From chemistry-request@server.ccl.net Tue Apr 24 06:18:49 2001 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3OAIkI08162 for ; Tue, 24 Apr 2001 06:18:47 -0400 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.1/8.11.0) with ESMTP id f3OAIXs87784; Tue, 24 Apr 2001 12:18:34 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Tue, 24 Apr 2001 12:18:33 +0200 (EET) From: Arvydas Tamulis To: cc: Jelena Tamuliene , Subject: Calculations of Localized Orbitals Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, We have performed Gaussian98 DFT geometry optimization of the copper white phosphorus complex [Cu(Cl2)(CH3OH)(NH3)(P4)]0 and now whish to find the localized orbitals in this complex. We tried to obtain these localized orbitals by GAUSSIAN 98 package, however, the calculation of the localize orbital of the above complex applied AIM=BO command was not succesfull. Maybe you can advise other methods for calculations the localized orbitals existing in the GAUSSIAN 98 or in our possessing GAMESS-US and DALTON packages (or in other free packages). Thanking your in advance. With best regards, Arvydas Tamulis c/o Jelena Tamuliene ****************************************************** Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, Theoretical Molecular Electronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/ fax: +(370-2)-225361 or +(370-2)-224694 Phone: +(370-2)-620861 Home address: Didlaukio 27-40, Vilnius 2057, Lithuania Phone: +(370-2)-778743 From chemistry-request@server.ccl.net Tue Apr 24 06:24:06 2001 Received: from leonis.nus.edu.sg ([137.132.1.18]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3OAO4I08238 for ; Tue, 24 Apr 2001 06:24:05 -0400 Received: from Debug (nobody@mail.bic.nus.edu.sg [137.132.19.75]) by leonis.nus.edu.sg (8.10.0/8.10.0) with SMTP id f3OANhI15092; Tue, 24 Apr 2001 18:23:43 +0800 (SST) Message-Id: <200104241023.f3OANhI15092@leonis.nus.edu.sg> To: Manoj Pal , chemistry@ccl.net, pdb-l@rcsb.org From: Subject: reg.molscript manual Date: Tue, 24 Apr 2001 10:23:47 GMT X-Mailer: Endymion MailMan Professional Edition v3.0.33 Hi, I'm not able to get molscript manual. If anybody knows the website please let me know. Thanks in advance. with regards govind. From chemistry-request@server.ccl.net Tue Apr 24 06:25:01 2001 Received: from leonis.nus.edu.sg ([137.132.1.18]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3OAP0I08250 for ; Tue, 24 Apr 2001 06:25:00 -0400 Received: from Debug (nobody@mail.bic.nus.edu.sg [137.132.19.75]) by leonis.nus.edu.sg (8.10.0/8.10.0) with SMTP id f3OANEI15011; Tue, 24 Apr 2001 18:23:24 +0800 (SST) Message-Id: <200104241023.f3OANEI15011@leonis.nus.edu.sg> To: Manoj Pal , chemistry@ccl.net, pdb-l@rcsb.org From: Subject: Re: Fuzzy logic in protein secondary structure prediction. Date: Tue, 24 Apr 2001 10:23:28 GMT X-Mailer: Endymion MailMan Professional Edition v3.0.33 Hi, I'm not able to get molscript manual. If anybody knows the website please let me know. Thanks in advance. with regards govind. From chemistry-request@server.ccl.net Tue Apr 24 08:05:49 2001 Received: from mailgate.dfh.dk ([130.225.176.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3OC5mI09706 for ; Tue, 24 Apr 2001 08:05:48 -0400 Received: from [130.225.225.237] (dhcp225-237.dfh.dk [130.225.225.237]) by mailgate.dfh.dk (8.9.3/8.9.3) with ESMTP id OAA29076 for ; Tue, 24 Apr 2001 14:04:33 +0200 X-Sender: fsj@pophost.dfh.dk Message-Id: Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Date: Tue, 24 Apr 2001 14:02:07 +0200 To: chemistry@ccl.net From: Flemming Steen Jorgensen Subject: ADME minisymposium, Copenhagen June 21, 2001 Dear Colleague, We are pleased to announce a mini-symposium on: ADME in Drug Research Tools for Evaluation and Prediction of Absorption, Distribution, Metabolism and Excretion Thursday, June 21, 2001, 9.00-16.00 Royal Danish School of Pharmacy Copenhagen, Denmark Speakers include: The use of ADME in the discovery of orally active growth hormone secretagogues - a case study Michael Ankersen, Novo Nordisk, Denmark ADMEscreen: Correlating surface activity of drugs to their ADME Paavo K.J. Kinnunen, University of Helsinki, Finland Cell culture methods for prediction of intestinal drug absorption Staffan Tavelin, Uppsala University, Sweden Computational and mechanism-based prediction of metabolism by Cytochrome P450s Nico P.E. Vermeulen, Vrije Universiteit, The Netherlands In silico ADME in action Anne Hersey, GlaxoSmithKline, U.K. Poor Aqueous Solubility - An Industry Wide Problem in ADME Screening Christopher