From chemistry-request@ccl.net Mon Sep 22 17:41:56 2003 Received: from atom.chem.iupui.edu (atom.chem.iupui.edu [134.68.137.125]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8MLfPmK015762 for ; Mon, 22 Sep 2003 17:41:25 -0400 Received: from chem.iupui.edu (unknown [134.68.137.128]) by atom.chem.iupui.edu (Postfix) with ESMTP id 9F9A8240904; Mon, 22 Sep 2003 16:40:28 -0500 (CDT) Message-ID: <3F6F7AE9.68558CD8!at!chem.iupui.edu> Date: Mon, 22 Sep 2003 16:43:54 -0600 From: "Boyd, D." X-Mailer: Mozilla 4.79C-CCK-MCD {C-UDP; EBM-APPLE} (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: OSC CCL , QSAR & Modelling Society Subject: Alzheimer's Disease Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Colleagues, A symposium on molecular modeling related to Alzheimer's Disease will be held at the 36th Central Regional American Chemical Society Meeting in Indianapolis, June 2-4, 2004. This is one of the larger regional meetings. Topics of interest: computational chemistry, molecular simulations, docking, QSAR, etc., related to amyloid peptides beta-secretase beta-amyloid precursor protein (APP) presenilin acetyl cholinesterase etc. Please let me know by October 15 if you are interested in presenting a paper. Thanks, Don Donald B. Boyd, Ph.D. Research Professor of Chemistry http://chem.iupui.edu/ Department of Chemistry Indiana University-Purdue University at Indianapolis Indianapolis, Indiana 46202-3274, U.S.A. E-mail boyd!at!chem.iupui.edu From chemistry-request@ccl.net Mon Sep 22 08:01:18 2003 Received: from puga.vdu.lt (puga.vdu.lt [193.219.38.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8MC1BmK015546 for ; Mon, 22 Sep 2003 08:01:13 -0400 Received: from amavis by puga.vdu.lt with scanned-ok for chemistry..at..ccl.net id 1A1PNF-0002Ps-00; Mon, 22 Sep 2003 15:01:01 +0300 Received: from vaidila.vdu.lt ([193.219.38.52] ident=mail) by puga.vdu.lt with esmtp for chemistry..at..ccl.net id 1A1PNF-0002Pj-00; Mon, 22 Sep 2003 15:01:01 +0300 Received: from vejas.vdu.lt ([193.219.38.82] helo=localhost) by vaidila.vdu.lt with esmtp for chemistry..at..ccl.net id 1A1PNJ-0005RS-00; Mon, 22 Sep 2003 14:01:05 +0200 Date: Mon, 22 Sep 2003 15:01:05 +0300 From: Arturas X-Mailer: The Bat! (v1.62i) Reply-To: Arturas Organization: SemteX X-Priority: 3 (Normal) Message-ID: <141162427548.20030922150105..at..vaidila.vdu.lt> To: chemistry..at..ccl.net Subject: PCM In-Reply-To: <3E7A516D.8040300..at..u.washington.edu> References: <3E7A516D.8040300..at..u.washington.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS snapshot-20020300 X-Spam-Status: No, hits=3.4 required=7.0 tests=IN_REP_TO,RCVD_IN_NJABL,RCVD_IN_OSIRUSOFT_COM,REFERENCES, X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, PCM method (Gaussian) produce table of energies related to solvation effects. The last entry is: ------------------------------------------------------ DeltaG (solv) (kcal/mol) = ....... ------------------------------------------------------ What is exact physical meaning of that energy ? Is it 'pure' sovatation energy ? Arturas Z. - * - E-mail: a3arzi..at..vaidila.vdu.lt WWW : http://biologija.vdu.lt/person/ziemar From chemistry-request@ccl.net Sun Sep 21 23:52:25 2003 Received: from home.delsci.net (adsl-64-166-142-98.dsl.snfc21.pacbell.net [64.166.142.98]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8M3qJmK004455 for ; Sun, 21 Sep 2003 23:52:20 -0400 Received: from Ultra2 (router.delsci.net [192.168.0.1]) by home.delsci.net (8.11.6/8.11.6) with ESMTP id h8M3sxa26389; Sun, 21 Sep 2003 20:55:00 -0700 From: "Warren L. DeLano" To: "'Tal Lavy'" , Subject: RE: Software for generating conformations Date: Sun, 21 Sep 2003 20:52:15 -0700 Message-ID: <001301c380bc$e9ccb5a0$0c00a8c0@Ultra2> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 In-Reply-To: <200309211733.05639.tallavy..at..md.huji.ac.il> X-Spam-Status: No, hits=2.5 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,RCVD_IN_OSIRUSOFT_COM, X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Tal, PyMOL can do this kind of thing so long as you can uniquely specify the atoms which make up each torsion you wish to set... Usage: set_dihedral atom1, atom2, atom3, atom4, angle Example: set_dihedral 11/ca, 11/cb, 11/cg, 11/cd1, 180 You could use a short Python loop to automatically adjust the torsion(s) and then save the modified pdb files. For example, the following snippet: > from pymol import cmd for angle in (30, 65, 115, 40, 150): \ cmd.set_dihedral("11/ca","11/cb","11/cg","11/cd1",angle) \ cmd.save("mol_%d.pdb"%angle) generates a set of 5 PDB files which you can then plug into some external force-field minimizer. Cheers, Warren -- mailto:warren..at..delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request..at..ccl.net] On > Behalf Of Tal Lavy > Sent: Sunday, September 21, 2003 6:33 AM > To: CHEMISTRY..at..ccl.net > Subject: CCL:Software for generating conformations > > > > > Dear All, > > > I am looking for a free program that could generate (and output) > conformations of molecules, according to specifications of rotations > around > bonds, by the user. > > This means the user constructs the molecule and the program reads it in > PDB > format, then the user inputs a set of angles (30, 65, 115, 40, 150 etc..) > and > the program outputs the transformed coordinates for the structure. These > structures should then undergo a force field evaluation. > > Thank you very much, > > Tal > > > =========================================================== > Tal Lavy, > Molecular Modeling and Drug Design > Department of Medicinal Chemistry and Natural Products > School of Pharmacy > Hebrew University of Jerusalem > ISRAEL > Phone: 972-2-6757026 > Fax: 972-2-6758925 > e-mail: tallavy..at..md.huji.ac.il > > http://www.md.huji.ac.il/models > ============================================================ > > > > > -= This is automatically added to each message by the 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 Mon Sep 22 10:44:30 2003 Received: from 198.211.180.54 (65-102-243-75.dnvr.qwest.net [65.102.243.75]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h8MEhmmK022194 for ; Mon, 22 Sep 2003 10:43:51 -0400 Message-Id: <200309221443.h8MEhmmK022194..at..server.ccl.net> From: "Gregory Banik" To: Subject: New Software for Chemical Education Sender: "Gregory Banik" Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit Date: Mon, 22 Sep 2003 08:41:59 -0600 Reply-To: "Gregory Banik" X-Spam-Status: No, hits=0.9 required=7.0 tests=NO_COST version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Colleague: I am pleased to announce Bio-Rad's new software tool for teaching key concepts in organic and analytical chemistry: the Academic Edition of Bio-Rad's KnowItAll(R) Informatics System. The KnowItAll Academic Edition is available by download at no charge for professors, other faculty and staff, and students at degree-granting institutions (see website URL information below). As the winner of Scientific Computing & Instrumentation magazine's Reader's Choice Award for Best Spectroscopy Software in 2001, 2002, and 2003, we proudly offer this high quality teaching resource to the professors and students of today--the professors and scientists of tomorrow. The KnowItAll Academic Edition represents the combination of the renowned Sadtler spectral data and software with the highly regarded ChemWindow software (from the former Softshell company, now part of Bio-Rad). The new program includes: - Applications for chemical structure drawing and reporting, - A teaching version of the well-known Perch software for proton NMR spectrum prediction and simulation, - Applications for processing NMR, IR, and Raman spectra, - Applications for IR and Raman spectroscopy functional group analysis, - The Sadtler Handbook of Infrared Spectra in a new web format, - An application for 3D structure creation and visualization, - An application for symmetry and point group analysis, and - Clipart for laboratory glassware and chemical engineering symbols. I recently described the KnowItAll Academic Edition in two talks at the ACS meeting in New York. A recording of a recent webcast of these combined presentations is available on our WebEx site at http://bio-radevents.webex.com (please click on the "Recorded Events" link on the left). The presentation will give you ideas about how you can use KnowItAll to teach key concepts in organic and analytical chemistry. Please visit our web site at http://www.knowitall.com/academic to download your copy of the KnowItAll Academic Edition--Bio-Rad wants to help you make each of your students a KnowItAll in chemistry! Best regards, Gregory M. Banik, Ph.D. General Manager Bio-Rad Laboratories, Inc. Informatics Division 3316 Spring Garden Street Philadelphia, PA 19104 USA Web: http://www.knowitall.com/academic If you would rather not receive e-mail from the Bio-Rad Informatics Division, click on the following link, and you will be removed from our database. http://www.knowitall.com/subunsub/unsub.asp?email=chemistry..at..www.ccl.net