From chemistry-request@server.ccl.net Tue Sep 14 04:34:46 1999 Received: from york.ac.uk (pump3.york.ac.uk [144.32.128.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA20215 for ; Tue, 14 Sep 1999 04:34:45 -0400 Received: from ebor.york.ac.uk (ebor.york.ac.uk [144.32.128.95]) by york.ac.uk (8.9.3/8.9.3) with SMTP id JAA09336 for ; Tue, 14 Sep 1999 09:27:07 +0100 (BST) Date: Tue, 14 Sep 1999 09:27:08 +0100 (BST) From: "M.Reinhold" To: chemistry newsgroup Subject: CeriusII Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCler, since months we are puzzled about a particular problem with CeriusII. As some people out there might have more experience with this software than we have, I dare to post this question here, even if it is slightly off the main topic. We run ADF calculations through the Cerius II interface. The calculations ends without problems and the file can be read in by Cerius without problems. We are able to visualise frequencies and get information about the orbital orders in our systems. However, sometimes when we try to look at the orbital surfaces (e.g. read in the t41.* file) Cerius tells us that it cannot do this (something about the density map). This only occurs sometimes and we could not quite figure out if it is related to certain aspects in the calculations we do (e.g. symmetry, etc). Any help would be most appreciated. Meike reply to: mr113@york.ac.uk M. Reinhold PhD student Chemistry Department room C130 University of York From chemistry-request@server.ccl.net Tue Sep 14 04:53:30 1999 Received: from bjhal3.imf.kvl.dk (bjhal3.imf.kvl.dk [130.225.40.186]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA20334 for ; Tue, 14 Sep 1999 04:53:30 -0400 From: larso@bjhal3.imf.kvl.dk Received: (from larso@localhost) by bjhal3.imf.kvl.dk (8.8.7/8.8.7) id KAA02689 for chemistry@ccl.net; Tue, 14 Sep 1999 10:49:52 +0200 Date: Tue, 14 Sep 1999 10:49:52 +0200 Message-Id: <199909140849.KAA02689@bjhal3.imf.kvl.dk> To: chemistry@ccl.net Subject: geometry optimizations using oniom Hi everybody I have had some problems performing geometry optimizations using the oniom method i gaussian 98. I work with a metallo enzyme. The nearest parts of the coordinating amino acid residues and the metal ion are treated on b3lyp level, whereas pm3 is used for the rest. I freeze the alpha carbons of the aminoacids next to the coordinating aminoacid residues relative to each other to mimic the restriction that the backbone put on the active site. One of the calculations seemed to work fine. It ran about 35 cycles. I then restarted it from cycle nr 24, because it had the smallest forces, and all of a sudden I got the error message : Incomplete coordinate system. Try restarting with Geom=Check Guess=Read Opt=(ReadFC,NewRedundant) Incomplete coordinate system. Error termination via Lnk1e in /usr/local/g98/l103.exe. Sometimes I have also had this message already after the first cycle. What does this message mean? Is there any way you can avoid this error? Best regards Lars PS My e-mail address is : larso@dina.kvl.dk From chemistry-request@server.ccl.net Tue Sep 14 06:26:01 1999 Received: from rs5.thch.uni-bonn.de (rs5.thch.uni-bonn.de [131.220.44.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA20687 for ; Tue, 14 Sep 1999 06:25:53 -0400 Received: (from bernd@localhost) by rs5.thch.uni-bonn.de (8.8.8/8.8.5) id MAA16123 for chemistry@www.ccl.net; Tue, 14 Sep 1999 12:20:27 +0200 From: Bernd Engels Message-Id: <199909141020.MAA16123@rs5.thch.uni-bonn.de> Subject: excalator method To: chemistry@server.ccl.net (Computational Chemistry List) Date: Tue, 14 Sep 1999 12:20:26 +0200 (MES) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit dear CCL'er I looking for an algorithm or formular for the so called 'escalator method'. As I heard the escalator method gives you the approximate eigenvalues of an (n+1) times (n+1) matrix if you know the eigenvalues of the n times n matrix. As I heard the excalator method was used in one of the first versions of the MRD-CI code, but was later replaced by the Epstein-Nesbet method. I looked in the net and in numerical recipies but I couldn't find it. Any