26:02 -0400 Received: from cooker (helo=localhost) by august.V-LO.krakow.pl with local-esmtp id 19Qncv-0000qS-00 for >ccl.net>; Fri, 13 Jun 2003 14:25:53 +0200 Date: Fri, 13 Jun 2003 14:25:53 +0200 (CEST) From: Wojciech Migda >v-lo.krakow.pl> To: CHEMISTRY<>ccl.net Subject: CCL: problems with NBO under g03 Message-ID: >august.V-LO.krakow.pl> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am performing NBO analysis of few conformers using the B3LYP functional using Gaussian03 suite. Some of the jobs finished OK, but some did not. Here is an example: NEXT STEP: Evaluate the energy of the new density matrix that has been constructed from the deleted NBO Fock matrix by doing one SCF cycle. Requested convergence on RMS density matrix=1.00D-08 within 1 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. Integral accuracy reduced to 1.0D-05 until final iterations. Spurious integrated density or basis function: NE= 112 NElCor= 0 El error=1.33D-01 rel=1.19D-03 Tolerance=1.00D-03 Shell 49 absolute error=2.10D-04 Tolerance=1.20D-02 Shell 32 signed error=1.66D-04 Tolerance=1.00D-01 Inaccurate quadrature in CalDSu. Error termination via Lnk1e in /usr_ext1/gaussian03/g03/l502.exe at Thu Jun 5 12:12:21 2003. Here is an input example: # B3LYP/6-31G scf=tight extrabasis Pop=NBODel ace3meme 001 NBO 0 1 C -2.270609 -1.011243 1.694649 C -1.811376 -1.734650 2.792965 C -0.522851 -2.268014 2.776627 C 0.282744 -2.066293 1.659066 C -0.163496 -1.330043 0.552245 C -1.469583 -0.791039 0.563789 C 0.801747 -1.142593 -0.600345 O 1.673819 -0.016651 -0.364289 C 1.649744 1.053842 -1.311273 O 0.319917 1.528623 -1.504622 C -0.383079 1.976894 -0.336063 C -1.842327 1.550689 -0.443122 C -2.048541 0.024954 -0.578211 H -3.281431 -0.609607 1.704866 H -2.459800 -1.889590 3.650650 H -0.152702 -2.842321 3.620777 H 1.285386 -2.485917 1.635255 C 2.568848 2.122040 -0.716116 C 2.124344 0.613607 -2.696992 H 0.067615 1.541069 0.560835 H -0.311254 3.070125 -0.264144 H 0.269901 -1.016887 -1.544348 H 1.441624 -2.027587 -0.685884 H -2.302772 2.043323 -1.307978 H -2.365126 1.917850 0.449649 H -1.633307 -0.294851 -1.537019 H -3.126268 -0.166300 -0.632275 H 2.582681 3.002912 -1.363329 H 2.229405 2.415644 0.279491 H 3.585510 1.732528 -0.624696 H 2.139129 1.469600 -3.376197 H 3.131920 0.195921 -2.628818 H 1.456457 -0.138987 -3.122534 O 0 sp 1 1.00 0.0845 1.00 1.00 d 1 1.00 0.80 1.00 **** C 0 d 1 1.00 0.80 1.00 **** H 0 p 1 1.00 1.10 1.00 **** $NBO $END $DEL NOSTAR $END What is wrong? Yours, Wojciech Migda, migda<>chemia.uj.edu.pl Department of Organic Chemistry Faculty of Chemistry Jagiellonian University Krakow, POLAND From chemistry-request@ccl.net Fri Jun 13 08:30:41 2003 Received: from facstaff.wesleyan.edu (facstaff.wesleyan.edu [129.133.1.61]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5DCUekr005642 for >ccl.net>; Fri, 13 Jun 2003 08:30:40 -0400 Received: from facstaff.wesleyan.edu (localhost [127.0.0.1]) by facstaff.wesleyan.edu (8.12.8/8.12.6) with ESMTP id h5DCUVqW019912 for >ccl.net>; Fri, 13 Jun 2003 08:30:31 -0400 (EDT) Received: from localhost (yliu@localhost) by facstaff.wesleyan.edu (8.12.8/8.12.6/Submit) with ESMTP id h5DCUUfj019909 for >ccl.net>; Fri, 13 Jun 2003 08:30:30 -0400 (EDT) X-Authentication-Warning: facstaff.wesleyan.edu: yliu owned process doing -bs Date: Fri, 13 Jun 2003 08:30:30 -0400 (EDT) From: Michael Liu >wesleyan.edu> To: chemistry<>ccl.net Subject: SDF file format definition Message-ID: >facstaff.wesleyan.