From mito@aqua.chem.nagoya-u.ac.jp Mon Sep 11 03:15:06 1995 Received: from aqua.chem.nagoya-u.ac.jp for mito@aqua.chem.nagoya-u.ac.jp by www.ccl.net (8.6.10/950822.1) id DAA07933; Mon, 11 Sep 1995 03:14:15 -0400 Received: (from mito@localhost) by aqua.chem.nagoya-u.ac.jp (8.6.9+2.4W/3.3Wb-94112516) id QAA26617; Mon, 11 Sep 1995 16:02:02 +0900 Date: Mon, 11 Sep 1995 16:02:02 +0900 From: Masakatsu Ito Message-Id: <199509110702.QAA26617@aqua.chem.nagoya-u.ac.jp> To: chemistry@www.ccl.net Subject: Using valence double zeta basis in MOLPRO94? Dear colleagues, Can somebody out there give me some advice or sample inputs as an example of how to define your own primitives and contractions within the MOLPRO94 package? I want to use Dunning/Hay "valence double zeta" basis set (T.H.Dunning, Jr., P.J.Hay Chapter 1 in "Methods of Electronic Structure Theory", H.F.Schaefer III, Ed. Plenum Press, N.Y. 1977, pp 1-27). MOLPRO basis set library does not include this basis set, so I have to define the primitives and contractions. There is no example of this kind in the manual, although the syntax for contracted set definitions is described in chapter 10. Thanks in advance. Masakatsu Ito Department of Structual Molecular Science The Graduate University for Advanced Studies Tel 81(Japan)-52-789-3656 Fax 81(Japan)-52-789-3551 E-mail mito@aqua.chem.nagoya-u.ac.jp From qocruces@usc.es Mon Sep 11 05:15:09 1995 Received: from uscmail.usc.es for qocruces@usc.es by www.ccl.net (8.6.10/950822.1) id FAA09120; Mon, 11 Sep 1995 05:05:35 -0400 Received: from qobrue.usc.es by uscmail.usc.es (5.67b/1.34) id AA11312; Mon, 11 Sep 1995 11:10:50 +0200 Date: Mon, 11 Sep 1995 11:10:50 +0200 Message-Id: <199509110910.AA11312@uscmail.usc.es> X-Sender: qocruces@uscmail.usc.es X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: qocruces@usc.es (Jacobo Cruces) Subject: Problems with XMol Dear Netters: We have installed XMol 1.3.1 in our Silicon Graphics Indigo (R4000, IRIX 4.0.5F) and when we tried to run the program we get the following error message: xmol: bad file number Has anyone found this error before? We would appreciate any help. Another question: Does anybody know if there is a version of Xmol for Power Macintosh? Thank you. Jacobo Cruces Colado Department of Organic Chemistry University of Santiago de Compostela Avda. de las Ciencias s/n 15706 SPAIN e-mail: qocruces@uscmail.usc.es jcruces@sfdzuma.usc.es From thouvenin@pobox.oleane.com Mon Sep 11 05:30:09 1995 Received: from relay2.oleane.net for thouvenin@pobox.oleane.com by www.ccl.net (8.6.10/950822.1) id FAA09227; Mon, 11 Sep 1995 05:23:40 -0400 Received: from unknown (thouveni.pobox.oleane.com [194.2.6.61]) by relay2.oleane.net (8.6.12/8.6.10) with SMTP id LAA01808 for ; Mon, 11 Sep 1995 11:23:38 +0200 Message-ID: Read-Receipt-To: thouvenin philippe Return-Receipt-To: thouvenin@pobox.oleane.com Priority: Normal To: ccl MIME-Version: 1.0 From: thouvenin philippe Subject: The best computational method(s) to compute the HOMO. Date: Mon, 11 Sep 95 11:22:01 +0200 (CET) Content-Type: text/plain; charset=US-ASCII; X-MAPIextension=".TXT" Content-Transfer-Encoding: 7bit I wish to compare the reactivity of various molecules in the ground state. I use the energie of the HOMO, computed with a quantum mechanics semi-empirical method, as one index of this reactivity. The molecules are cyclic conjugated systems (5 members, 6 members, 7 members, bicyclic systems, ...) with donor substituants. I would like to know if there is a semi-empirical method which is more suitable to use (AM1, PM3, ...) or if I have to use an ab initio method to compare the HOMO's. In addition, is there one computational