suggestions? If the topic is of interest, I will summarize. Bernd Engels Institut fuer Organische Chemie Wuerzburg From chemistry-request@server.ccl.net Mon Sep 13 13:11:22 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA15204 for ; Mon, 13 Sep 1999 13:11:22 -0400 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id NAA13721 for ; Mon, 13 Sep 1999 13:05:56 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <37DD3013.E918E759@syr.edu> Date: Mon, 13 Sep 1999 13:10:43 -0400 From: Deepak Singh Organization: Dept. of Chem & Biochem, Syracuse University X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: MD text Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everyone. Sometime ago I asked the following question "Can someone suggest an advanced text which covers MD simulations (particularly for proteins) and covers a broad range of aspects aspects incl. algorithms, trajectory evaluation, important results etc. I think McCammon and Harvey while good is a little dated, while the book "Computer Simulations of liquids" is out of print and impossible to get hold of through any means at my disposal. Rappaport is the other one I have looked at and it is not quite what I am looking for." Thank you to everyone who replied. Almost everyone who wrote to me recommended Frenkel/Smit - "Understanding molecular simulation" - Acad.Press, 1996, ISBN 0-12-267370-0 I must agree that this is an excellent book and very Similar to Allen and Tildesley's "Computer Simulation of Liquids". Other books recommended include Andrew R. Leach, Molecular Modeling: Principles & Applications, Addison Wesley Longman Ltd., Essex, 1996. Haile, Molecular Dynamics Simulation (on a similar level as Allen/Tildesley) Just a note .. Allen and Tildesley is BACK!!! regards Deepak. -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Mon Sep 13 18:09:03 1999 Received: from smtp2.san.cerf.net (smtp2.san.cerf.net [192.215.81.42]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA17712 for ; Mon, 13 Sep 1999 18:09:02 -0400 Received: from nic.cerf.net (nic.cerf.net [192.102.249.3]) by smtp2.san.cerf.net (8.8.8/10.1.96) with ESMTP id VAA12304 for ; Mon, 13 Sep 1999 21:03:24 GMT Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by nic.cerf.net (1.1.1/8.8.8) with ESMTP id OAA29915 for ; Mon, 13 Sep 1999 14:01:57 -0700 (PDT) Received: (from daemon@localhost) by bioc1.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id OAA25363; Mon, 13 Sep 1999 14:00:21 -0700 (PDT) Received: from gxf-pc.msi.com(146.202.11.21) by bioc1.msi.com via smap (V2.0) id xma025341; Mon, 13 Sep 99 13:59:51 -0700 Message-Id: <3.0.6.32.19990913140134.008ff600@sparky.msi.com> X-Sender: nxt@sparky.msi.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Mon, 13 Sep 1999 14:01:34 -0700 To: Keith Refson , Reinaldo Pis Diez From: Noppawan Tanpipat Subject: Re: CCL:Ab initio MD codes again Cc: chemistry@ccl.net In-Reply-To: <14301.18921.401079.283684@gargle.gargle.HOWL> References: <3.0.1.32.19990913131606.0069d51c@dalton.quimica.unlp.edu.ar> <3.0.1.32.19990913131606.0069d51c@dalton.quimica.unlp.edu.ar> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To add to the collection below, DMol3 - a local-orbital molecular and periodic DFT code from MSI - also does MD and simmulated annealing. Noppawan Tanpipat At 08:00 PM 9/13/99 +0100, Keith Refson wrote: >Reinaldo Pis Diez writes: > > Does anybody know if any of the AI-MD codes mentioned by Andrzej > > Szymoszek allow the treatment of spin-polarized systems? > > The fhi98md code doesn't do it as far as I know. I wonder if VASP and the > > Parrinello's code do. > >Both VASP and CASTEP are able to do spin-polarized calculations. So >can one more plane-wave code which was not mentioned, FEMD, written by >Ali Alavi now at Queens University, Belfast. I don't know his >position on sharing the code however. > >It is perhaps also worth mentioning that CASTEP is available free of >charge in source code form to all UK academics under an agreement >between MSI and the UK Car-Parrinello consortium. > >I can't find the original question to see the exact scope, but you can >also perform ab-initio MD with