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-ECS-MailScanner: Found to be clean Hi, Could anyone please point to me where can I find the definition of SDF file format on internet if I do not want to go to the orginal paper? Thank you very much in advance. Mike From chemistry-request@ccl.net Fri Jun 13 08:14:04 2003 Received: from ufpe.br (h249.ip179.ufpe.br [150.161.179.249] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with SMTP id h5DCE3kr005263 for >ccl.net>; Fri, 13 Jun 2003 08:14:04 -0400 Received: (qmail 12787 invoked from network); 13 Jun 2003 12:17:43 -0000 Received: from webmail.ufpe.br (HELO ufpe.br) (150.161.179.200) by 0 with SMTP; 13 Jun 2003 12:17:43 -0000 Received: from 150.161.174.74 (SquirrelMail authenticated user zaldini) by www.webmail.ufpe.br with HTTP; Fri, 13 Jun 2003 09:12:53 -0300 (BRT) Message-ID: <1272.150.161.174.74.1055506373.squirrel<>www.webmail.ufpe.br> Date: Fri, 13 Jun 2003 09:12:53 -0300 (BRT) Subject: CCL: FORTRAN & C communication From: >ufpe.br> To: >ccl.net> X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, I would like to find some good reference ou instruction about the communication between program codes written in FORTRAN and C. Thanks in advance. Prof. Marcelo Z. Hernandes UFPE - Brazil From chemistry-request@ccl.net Fri Jun 13 11:42:32 2003 Received: from haney.hbond.com (haney.hbond.com [207.137.2.252]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5DFgUkr016560 for ; Fri, 13 Jun 2003 11:42:31 -0400 Received: (from haney@localhost) by haney.hbond.com (8.9.3/8.9.3) id IAA01302; Fri, 13 Jun 2003 08:42:26 -0700 From: "Dr. David N. Haney" Message-Id: <200306131542.IAA01302^at^haney.hbond.com> Subject: Re: CCL:SDF file format definition To: yliu^at^wesleyan.edu (Michael Liu) Date: Fri, 13 Jun 2003 08:42:25 -0700 (PDT) Cc: chemistry^at^ccl.net In-Reply-To: from "Michael Liu" at Jun 13, 2003 08:30:30 AM X-Mailer: ELM [version 2.5 PL5] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mike: SDF and MOL are MDL file formats. MDL provides information about them at: www.mdl.com/downloads/ctfile/ctfile_subs.html. > Hi, > > Could anyone please point to me where can I find the definition of SDF > file format on internet if I do not want to go to the orginal paper? > > Thank you very much in advance. > > Mike -- ######### David N. Haney, Ph.D. ######### # Haney Associates Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney^at^hbond.com # ################# ##################### From chemistry-request@ccl.net Fri Jun 13 11:42:30 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5DFgOkr016548 for ; Fri, 13 Jun 2003 11:42:30 -0400 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h5DFgNZA035601 for ; Fri, 13 Jun 2003 17:42:23 +0200 (CEST) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id h5DFgNPm401795; Fri, 13 Jun 2003 17:42:23 +0200 (MEST) Date: Fri, 13 Jun 2003 17:42:23 +0200 (MEST) From: Michel Petitjean Message-Id: <200306131542.h5DFgNPm401795.-at-.ds10.itodys.jussieu.fr> To: chemistry.-at-.ccl.net Subject: CCL:Re: FORTRAN & C communication X-Antivirus: scanned by sophie at shiva.jussieu.fr To: Subject: CCL:Re: FORTRAN & C communication Calling fortran from C: transmit all arguments with pointers. No problem should occur with scalar or arrays of integers or reals (or double precision reals). Calling C from fortran: use built-in functions such as %val, %adr,... when transmitting arguments, if available on your compiler. Multi-indiced arrays are stored according varying the first index first in fortran, and according varying first the last index in C. When compiling fortran on sgi, use