method more adapted than another one regarding to the structures of the molecules ? Thank you very much in advance for all the responses I hope to receive. Sincerely yours. Roger ROZOT, PhD e-mail : thouvenin@pobox.oleane.com (You have to indicate my name in the mail.) From patrick@hartree1.rug.ac.be Mon Sep 11 06:15:09 1995 Received: from mserv.rug.ac.be for patrick@hartree1.rug.ac.be by www.ccl.net (8.6.10/950822.1) id GAA09643; Mon, 11 Sep 1995 06:12:15 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA07686 (5.67b/IDA-1.5 for ); Mon, 11 Sep 1995 12:12:06 +0200 Received: from hartree1.rug.ac.be by allserv.rug.ac.be (5.x/SMI-SVR4) id AA23623; Mon, 11 Sep 1995 12:12:04 +0200 Received: by hartree1.rug.ac.be (AIX 3.2/UCB 5.64/4.03) id AA15761; Mon, 11 Sep 1995 12:10:46 +0200 Date: Mon, 11 Sep 1995 12:10:40 +0200 (DFT) From: Patrick Bultinck To: CCL Subject: Stuttgart Pseudopotentials, GAMESS Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear, Has anybody got some example input file(s) for calculations with GAMESS or GAUSSIAN, that use pseudopotentials of the Stuttgart Group (Stoll-Preuss). Where can I get the latest revision of these ECP's ? Thanks, Patrick Bultinck From mcblimts@leonis.nus.sg Mon Sep 11 06:17:27 1995 Received: from sable.nus.sg for mcblimts@leonis.nus.sg by www.ccl.net (8.6.10/950822.1) id GAA09655; Mon, 11 Sep 1995 06:14:16 -0400 Received: from leonis.nus.sg (leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.6.10/8.6.9) with ESMTP id SAA14518 for ; Mon, 11 Sep 1995 18:13:49 +0800 Received: (from mcblimts@localhost) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) id SAA10047; Mon, 11 Sep 1995 18:13:48 +0800 Date: Mon, 11 Sep 1995 18:13:48 +0800 (SST) From: Lim Teck Sin To: ccl Subject: Flexible docking software Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, It seems that many of the molecular docking packages only handle rigid molecules. Anyone knows of any packages (public-domain or commerical or yet-to-be-released-versions) that perform 'flexible' docking? Thanks. best regards - teck-sin From mcblimts@leonis.nus.sg Mon Sep 11 06:15:04 1995 Received: from sable.nus.sg for mcblimts@leonis.nus.sg by www.ccl.net (8.6.10/950822.1) id GAA09655; Mon, 11 Sep 1995 06:14:16 -0400 Received: from leonis.nus.sg (leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.6.10/8.6.9) with ESMTP id SAA14518 for ; Mon, 11 Sep 1995 18:13:49 +0800 Received: (from mcblimts@localhost) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) id SAA10047; Mon, 11 Sep 1995 18:13:48 +0800 Date: Mon, 11 Sep 1995 18:13:48 +0800 (SST) From: Lim Teck Sin To: ccl Subject: Flexible docking software Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: R Hi, It seems that many of the molecular docking packages only handle rigid molecules. Anyone knows of any packages (public-domain or commerical or yet-to-be-released-versions) that perform 'flexible' docking? Thanks. best regards - teck-sin From smb@smb.chem.niu.edu Mon Sep 11 10:00:11 1995 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.10/950822.1) id JAA12667; Mon, 11 Sep 1995 09:45:43 -0400 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA10766 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net>); Mon, 11 Sep 1995 08:45:50 -0500 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA09532; Mon, 11 Sep 95 08:37:40 -0500 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA17999; Mon, 11 Sep 95 08:37:39 -0500 Date: Mon, 11 Sep 95 08:37:39 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9509111337.AA17999@smb.chem.niu.edu> To: CHEMISTRY@www.ccl.net Subject: Proceedings of ECCC2 on THEOCHEM The Scientific Organizing