A. Lipinski, Pfizer, U.S.A. Geneva Please note that admission is free, but registration is required. See at http://www.dfh.dk/activities/gradschool/ for program, abstracts and registration. I apologize to those who receive multiple copies of this email. Please distribute this call to all interested parties. Regards, Flemming ######################################### # Flemming Steen Jorgensen Associate professor, Ph.D. # Royal Danish School of Pharmacy # Department of Medicinal Chemistry Phone +45 35 30 63 78 # Universitetsparken 2 Fax +45 35 30 60 40 # DK-2100 Copenhagen E-mail fsj@dfh.dk # Denmark ######################################### From chemistry-request@server.ccl.net Tue Apr 24 03:15:30 2001 Received: from maties.sun.ac.za ([146.232.128.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3O7FPI07361 for ; Tue, 24 Apr 2001 03:15:27 -0400 Received: from akad.sun.ac.za ([146.232.80.254]) by maties.sun.ac.za with esmtp (Exim 3.22 #1) id 14rx2D-0006VP-00 for chemistry@ccl.net; Tue, 24 Apr 2001 09:14:53 +0200 Received: from SUN_AKAD/SpoolDir by AKAD.SUN.AC.ZA (Mercury 1.48); 24 Apr 01 09:14:51 +0200 Received: from SpoolDir by SUN_AKAD (Mercury 1.48); 24 Apr 01 09:14:42 +0200 From: "Mnr GA Venter" Organization: Stellenbosch University To: chemistry@ccl.net Date: Tue, 24 Apr 2001 09:14:34 +0200 MIME-Version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Subject: Incorrect wavefunction read in Gaussian98 Message-ID: <3AE543F4.369.3465664@localhost> Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12c) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by server.ccl.net id f3O7FUI07363 Hi I am modeling first row transition metal ozone complexes with Gaussian98. At some point in my calculations I test for the stability of the wavefunction using the Gaussian98 command STABLE=OPT. When the program finds an instability it is corrected and a new, lower energy is calculated. I then attempt to optimize the geometry using the stabilized wavefunction as starting guess via the GUESS=READ command. The problem is that the program sometimes uses the new stabilized wavefunction’s energy and sometimes reverts back to the unstabilized wavefunction’s energy. It seems to do this indiscriminately. The only differences between the input files are the central atom and the associated multiplicity. Thanks in advance. Gerhard gaventer@maties.sun.ac.za -------------------------------------- Gerhard Venter Department of Chemistry University of Stellenbosch Private Bag X1 7602 Matieland South Africa --------------------------------------- From chemistry-request@server.ccl.net Tue Apr 24 10:31:27 2001 Received: from berzerk.gpcc.itd.umich.edu (smtp@[141.211.2.162]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3OEVRI10848 for ; Tue, 24 Apr 2001 10:31:27 -0400 Received: from breakout.gpcc.itd.umich.edu (smtp@breakout.gpcc.itd.umich.edu [141.211.2.141]) by berzerk.gpcc.itd.umich.edu (8.8.8/4.3-mailhub) with ESMTP id KAA14555; Tue, 24 Apr 2001 10:31:19 -0400 (EDT) Received: from localhost (peisach@localhost) by breakout.gpcc.itd.umich.edu (8.8.8/5.1-client) with ESMTP id KAA29329; Tue, 24 Apr 2001 10:31:18 -0400 (EDT) Precedence: first-class Date: Tue, 24 Apr 2001 10:31:18 -0400 (EDT) From: Daniel Peisach X-Sender: peisach@breakout.gpcc.itd.umich.edu To: govind@bic.nus.edu.sg cc: Manoj Pal , chemistry@ccl.net, pdb-l@rcsb.org Subject: Re: reg.molscript manual In-Reply-To: <200104241023.f3OANhI15092@leonis.nus.edu.sg> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > I'm not able to get molscript manual. If anybody knows the website > please let me know. http://www.avatar.se/molscript/doc/molscript.html -Dan From chemistry-request@server.ccl.net Tue Apr 24 11:05:22 2001 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3OF5MI11293 for ; Tue, 24 Apr 2001 11:05:22 -0400 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id f3OF5LN21965 for ; Tue, 24 Apr 2001 10:05:21 -0500 (CDT) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id KAA21518 for chemistry@ccl.net; Tue, 24 Apr 2001 10:05:21 -0500 (CDT) Date: Tue, 24 Apr 2001 10:05:20 -0500 From: John Stone To: chemistry@ccl.net Subject: Announce: VMD 1.6.1 Released! Message-ID: <20010424100519.B21503@geneseo.ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.7i VMD "Visual Molecular Dynamics" 1.6.1 Announcement -------------------------------------------------- The Theoretical Biophysics group at the Beckman Institute For Advanced Science and Technology, the University of Illinois (U-C), is proud to announce the public release of VMD 1.6.1. VMD is a package for the visualization and analysis of biomolecular systems. This software is distributed free of charge and includes source code, documentation, and precompiled binaries for Compaq, IBM, HP, Linux, MacOS-X, Sun, and SGI Unix systems, as well as Microsoft Windows 95/98/ME/NT/2K. The VMD documentation includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer. VMD development is supported by the NIH National Center for Research Resources. A full description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ The authors request that any published work which utilizes VMD includes a reference to the VMD web page and/or the following reference: Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. The Theoretical Biophysics group encourages VMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. We are eager to hear from you, and thank you for using our software! John Stone vmd@ks.uiuc.edu April 22, 2001 README file for VMD 1.6.1 --------------------------------------------------------------------------- What is VMD? See also http://www.ks.uiuc.edu/Research/vmd/ --------------------------------------------------------------------- VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. The program has many features, which include: o No limit on the number of molecules, atoms, residues or number of animation frames, except available memory. o Many molecular rendering and coloring methods. o Stereoscopic display capability using Red/Blue or LCD shutter glasses. o Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more). o Ability to write the current image to a file which may be processed by a number of popular raytracing and image rendering packages, including POV-Ray, Radiance, Raster3D, Rayshade, and Tachyon. o Integration with the program 'Babel' which allows VMD to read many molecular data file formats. Even without the use of Babel, VMD can read PDB files, as well as CHARMM- and X-PLOR compatible binary DCD files and X-PLOR compatible PSF files. o Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities. o Extensions to the Tcl and Python languages which enable researchers to write their own routines for molecular analysis. o Modular, extensible source code using an object-oriented design in C++, with a programmer's guide outlining the source code structure. o Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical Biophysics Group at the University of Illinois. See the NAMD WWW home page for more information: http://www.ks.uiuc.edu/Research/namd o VMD can be used to interactively display and control an MD simulation using NAMD or Protomol. o Integration with the BioCoRE collaborative research environment. VMD can "publish" molecular graphics scripts to BioCoRE, so that BioCoRE collaborators can work together over the internet. See the BioCoRE WWW home page for more information: http://www.ks.uiuc.edu/Research/biocore What's new in VMD 1.6.1? ------------------------ New Features o Some builds of VMD now support multiprocessor acceleration and multithreading for improved I/O performance even on uniprocessors. o Multithreaded IMD socket I/O for improved performance on high latency networks and with slow simulations. o Ported VMD to MacOS-X using Mesa, requires XFree86 be installed. o Support for 64-bit versions of VMD on IRIX 6.x and Solaris 2.x, using R10000 class SGI CPUs, and UltraSPARC class Sun CPUs. The 64-bit versions are capable of working with files larger than 2GB, and can use more than 4GB of main memory if necessary. o New "getbonds" and "setbonds" commands for Tcl and Python atom selections. Replaces older "bond" command. o New real-time implementation of anaglyph (red/blue) stereo for people without LCD glasses, but with quad-buffered stereo hardware on their machine. o New atom selection keyword 'exwithin', eliminates need for a commonly used complex combination of atom selections '(within 3 of X) and not X'. o Works with BioCoRE. VMD can now "publish" configuration files to a BioCoRE notebook, such that collaborators can work together on VMD visualizations, using BioCoRE as their common workplace. General Improvements and Bug Fixes o Tcl "atomselect get" speed increased by 10-30x for large molecules for numeric selections. String-based selections slightly slower, but a good improvement for the common performance intensive use-cases. o Increased speed of "lines" representation drawing and animation by a factor of 3, allowing interactive rotation of huge systems in lines mode (4 million atom water box at 2 seconds per