the -Wf,-noappend flag, and when compiling fortran on compaq unix, use the -assume nounderscore flag. Owing to the time lost for maintaining non-portable applications mixing languages, it is sometimes better to reprogramme all in a single language. For numerical applications and formatted i/o, I find that fortran is quite easier than C (I know that some people do not agree). If you encounter difficulties, ask questions on the comp.lang.fortran newsgroup. It is read by experienced developpers. Michel Petitjean, Email: petitjean.-at-.itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean.-at-.ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html asked: >Dear CCLers, > >I would like to find some good reference ou instruction about the >communication between program codes written in FORTRAN and C. >Thanks in advance. > >Prof. Marcelo Z. Hernandes >UFPE - Brazil From chemistry-request@ccl.net Fri Jun 13 10:37:20 2003 Received: from novalfsmtp2.novsvcs.net (smtp2.novsvcs.net [192.208.44.111]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5DEbJkr012607 for ; Fri, 13 Jun 2003 10:37:20 -0400 Received: from ukrgsmtp02.cp.chbs ([147.167.242.114]) by novalfsmtp2.novsvcs.net (8.10.2/8.9.3) with ESMTP id h5DEbIV05086; Fri, 13 Jun 2003 10:37:18 -0400 Received: from ukrgmsxhub10.cp.chbs (ukrgmsxhub10.cp.chbs [147.167.242.94]) by ukrgsmtp02.cp.chbs (Build 103 8.9.3p2/NT-8.9.3) with ESMTP id PAA00849; Fri, 13 Jun 2003 15:37:19 +0100 From: graham.mullier^at^syngenta.com Received: by ukrgmsxhub10.cp.chbs with Internet Mail Service (5.5.2653.19) id ; Fri, 13 Jun 2003 15:37:17 +0100 Message-ID: <0B27450D68F1D511993E0001FA7ED2B3025E5035^at^ukjhmbx12.ukjh.zeneca.com> To: yliu^at^wesleyan.edu Cc: chemistry^at^ccl.net Subject: RE: SDF file format definition Date: Fri, 13 Jun 2003 15:37:15 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain MDL web site, see also previous post in this group and I'm feeling generous so here's the last URL I posted: http://www.mdli.com/downloads/literature/ctfile.pdf Graham Graham Mullier Chemoinformatics Team Leader, Chemistry Design Group, Syngenta, Bracknell, RG42 6EY, UK. direct line: +44 (0) 1344 414163 -----Original Message----- From: Michael Liu [mailto:yliu^at^wesleyan.edu] Sent: 13 June 2003 13:31 To: chemistry^at^ccl.net Subject: CCL:SDF file format definition Hi, Could anyone please point to me where can I find the definition of SDF file format on internet if I do not want to go to the orginal paper? Thank you very much in advance. Mike -= This is automatically added to each message by 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 mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl^at^ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Fri Jun 13 10:08:50 2003 Received: from mail.webcable.com.br (mail.webcable.com.br [200.189.175.162]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5DE8kkr010325 for ; Fri, 13 Jun 2003 10:08:50 -0400 Received: from localhost ([127.0.0.1] helo=webcable.com.br) by mail.webcable.com.br with esmtp (Exim 3.36 #1) id 19QpJg-0006db-00; Fri, 13 Jun 2003 11:14:08 -0300 From: "Dinbmica" To: chemistry^at^ccl.net Subject: CCL: NDDO semiempirical parameters Date: Fri, 13 Jun 2003 11:14:08 -0300 Message-Id: <20030613111408.M52463^at^webcable.com.br> X-Mailer: Open WebMail 1.63 20020319 X-OriginatingIP: 200.183.85.218 (dinamica^at^webcable.com.br) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Dear CCLers,, I have a couple of questions about semiempirical parameters in NDDO methods (MNDO, AM1...): 1) Do you have any routine or the iterative formulas to obtain the derived parameters, rho1 and rho2, from the optimized ones (namely 1 center 2 electron integrals, g_ij, and zeta_i) ?? 