Committee of the Second Electronic Computational Chemistry Conference (ECCC-2) would like to announce that the proceedings of this conference will be published in a special issue of THEOCHEM. Elsevier, the publisher of THEOCHEM, is committed to producing a proceedings that captures the excitement and special attributes of the ECCC-2. This includes publication of some of the discussions and incorporation of the color images, movies, hyperactive molecules, etc. on the Elsevier web site. The conference will accept both papers and poster. The papers will be peer-reviewed for scientific and editorial content for acceptance in the special issue of THEOCHEM, while the posters will appear only on the web and will be removed at the end of the conference. Further information on ECCC-2 can be obtained on the World-Wide Web at URL: http://hackberry.chem.niu.edu/ECCC2 Deadline for submission of abstracts is SEPTEMBER 29, 1995. The Scientific Organizing Committee, Steven Bachrach Don Boyd David Dixon Stephen Gray Toni Kazic Henry Rzepa Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From nauss@ucmod2.che.uc.EDU Mon Sep 11 10:30:11 1995 Received: from phem3 for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.10/950822.1) id KAA13488; Mon, 11 Sep 1995 10:24:22 -0400 Received: from UCBEH.SAN.UC.EDU (SMTPUSER@UCBEH) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HV5AAQE5K08Y6A7Z@phem3.acs.ohio-state.edu>; Mon, 11 Sep 1995 10:24:15 EDT Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-4 #7238) id <01HV5A9K1YSW03R10E@UCBEH.SAN.UC.EDU> for chemistry@www.ccl.net; Mon, 11 Sep 1995 10:23:19 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:chemistry@www.ccl.net id AA03575; Mon, 11 Sep 1995 10:30:04 -0400 Date: Mon, 11 Sep 1995 10:30:04 -0400 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Program called PROBE To: chemistry@www.ccl.net Reply-to: nauss@ucmod2.che.uc.EDU Message-id: <9509111430.AA03575@ucmod2.che.uc.EDU> Content-transfer-encoding: 7BIT Has anyone any information regarding a program called PROBE? Specifically, I'd like a journal citation or such so that I can find out more about it. It is written by Inna Dubchak, Stephen Holbrook, and Sung-Hou Kim at U. Cal-Berkley. Also, any user comments would be useful. Thanks in advance... Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC http://www.che.uc.edu/~nauss * **************************************************************************** From brownr@bohr.pprd.abbott.com Mon Sep 11 10:45:11 1995 Received: from abtlabs.pprd.abbott.com for brownr@bohr.pprd.abbott.com by www.ccl.net (8.6.10/950822.1) id KAA13831; Mon, 11 Sep 1995 10:44:10 -0400 Received: from bohr.pprd.abbott.com by abtlabs.pprd.abbott.com with SMTP id AA27330 (5.65c/IDA-1.4.4 for ); Mon, 11 Sep 1995 09:44:00 -0500 Received: by bohr.pprd.abbott.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA22133; Mon, 11 Sep 95 09:43:51 -0500 From: "Robert Brown" Message-Id: <9509110943.ZM22131@bohr.pprd.abbott.com> Date: Mon, 11 Sep 1995 09:43:51 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chminf-l@iubvm.ucs.indiana.edu, mol-diversity@listserv.arizona.edu, chem_comp@mailbase.ac.uk, chemind-l@derwent.co.uk, chemistry@www.ccl.net Subject: Spring ACS - Call for Papers Reminder Cc: brownr@bohr.pprd.abbott.com Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 2nd Call for Papers A symposium entitled "Handling the Information Explosion in Combinatorial Chemistry" will be held in the Division of Chemical Information (CINF) of the ACS at the 1996 Spring Meeting, New Orleans, March 24-29 1996. The symposium will focus on the problems of handling the massive amount of chemical