two other non-plane-wave codes I know >of, SIESTA which is a local-orbital periodic DFT code from Madrid >(P. Ordejon et al Phys. Rev B51 (1995) 1456-1476), and WIEN95 (98?) >which is a LAPW code from Karl-Heinz Schwarz's group in Vienna. I >can't be sure, but I also have a vague recollection that AMD >(Amsterdam Density Functional) also does MD. > >Keith Refson > >-- >Dr Keith Refson, "Paradigm is a word too often used by those who would >Dept of Earth Sciences like to have a new idea but cannot think of one." >Parks Road, -- Mervyn King, Deputy Governor, Bank of England >Oxford OX1 3PR, UK >Keith.Refson@ Tel: 01865 272026 > earth.ox.ac.uk Fax: 01865 272072 > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Tue Sep 14 09:13:28 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA22089 for ; Tue, 14 Sep 1999 09:13:24 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id JAA29685 for ; Tue, 14 Sep 1999 09:07:22 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id PAA14784 for ; Tue, 14 Sep 1999 15:07:10 +0200 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: CCL Subject: non-linear least squares Date: Tue, 14 Sep 1999 15:02:27 +0200 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <99091415070900.10751@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id JAA22090 Dear All, does anybody know of good OpenSource routines to perform unconstraint non-linear least squares fits, preferably in C++; C or FORTRAN are ok as well, though. Best would be a storage conserving implementation. Usage of BLAS would be nice, but I could probably change it accordingly by myself. I know of MINPACK codes lmstr and lmdif, nl2sol from TOMS and LINALG from CEPHES. Can anybody comment on these ? Does anybody know of new publications of any such algorithms ? Thanks in advance, -- Jochen Heinrich-Heine-Universität Düsseldorf jochen@uni-duesseldorf.de Institut für Physikalische Chemie I phone ++49-211-8113681 Universitätsstr. 26.43.02.29 fax ++49-211-8115195 40225 Düsseldorf, Germany www-public.rz.uni-duesseldorf.de/~jochen From chemistry-request@server.ccl.net Tue Sep 14 19:24:28 1999 Received: from tiger.jsums.edu (tiger.jsums.edu [143.132.85.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA24459 for ; Tue, 14 Sep 1999 19:24:28 -0400 Received: (from jerzy@localhost) by tiger.jsums.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) id SAA99588 for CHEMISTRY@ccl.net; Tue, 14 Sep 1999 18:12:27 -0500 (CDT) Date: Tue, 14 Sep 1999 18:12:27 -0500 (CDT) From: jerzy@tiger.jsums.edu (Jerzy Leszczynski) Message-Id: <199909142312.SAA99588@tiger.jsums.edu> To: CHEMISTRY@ccl.net Subject: 99.11.05 8th CCTCC Meeting (Conf Curr Trends Comp Chem) 8th CCTCC - Second Announcement Dear Colleague: We are pleased to announce the eighth conference on Current Trends in Computational Chemistry. This symposium, organized by Jackson State University, will cover all areas of computational chemistry as well as quantum chemistry. The local host of the conference is the US Army Corps of Engineers Waterways Experiment Station (WES) in Vicksburg, Mississippi. The meeting will be held at the Holiday Inn of Vicksburg, Mississippi (40 miles west of Jackson) on November 5th and 6th, 1999. The format consists of a series of plenary lectures and poster presentations on Friday and Saturday covering applications as well as theory. In addition, a banquet is scheduled for Friday evening and a dinner and reception for Saturday evening. The 8th conference will also feature another talk given in the ancillary "Noble Lecture Series." This series was initiated during the 6th CCTCC by a remarkable presentation by Istvan Hargittai entitled "The Molecules Among Us: Conversations with Famous Chemists" and followed by a lecture "Past and Future of the Fullerene Story" delivered by Eiji Osawa during the 7th CCTCC. The lectures in this series are presented in a relaxed, after-dinner atmosphere by the noble speakers and are devoted to noble scientific events and people. As such, it is an exceptional lecture to the conference and, contrary to the regular talks, might not necessarily report any Current findings. This year the talk will