frame.) o Significant improvements in responsiveness in the the graphics form "atom name lists" for large molecules with hundreds of thousands of atoms. Very large name lists now display 10 to 30 times faster. o Increased the number of colors in the color scale map from 16 to 1024. o Significant updates to Python callback mechanism. o Fixed a minor EOF failure in G96 file reader o Built with FLTK 1.0.10 on all platforms. o Fixed PRs (bugs): 134, 136, 139, 140, 141, 145, 146, 148, 150, 151, 152, 153 User Interface Changes o The rmsd fit routines can be brought up without needing to source a fully qualified pathname in the VMD installation directory o Updated the "Sim" form to improve the IMD interface User Documentation Updates o Updated interactive molecular dynamics (IMD) features for the current implementation o Documentation for new anaglyph stereo feature o Documented new RMSD fit startup feature Known bugs ---------- Please visit the VMD web site for information on known bugs, workarounds, and fixes: http://www.ks.uiuc.edu/Research/vmd/ Cost and Availability --------------------- BioCoRE, JMV, MDTools, NAMD, VMD and the Structural Biology Software Database represent the broad efforts of the Theoretical Biophysics Group, an NIH Resource for Macromolecular Modeling and Bioinformatics, designed to develop and distribute free, effective tools (with source code) for molecular dynamics studies in structural biology. For more information, see: http://www.ks.uiuc.edu/Research/biocore/ http://www.ks.uiuc.edu/Research/NAMD/ http://www.ks.uiuc.edu/Research/VMD/ http://www.ks.uiuc.edu/Development/biosoftdb/ http://www.ks.uiuc.edu/Development/JMV/ http://www.ks.uiuc.edu/Development/MDTools/ The VMD project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969). Disclaimer and Copyright ------------------------ VMD is Copyright (c) 1995-2001 the Board of Trustees of the University of Illinois and others. The terms for using, copying, modifying, and distributing VMD are specified in the file LICENSE. If you use VMD in a way you think is interesting or novel, we would like to know about it. The authors request that any published work which utilizes VMD includes a reference to the VMD web page: http://www.ks.uiuc.edu/Research/vmd/ and/or the following reference: Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. Documentation ------------- Three VMD manuals are available which describe how to install, use, and modify VMD. The VMD installation guide, is contained in the VMD distribution in the file "doc/ig.ps". The User's Guide and Programmer's Guide are available separately (due to size) from the VMD web site. Quick help may be accessed by pressing the "Help" button on the main VMD form, or by typing help in the VMD command window. This will bring up the VMD quick help page, and will lead you to several other VMD help files and manuals. Quick Installation Instructions ------------------------------- The Windows version of VMD is distributed as a self-extracting archive, and should be entirely self explanatory. Detailed instructions for compiling this version of VMD can be found in the installation guide. For quick installation of the binary distribution for Unix do the following: 1) uncompress and untar the distribution into a working directory. In this working directory, there are several subdirectories such as bin, src, doc, data, as well as this README and a configure script. Change to this working directory after the unpacking is complete. 2) Edit the file 'configure'; change the values for the $install_library_dir and $install_bin_dir to a directory in which vmd data files and executables should be installed: $install_bin_dir is the location of the startup script 'vmd'. It should be located in the path of users interested in running VMD. $install_library_dir is the location of all other VMD files. This included the binary and helper scripts. It should not be in the path. 3) A Makefile must be generated based on these configuration variables by running "./configure". 