information generated by combinatorial chemistry projects. Presentations are invited which discuss the problems of registration of libraries and their components; searching in combinatorial library databases; tracking of libraries, components and precursors; and ties between chemical information systems and automated synthesis and screening. Contributions are invited from software vendors and papers from end-users describing their experiences using commercial combinatorial chemistry software, developing in-house systems or integrating combinations of the two are particularly welcome. If you are interested in contributing to this symposium, please email or fax a title and short summary highlighting the topics you wish to address as soon as possible and no later than October 16th. Official ACS abstracts are due by 1st Novemeber. Please send your summary and any enquiries to: Mark G. Bures, Robert D. Brown, Yvonne C. Martin Abbott Laboratories, D47E/AP10, 100 Abbott Park Road Abbott Park, IL 60064-3500. Phone: (708) 937 4981 (secretary) Fax: (708) 937 2625 Internet: mark.bures@abbott.com, brownr@abbott.com, yvonne.martin@abbott.com. -- ************************************************************************* Robert Brown, PhD * Phone (708) 937 4036 Abbott Laboratories * Fax (708) 937 2625 AP10/47E * e-mail brownr@abbott.com 100 Abbott Park Road * Abbott Park * IL 60064-3500 * ************************************************************************* From jkl@ccl.net Mon Sep 11 11:30:12 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA14636; Mon, 11 Sep 1995 11:20:00 -0400 Received: from harris.cc.strath.ac.uk for cbas25@ccsun.strath.ac.uk by bedrock.ccl.net (8.6.10/950822.1) id LAA17866; Mon, 11 Sep 1995 11:19:58 -0400 Received: from skye.cc.strath.ac.uk by harris.cc.strath.ac.uk with SMTP (PP); Mon, 11 Sep 1995 15:55:48 +0100 Received: by skye.cc.strath.ac.uk (5.x) id AA19316; Mon, 11 Sep 1995 15:57:50 +0100 From: cbas25 Message-Id: <9509111457.AA19316@skye.cc.strath.ac.uk> Subject: URL for INTERPROBE To: CHEMISTRY@ccl.net Date: Mon, 11 Sep 1995 15:57:50 +0100 (BST) Cc: cbas25@strath.ac.uk X-Mailer: ELM [version 2.4 PL23] Content-Type: text Dear colleagues, I wish to announce that INTERPROBE CHEMICAL SERVICES now has a world-wide-web page at:- http://interchem.chem.strath.ac.uk/inter/interprobe.html View this page for latest information about INTERCHEM and other programs available from INTERPROBE:- INTERCHEM (Multipurpose molecular modeling program) PRESTO (Protein sequence analysis program) CHEMSPREAD (Statistical analysis program) THREEDOM (3D Database searching) AUTOBUILD (To generate families of 3D structures) Peter Bladon email cbas25@strath.ac.uk Phone/Fax +44-141-776-1718 From jkl@ccl.net Mon Sep 11 12:00:14 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA15331; Mon, 11 Sep 1995 11:49:21 -0400 Received: from wugate.wustl.edu for reichertd@mirlink.wustl.edu by bedrock.ccl.net (8.6.10/950822.1) id LAA18322; Mon, 11 Sep 1995 11:49:20 -0400 Received: from mirlink.wustl.edu (mirlink.wustl.edu [128.252.155.1]) by wugate.wustl.edu (8.6.12/8.6.11) with SMTP id KAA01982 for ; Mon, 11 Sep 1995 10:49:20 -0500 Message-Id: <199509111549.KAA01982@wugate.wustl.edu> Date: 11 Sep 1995 10:47:22 U From: "David Reichert" Subject: Tc Modeling To: "CCL" Hello, Is anyone familiar with any semi-empirical or ab initio calculations done on Tc(V) oxo compounds? I've been unable to find any reports in the literature except for some molecular mechanics work. Thanks in advance, David E. Reichert, Ph.D. Mallinckrodt Inst. of Radiology Washington University School of Medicine e-mail: reichertd@mirlink.wustl.edu