be delivered by Michael Kasha, Florida State University. We are planning to publish extended abstracts (up to four pagers each) of all invited talks and poster presentations. Original scientific contributions will be published in a special issue of the Journal of Molecular Structure (TEOCHEM). Manuscripts for inclusion in the special issue should be submitted in triplicate upon arrival at the registration desk. Submitted papers will be subject to the journal's standard referee procedures. Abstracts are due by September 30, 1999. Sincerely, Jerzy Leszczynski Chairman of the Organizing Committee 8th CONFERENCE ON Current Trends In Computational Chemistry NOVEMBER 5 & 6, 1999, Vicksburg, Mississippi 1. NAME:_______________________________________________________________________ 2. MAILING ADDRESS:____________________________________________________________ _______________________________________________________________________________ TELEPNONE:_______________FAX:_______________E-MAIL:_______________________ 2. If you wish to present a poster, please indicate the title below. All abstracts are due by September 30, 1999 (up to 4 pagers in length, presenting author underlined, photo ready quality, in duplicate) to ensure publication in the Conference Materials. TITLE:_________________________________________________________________________ _______________________________________________________________________________ AUTHORS: ______________________________________________________________________ 3. Conference materials, banquet and reception fee, all meals from breakfast Friday through dinner Saturday, coffee, and refreshments are included per paid participant. MAKE CHECKS PAYABLE TO: Current Trends in Computational Chemistry. Registration fee before September 1, 1999 US$ 150.00 $_____ Registration fee thereafter 200.00 $_____ Registration fee at student discount 75.00 $_____ 4. HOUSING: the organizers will not make housing reservations. To reserve a room at the special conference rate of $50.00-$60.00 per room, contact the Holiday Inn of Vicksburg, 3330 Clay Street, Vicksburg, MS 39180, Tel: (601) 636-4551, fax: (601) 636-4552. Reservations should be arranged with the Holiday Inn prior to October 10, 1999. I do____do not____plan to stay at the conference hotel I do____do not____plan to submit a paper to the special issue of TEOCHEM ________________ Signature http://tiger.jsums.edu/~cctcc/conf_ homepage.html Department of Chemistry, Jackson State University, Jackson, MS 39217, USA Conference Chairman: Jerzy Leszczynski, Tel: 601-973-3482, Email: jerzy2.iris5.jsums.edu; Conference Secretary: Ms. Shonda R. Allen, Tel: 601-973-3723, Email: srallen@stallion.jsums.edu List of Invited Speakers Misako Aida Hiroshima University Modeling of Reactions in Solution by Means of Ab Initio MD Issac B. Bersuker The University of Texas at Austin A Method of Combined Quantum Mechnical/Molecular Mechanics (QM/MM) Modeling for Large Transition Metal Systems with Charge Transfer Between QM and MM Sites Ernest Roy Davidson Indiana University Theoretical Interpretation of Photoelectron Spectra for Some Molecules and Clusters Martin Field Institut de Biologie Structurale, Grenoble Molecular Simulations using Hybrid Quantum Mechanical and Molecular Mechanical Potentials William L. Jorgenson Yale University What's New with Water, Reactions & Properties Predictions Michael Kasha Florida State University TBA Morris Krauss Center for Advanced Research in Biotechnology Binding Spectroscopy and Transition States in the Active Site of Chorismate Mutase Jan Lanbanowski Ohio Supercomputer Center Chemistry and Internet Mario Raimondi Universita' di Milano Non Orthogonal Approaches to the Determination of Intermolecular Potentials George Ch. Schatz Northwestern University Optical Properties of Metal Nanoparticles and Nanoparticle Aggregates Important in Biosensors Ajit J. Thakkar University of New Brunswick Connections Among Bond Orders, Polarizabilities and Aromaticity Harel Y. Weinstein Mount Sinai School of Medicine Specificity and Dynamics in Reguation of Gene Expression: The Rules of the TATA Box From