4) After configuration is complete, cd to the src directory, and type "make install". This will install VMD in the two directories listed above. Note that running "make install" twice will print error messages because you are attempting to overwrite some read-only files. This should be fine. 5) When installed, type 'vmd' to start (make sure the $install_bin_dir directory is in your path). Required Libraries ------------------ VMD requires several libraries and programs for various of its functions. In particular, it uses GL or OpenGL based 3-D rendering, and will require that you have the appropriate GL or OpenGL libraries on your system. Other programs are required by some of VMD's optional features. Please visit the VMD web site for more information: http://www.ks.uiuc.edu/Research/vmd/ For problems, questions, or suggestions, send e-mail to 'vmd@ks.uiuc.edu'. VMD Development Team Theoretical Biophysics Group University of Illinois and Beckman Institute 405 N. Matthews Urbana, IL 61801 TBG: http://www.ks.uiuc.edu/ VMD: http://www.ks.uiuc.edu/Research/vmd/ README for VMD; last modified April 22, 2001 by John Stone -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@server.ccl.net Tue Apr 24 11:41:22 2001 Received: from neriserv.chim.unisi.it (IDENT:root@[192.167.124.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3OFfLI11729 for ; Tue, 24 Apr 2001 11:41:21 -0400 Received: from neriserv.chim.unisi.it (magoserver.bio-mol.unisi.it [192.167.124.8]) by neriserv.chim.unisi.it (8.9.3/8.9.3) with ESMTP id QAA00516 for ; Tue, 24 Apr 2001 16:10:26 +0200 Sender: andrea@neriserv.chim.unisi.it Message-ID: <3AE5ADC1.A7123F17@neriserv.chim.unisi.it> Date: Tue, 24 Apr 2001 18:45:53 +0200 From: Andrea Bernini Organization: Diparttimento Biologia Molecolare X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.17-21mdk i586) X-Accept-Language: en, it MIME-Version: 1.0 To: Computational Chemistry list Subject: Autock + NMR restraints Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I've already succsessfully used Autodock to fit an organic molecule into a macromolecule pocket, now I would like to repeat the process introducing a few NMR-derived intermolecular restraints to drive the docking, is there any way of doing this? Thanks in advance, ciao, Andrea. ______________________________________________ Andrea Bernini, Dr Molecular Biology Dept. University of Siena Via Fiorentina 1, 53100 Siena, Italy Phone +39 577 234911 Fax +39 577 234903 From chemistry-request@server.ccl.net Tue Apr 24 12:27:32 2001 Received: from jaguar.it.wsu.edu (root@[134.121.0.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3OGRWI12034 for ; Tue, 24 Apr 2001 12:27:32 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by jaguar.it.wsu.edu (8.9.3/8.9.3) with SMTP id JAA04075; Tue, 24 Apr 2001 09:26:15 -0700 (PDT) Message-ID: <006801c0ccdb$4944be80$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Mnr GA Venter" , References: <3AE543F4.369.3465664@localhost> Subject: Re: CCL:Incorrect wavefunction read in Gaussian98 Date: Tue, 24 Apr 2001 09:26:15 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello, When you attempt to read in the stable wave function you will need to set the switch "nosymm" for the keyword "scf" and you will want to employ the keyword/switch combination geom(allcheckpoint). The geom(allcheckpoint) will allow the wave function's guess multiplicity to be whatever noninteger value the stable(opt) routine resulted. Don't forget that the allcheckpoint switch means that both the comment line and the charge, multiplicity line are read from the checkpoint file. Here is an example: %chk=d:\g98wcalcs\test.chk #P RHF/STO-3G pop(full) gfinput iop(6/7=3) stable(opt) Stability Test on Molecular Hydrogen with the STO-3G Basis 0 1 H H 1 r1 r1 0.775 --LINK1-- %chk=d:\g98wcalcs\test.chk #P UHF chkbasis pop(full) gfinput iop(6/7=3) guess(read) scf(nosymm) geom(allcheckpoint) This seems to work for me (credit goes to Joseph Ochterski at Gaussian, Inc. for the solution). Now I only wish that the results from a stability calculation made more sense. Just about every RHF wave function is instable it seems, and just about every stable wave function has spin-contamination... Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Mnr GA Venter" To: Sent: Tuesday, April 24, 2001 12:14 AM Subject: CCL:Incorrect wavefunction read in Gaussian98 > Hi > > I am modeling first row transition metal ozone complexes with Gaussian98. At > some point in my calculations I test for the stability of the wavefunction using > the Gaussian98 command STABLE=OPT. When the program finds an > instability it is corrected and a new, lower energy is calculated. I then attempt > to optimize the geometry using the stabilized wavefunction as starting guess > via the GUESS=READ command. The problem is that the program sometimes > uses the new stabilized wavefunction's energy and sometimes reverts back to > the unstabilized wavefunction's energy. It seems to do this indiscriminately. > The only differences between the input files are the central