From jkl@ccl.net Mon Sep 11 12:45:13 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA16285; Mon, 11 Sep 1995 12:34:49 -0400 Received: from gauss.uib.es for guillem@gauss.uib.es by bedrock.ccl.net (8.6.10/950822.1) id MAA18848; Mon, 11 Sep 1995 12:34:20 -0400 From: Received: by gauss.uib.es; id AA18429; Mon, 11 Sep 1995 18:34:46 +0100 Message-Id: <9509111734.AA18429@gauss.uib.es> To: chemistry@ccl.net Subject: NBO Manual Date: Mon, 11 Sep 95 18:34:45 +0100 X-Mts: smtp Dear Netters, I would like to know if somebody could share with me an electronic (text or postcript) copy of the NBO manual (available via FTP or WWW). I have already done a search into the CCL archive, but infortunately the copy that resides in: /chemistry/software/SOURCES/FORTRAN/nbo/junk/nbo.txt has several pages corrupted (from p.35 to p.61) and therefore is unreadable. Many thanks for your help, G. Suner ------------------------------------------------------------------------ Dr Guillermo A. Suner; Dep. de Quimica, UNIVERSITAT DE LES ILLES BALEARS E-07071-Palma de Mallorca, SPAIN. E-mail: guillem@gauss.uib.es Tel: + 34 71 173498 Fax: + 34 71 173426 WWW URL: http://www.uib.es/depart/dqu/dquo/suner.html From butcher@robles.callutheran.edu Mon Sep 11 16:15:16 1995 Received: from robles.callutheran.edu for butcher@robles.callutheran.edu by www.ccl.net (8.6.10/950822.1) id QAA20263; Mon, 11 Sep 1995 16:02:23 -0400 Received: from [199.107.206.245] by robles.callutheran.edu; (5.65/1.1.8.2/19Jan95-1238PM) id AA11312; Mon, 11 Sep 1995 13:03:07 -0700 Date: Mon, 11 Sep 1995 13:03:07 -0700 Message-Id: <9509112003.AA11312@robles.callutheran.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: butcher@robles.callutheran.edu (Kristine Butcher) Subject: Amsterdam DF calcs on a Dec Alpha Hello everyone, I am seeking information regarding the use of the Amsterdam Density Functional program package (ADF) on a Dec Alpha machine. Before I purchase the ADF program (to replace my trouble-prone Xalpha-scattered wave method) I want to make sure that I won't run into costly technical difficulties. I am on the faculty at a small, liberal-arts school with no money for last-minute RAM upgrades, etc. I will be using a Dec Alpha 2000/300 machine running OSF/1 3.2A as its operating system. It has 128 mB of RAM, with about half a gigabyte of disk space available to me. This machine is also our campus mail server, and host to several other Internet-related softwares (I have to share it with many people!). The clusters I will be studying are generally 30 atoms or fewer, and of relatively high symmetry. I would like to hear from anyone running ADF under same/similar conditions as to ease of installation, RAM and disk space recommendations, and any other considerations. Thank you, Kristine Butcher ************************************************************************** * Kristine D. Butcher butcher@robles.callutheran.edu * * Department of Chemistry * * California Lutheran University phone: (805) 493-3338 * * 60 West Olsen Rd. FAX: (805) 493-3479 * * Thousand Oaks, CA 91360 * ************************************************************************** From nauss@ucmod2.che.uc.EDU Mon Sep 11 16:45:15 1995 Received: from phem3 for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.10/950822.1) id QAA20897; Mon, 11 Sep 1995 16:44:45 -0400 Received: from UCBEH.SAN.UC.EDU (SMTPUSER@UCBEH) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HV5NK9ZZ4G8Y6E51@phem3.acs.ohio-state.edu>; Mon, 11 Sep 1995 16:44:34 EDT Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-4 #7238) id <01HV5NB491QA03R2MH@UCBEH.SAN.UC.EDU>; Mon, 11 Sep 1995 16:39:05 