chemistry-request@server.ccl.net Tue Sep 14 23:02:11 1999 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA25180 for ; Tue, 14 Sep 1999 23:02:08 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@ccl.net id AA19950; Wed, 15 Sep 99 10:55:41 -0700 Date: Wed, 15 Sep 1999 10:55:41 -0700 (PDT) From: Gao Ying To: CHEMISTRY@ccl.net Subject: Free CADD software release: LigBuilder v1.0 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, We announce here that LigBuilder v1.0 is now available. You can download it free via anonymous FTP to ftp2.ipc.pku.edu.cn/pub/software/LigBuilder. LigBuilder is a multiple-purposed program written for structure-based drug design procedure. Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket and subsequently screen them. In brief, main features of LigBuilder include: (1) The program analyzes the binding pocket of the target protein and derives the key interaction sites. A pharmacophore model is suggested and it could be applied to 3D database searching. (2) User can choose to develop ligand molecules by growing strategy or linking strategy. Either lead discovery or lead optimization tasks can be carried out. (3) Molecules are built up by using fragment as building blocks. Various kinds of structure manipulation are provided, such as growing, linking, and mutation. On-the-fly minimization of conformation is performed during the building-up procedure. The flexibility of the ligand molecules is considered. (4) Molecules are evolved by Genetic Algorithm. The fitness score of a molecule is evaluated by considering its chemical viability as well as binding affinity. (5) Chemical rules for judging "drug-likeness" are applied to screen the resultant molecules. Chemical stability, synthesis feasibility, and toxicity can also be taken into account by defining "forbidden structure" libraries. (6) All the input and output molecules are in popular format, i.e. protein in PDB format and ligand in Sybyl Mol2 format. The program is very easy to use and maintain. LigBuilder is written in C++ language and has been tested on UNIX, LINUX, and DOS platforms. If you encounter any problem while downloading the program, please contact Ms. Ying Gao at gao@ipc.pku.edu.cn. Please forward this mail to anyone who may concern. With best wishes, Molecular Design Laboratory, Institute of Physical Chemistry Peking University, Beijing, China From chemistry-request@server.ccl.net Tue Sep 14 23:06:00 1999 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA25199 for ; Tue, 14 Sep 1999 23:05:57 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@ccl.net id AA19970; Wed, 15 Sep 99 10:59:38 -0700 Date: Wed, 15 Sep 1999 10:59:37 -0700 (PDT) From: Gao Ying To: CHEMISTRY@ccl.net Subject: Free CADD software release: XLOGP v2.0 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, We announce here that XLOGP v2.0 is now available. You can download it free via anonymous FTP to ftp2.ipc.pku.edu.cn/pub/software/xlogp/. XLOGP is an atom-additive method for calculating the octanol/water partition coefficient(logP). It gives the logP value for a give compound by summing the contributions from component atoms and correction factors. In the current version of XLOGP, we have adopted a new atom classification scheme to deal with carbon, nitrogen, oxygen, sulfur, phosphorus, and halogen atoms. A new set of correction factors is also introduced. Compared to the original version (v1.1), XLOGP v2.0 is more robust and yields better statistical results. The comparison of various logP calculation procedures demonstrates that XLOGP v2.0 gives much better results than other atom-additive approaches and is at least comparable to some popular fragmental approaches. Because of the simple methodology, missing fragment problem does not occur to our method. XLOGP v2.0 is written in C++ and has been tested on UNIX, LINUX, and DOS platforms. If you encounter any problem while downloading the program, please contact Ms. Ying Gao at gao@ipc.pku.edu.cn. Please forward this mail to anyone who may concern. With best wishes, Molecular Design Laboratory, Institute of Physical Chemistry Peking University, Beijing, China