2) Can you suggest any references which explicitly comment on the individual influence of the NDDO parameters upon calculated molecular properties? E.g.: If one varies the resonance integrals (beta_i), what is the effect upon geometries? Or if one varies the one center one electron integrals (U_ii), what is the effect upon charge distribution? Thank you very much for your help, Guilherme Menegon IQUSP From chemistry-request@ccl.net Fri Jun 13 16:43:40 2003 Received: from sccrmhc13.attbi.com (sccrmhc13.attbi.com [204.127.202.64]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5DKhekr030991 for ; Fri, 13 Jun 2003 16:43:40 -0400 Received: from C1353359A (12-207-202-154.client.attbi.com[12.207.202.154](untrusted sender)) by attbi.com (sccrmhc13) with SMTP id <20030613204337016001ktcke>; Fri, 13 Jun 2003 20:43:37 +0000 Reply-To: From: "Mark Thompson" To: "Dinbmica" , Subject: CCL: NDDO semiempirical parameters Date: Fri, 13 Jun 2003 13:38:44 -0700 Message-ID: <000001c331eb$c845a970$0300a8c0~at~attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-Reply-To: <20030613111408.M52463~at~webcable.com.br> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 > I have a couple of questions about semiempirical parameters in > NDDO methods (MNDO, AM1...): > > 1) Do you have any routine or the iterative formulas to obtain > the derived parameters, rho1 and rho2, from the optimized ones > (namely 1 center 2 electron integrals, g_ij, and zeta_i) ?? Other than the discussion given in the original Thiel and Dewar papers, you pretty much have to write your own; its not too hard. (If you do find other sources on this, please summarize to the CCL). > 2) Can you suggest any references which explicitly comment on the > individual influence of the NDDO parameters upon calculated > molecular properties? > E.g.: If one varies the resonance integrals (beta_i), what is > the effect upon geometries? Or if one varies the one center one > electron integrals (U_ii), what is the effect upon charge distribution? The two original Jimmy Stewart PM3 references would be a good place to start (also email Jimmy himself). The references are : J.Comp.Chem 10, 209-220 (1989) J.Comp.Chem 10, 221-264 (1989) You can experiment with some of these param modifications, by hand, using ArgusLab. Simply modify the AM1, PM3, MNDO params (in am1.prm, pm3.prm, and mndo.prm) with a text editor and see what happens. Make sure you save copies of the original parameter files. Download it at http://www.arguslab.com Cheers, Mark ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 FAX: 206-440-3305 ArgusLab is available at: http://www.arguslab.com ================================= From chemistry-request@ccl.net Fri Jun 13 16:34:04 2003 Received: from parker.howard.edu ([138.238.147.154]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5DKXvkr030815 for ; Fri, 13 Jun 2003 16:34:02 -0400 Received: by PARKER with Internet Mail Service (5.5.2653.19) id ; Fri, 13 Jun 2003 16:33:57 -0400 Message-ID: From: "Ferber, Steven D" To: "'chemistry/at/ccl.net'" Subject: Converging frozen endpoint optimizations Date: Fri, 13 Jun 2003 16:33:55 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" To whom has a clue, I first apologize for asking such a general question - but since the search engines are down - I can't avoid it. Can anyone give me references (like in