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:chemistry@www.ccl.net id AA08047; Mon, 11 Sep 1995 16:43:47 -0400 Date: Mon, 11 Sep 1995 16:43:47 -0400 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Phi-Psi plots To: chemistry@www.ccl.net Cc: DIBUG@COMP.BIOZ.UNIBAS.CH Reply-to: nauss@ucmod2.che.uc.EDU Message-id: <9509112043.AA08047@ucmod2.che.uc.EDU> Content-transfer-encoding: 7BIT How do *you* handle phi-psi plots? We are working with some carbohydrate models and want to show contour maps for rotation about the glycosidic linkages. We also want to find the most favorable combination of phi/psi between two residues. (The specific residues involve are unusual sugars. So no one has made a study like this before.) The data is generated using Biosym's Discover using the rotors command. The output is a formatted *.tor file. I can get a reasonable plot using Biosym's InsightII with Analysis. Eventually, we would want to show the contours for publication illustrations. However, the plots from Analysis are truncated, i.e. the axes are shorter than -180 to +180 degrees. I am unable to expand the axes to the the range. Any suggestions on how to expand them? Also, the Biosym plot does not leave a lot of flexibility for drawing contours and labeling them for publication purposes. So what do others use? Would GNU-Plot be useful here? I'll summarize if I get any responses. Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC http://www.che.uc.edu/~nauss * **************************************************************************** From hcj@mazda.wavefun.com Mon Sep 11 18:00:16 1995 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.10/950822.1) id RAA21800; Mon, 11 Sep 1995 17:50:14 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA20961; Mon, 11 Sep 95 14:50:22 -0700 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma020958; Mon Sep 11 14:50:01 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@www.ccl.net id AA08209; Mon, 11 Sep 95 14:49:53 -0700 Date: Mon, 11 Sep 95 14:49:53 -0700 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9509112149.AA08209@mazda.wavefun.com> To: nauss@ucmod2.che.uc.EDU Cc: chemistry@www.ccl.net, DIBUG@COMP.BIOZ.UNIBAS.CH In-Reply-To: <9509112043.AA08047@ucmod2.che.uc.EDU> (nauss@ucmod2.che.uc.EDU) Subject: Re: CCL:Phi-Psi plots Reply-To: hcj@wavefun.com >>>>> "Jeffrey" == Jeffrey L Nauss writes: Jeffrey> How do *you* handle phi-psi plots? I wrote a small utility program to go along with Spartan. The program will generate a 2 or 3 dimensional gnuplot data file from the list of Spartan molecules resulting from conformational analysis (or reaction coordinate) calculations. This can then be used within gnuplot to generate a Phi plot, or a Phi-Psi plot using contours, meshes, etc. Feel free to drop me a note if you need more info. -Harry +-----------------------+------------------+-------------------------+ |Harry C. Johnson IV | ______________ | E-Mail: hcj@wavefun.com | |Computational Chemist | \ _________ / | Phone: (714)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (714)955-2118 | |18401 Von Karman | \ \\\\\/ | | |Suite 370 | \ \\/ | "Seems to me its all | |Irvine, CA 92715 | \/ | just chemistry" - RUSH | +-----------------------+------------------+-------------------------+ From jkl@ccl.net Mon Sep 11 18:16:31 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA22003; Mon, 11 Sep 1995 18:09:43 -0400 Received: from scisun.sci.ccny.cuny.edu for box@scisun.sci.ccny.cuny.edu by bedrock.ccl.net (8.6.10/950822.1) id SAA22451; Mon, 11 Sep 1995 18:09:42 -0400 Received: by scisun.sci.ccny.cuny.edu (4.1/SMI-4.1-CCNY-Science) id AA02921; Mon, 11 Sep 95 18:09:29 EDT Date: Mon, 11 Sep 1995 18:09:28 -0400 (EDT) From: "Vernon G. S. Box, Ph.D." To: hcj@wavefun.com Cc: steve_hardinger@qmail.fullerton.edu, chemistry@ccl.net Subject: Re: CCL:Animations and Spartan In-Reply-To: <9509080011.AA07591@mazda.wavefun.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 7 Sep 1995, Harry C. Johnson wrote: > >>>>> "Steve" == Steve Hardinger writes: > > Steve> I've been working with trying to animate the rotaion of > Steve> n-butane with Spartan. Everything works very well, but I > Steve> would like to improve the presentation. I'd like to know > Steve> (1) can I change the speed at which the frames are > Steve> presented, and (2) how can I get the view to stay the saem, > Steve> i.e, always along the c2-c3 bond axis? > > 1) There is no current way to control the speed of the animations. If > the animation is too fast (the usual case) you can generate more > conformers which will produce a smoother animation, or get a slower > machine 8^) Also the addition of surfaces will often slow things down > considerably, so there is often a trade off between the rate of > animation of the structure alone, and the structure with surfaces. > > Future versions of Spartan will most likely include some mechanism for > controlling the animation rate directly. > > 2) When animating a series of conformations it is usually desirable to > specify the 'NOMOVE' keyword in the setup dialog of the appropriate > energy calculation method (mechanics, semi-empirical, or ab initio). > Without NOMOVE the optimization methods will re-orient the molecule in > an attempt to recognize symmetry within the molecule. It is usually > also desirable to specify 'ENFORCE' and 'DUPLCHECK=NONE' in the > conformational analysis setup as well. This prevents the particular > dihedral of interest from changing as a result of optimization > (enforce), and also turns off duplicate checking. > > Hope this helps! > -Harry > > +-----------------------+------------------+-------------------------+ > +-----------------------+------------------+-------------------------+ Hi Guys STR3DI.EXE from Exorga Inc will do just what Harry wants, but with much less hassle. Contact Exorga at : P.O. Box 56, Colonia, NJ 07067 or look at their page at http://pages.prodigy.com/NJ/exorga/exorga.html VB From marcus@acsu.buffalo.edu Mon Sep 11 19:00:18 1995 Received: from destrier.acsu.buffalo.edu for marcus@acsu.buffalo.edu by www.ccl.net (8.6.10/950822.1) id SAA22336; Mon, 11 Sep 1995 18:49:16 -0400 Received: (marcus@localhost) by destrier.acsu.buffalo.edu (8.6.10/8.6.4) id SAA16627 for chemistry@www.ccl.net; Mon, 11 Sep 1995 18:49:16 -0400 From: Emil Marcus Message-Id: <199509112249.SAA16627@destrier.acsu.buffalo.edu> Subject: Re: CCL:Phi-Psi plots To: chemistry@www.ccl.net Date: Mon, 11 Sep 1995 18:49:15 -0400 (EDT) X-Mailer: ELM [version 2.4 PL22] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 889 && How do *you* handle phi-psi plots? && && Jeff Nauss && && -- Original Sender From: Address: nauss@ucmod2.che.uc.EDU && CHEMISTRY@www.ccl.net Please, contact Kenny K.H. Toh (ktoh@td2cad.intel.com) to tell you an "ftp" or "web" site where you may find his program PLOTMTV (fast multi-purpose program for X11-windows). I've used it to obtain contour plots and I am very pleased with it. You may also try Harvard ChartXL for the PC. It imports "lotus", "excel" and various "data" and "text" files and can also generate contour plots. Stanford Graphics for Windows is also a good option. With greetings, Emil Emil Marcus University at Buffalo and Roswell Park Cancer Institute Department of Biophysics Tel: (716) 845 - 4510 Fax: (716) 845 - 8906 marcus@acsu.buffalo.edu