the CCL archives) for tricks to converge an optimization with FROZEN ENDpoints (like parts of a poly-nucleotide). This is for subsequent vibrational normal mode calculation. I am using B3LYP/6-31+G* on g'98 with GDIIS optimization and ultrafine grid Integrals. Any hints would be greatly appreciated. Steven D. Ferber Grad Student - Physical BioCHEMISTRY Howard University Chemistry Dept. - D.C. sferber/at/howard.edu 202/806-4231 From jkl@ccl.net Fri Jun 13 15:06:12 2003 -0400 Return-Path: Received: from mtiwmhc11.worldnet.att.net (mtiwmhc11.worldnet.att.net [204.127.131.115]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h5DJ69g20264 for ; Fri, 13 Jun 2003 15:06:12 -0400 (EDT) Received: from hal (247.denver-08rh16rt.co.dial-access.att.net[12.86.39.247]) by mtiwmhc11.worldnet.att.net (mtiwmhc11) with SMTP id <200306131906051110069rrpe>; Fri, 13 Jun 2003 19:06:05 +0000 Message-Id: <4.2.0.58.20030613130308.00afb860(at)postoffice.worldnet.att.net> X-Sender: mrmopac(at)postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Fri, 13 Jun 2003 13:03:37 -0600 To: jkl(at)ccl.net From: "James J. P. Stewart" Subject: Re: CCL:NDDO semiempirical parameters Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_255821515==_.ALT" --=====================_255821515==_.ALT Guilherme Menegon asked, >1) Do you have any routine or the iterative formulas to obtain the derived >parameters, rho1 and rho2, from the optimized ones (namely 1 center 2 >electron integrals, g_ij, and zeta_i) ?? The recursive, iterative procedures for obtaining these parameters were first described in M. J. S. Dewar and W. Thiel. Ground States of Molecules, 38. The MNDO Method. Approximations and Parameters. J. Am. Chem. Soc., 99:4899-4907, 1977. For a brief discussion, please see: http://www.cachesoftware.com/mopac/Mopac2002manual/node447.html Jimmy ( @ @ ) .-------------oOOo----(_)----oOOo-------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: jstewart(at)fujitsu.com | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | | | USA .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo. | | .--------------------\ (----( )-------------------------------------. \_) ) / (_/ --=====================_255821515==_.ALT Content-Type: text/html; charset="us-ascii"
Guilherme Menegon asked,

1) Do you have any routine or the iterative formulas to obtain the derived parameters, rho1 and rho2, from the optimized ones (namely 1 center 2 electron integrals, g_ij, and zeta_i) ??

The recursive, iterative procedures for obtaining these parameters were first described in M. J. S. Dewar and W. Thiel. Ground States of Molecules, 38. The MNDO Method. Approximations and Parameters. J. Am. Chem. Soc., 99:4899-4907, 1977.

For a brief discussion, please see: http://www.cachesoftware.com/mopac/Mopac2002manual/node447.html

Jimmy


                     ( @ @ )
 .-------------oOOo----(_)----oOOo-------------------------------------.
 | James J. P. Stewart             |                                   |
 | Stewart Computational Chemistry | E-mail:  jstewart(at)fujitsu.com     |
 | 15210 Paddington Circle         |  39/03/15 N, 104/49/29 W          |
 | Colorado Springs CO 80921-2512  |                                   |
 | USA               .ooo0         | Phone: USA +(719) 488-9416        |
 |                   (   )   Oooo. |                                   |
 .--------------------\ (----(   )-------------------------------------.
                       \_)    ) /
                             (_/ --=====================_255821515==_.ALT--