atom and the > associated multiplicity. > > Thanks in advance. > Gerhard > gaventer@maties.sun.ac.za > > -------------------------------------- > Gerhard Venter > Department of Chemistry > University of Stellenbosch > Private Bag X1 > 7602 Matieland > South Africa > --------------------------------------- > > > -= 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 Apr 24 12:57:41 2001 Received: from alpha.cse.ucsc.edu ([128.114.48.14]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f3OGvfI12430 for ; Tue, 24 Apr 2001 12:57:41 -0400 Received: (from karplus@localhost) by alpha.cse.ucsc.edu (8.6.10/8.6.12) id JAA300652; Tue, 24 Apr 2001 09:57:34 -0700 Date: Tue, 24 Apr 2001 09:57:34 -0700 Message-Id: <200104241657.JAA300652@alpha.cse.ucsc.edu> From: Kevin Karplus To: govind@bic.nus.edu.sg CC: manoj@chem.iitkgp.ernet.in, chemistry@ccl.net, pdb-l@rcsb.org In-reply-to: <200104241023.f3OANhI15092@leonis.nus.edu.sg> (govind@bic.nus.edu.sg) Subject: Re: reg.molscript manual References: <200104241023.f3OANhI15092@leonis.nus.edu.sg> The molscript manual is found in less than a second by using the google.com search engine with molscript manual Why do people continue to ask for websites that are so easily found? Please, folks, use this list for questions where expert advice and discussion is needed, not for questions that any high school student should be able to answer. From chemistry-request@server.ccl.net Tue Apr 24 15:21:49 2001 Received: from rhenium ([194.73.73.93]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3OJLmI13232 for ; Tue, 24 Apr 2001 15:21:48 -0400 Received: from [62.7.82.20] (helo=[192.168.0.2]) by rhenium with esmtp (Exim 3.03 #83) id 14s8KG-0004MO-00; Tue, 24 Apr 2001 20:18:16 +0100 Date: Tue, 24 Apr 2001 20:18:38 +0100 (GMT Daylight Time) From: Geoff Barton To: Kevin Karplus cc: govind@bic.nus.edu.sg, manoj@chem.iitkgp.ernet.in, chemistry@ccl.net, pdb-l@rcsb.org Subject: Re: reg.molscript manual In-Reply-To: <200104241657.JAA300652@alpha.cse.ucsc.edu> Message-ID: X-X-Sender: geoff@alpha1.ebi.ac.uk MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Kevin, Some possible answers to your questions. 1. Not everyone in the world is as priviliged as you and me in the speed and ease with which they can connect to the internet. 2. Not everyone in the world has English as their first language and so the internet can be hard to navigate and learn. Oh yes, and since few countries in the world use the US education system why should you expect people to know what a 'High School' is or how old you have to be to go to one? Please, lets keep this list helpful to all levels of questions related to structure. The URL you forgot to add to your email is: http://www.avatar.se/molscript/doc/molscript.html and yes, it can be found with www.google.co.uk Geoff. On Tue, 24 Apr 2001, Kevin Karplus wrote: > The molscript manual is found in less than a second by using the google.com > search engine with > molscript manual > > Why do people continue to ask for websites that are so easily found? > Please, folks, use this list for questions where expert advice and > discussion is needed, not for questions that any high school student > should be able to answer. > ------------------ Geoff Barton, EMBL-European Bioinformatics Institute, Genome Campus, Hinxton, Cambs CB10 1SD, U.K., mailto:geoff@ebi.ac.uk http://barton.ebi.ac.uk, Tel: +44 1223 494414, Fax: +44 1223 494496 From chemistry-request@server.ccl.net Tue Apr 24 14:47:12 2001 Received: from smtp.csc.fi ([193.166.0.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3OIlBI13081 for ; Tue, 24 Apr 2001 14:47:12 -0400 Received: from isosirri (ts1-140.csc.fi [193.166.2.140]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with SMTP id VAA21573 for ; Tue, 24 Apr 2001 21:47:11 +0300 From: "Leif Laaksonen" To: "Chemistry@Ccl. Net" Subject: Interested in testing the display of Delpi surfaces with gOpenMol? Date: Tue, 24 Apr 2001 21:50:41 +0300 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_001B_01C0CD08.9B6342E0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_001B_01C0CD08.9B6342E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Hi, I have made two small conversion programs that converts the Delpi (http://trantor.bioc.columbia.edu/delphi/) *.phi potential maps and INSIGHT format *.phi potential maps to a format used by gOpenMol. If there is somebody who is using gOpenMol and Delpi and wants to help me I would appreciate a bit of testing to be sure I got the conversion right. Please answer me directly and I'll mail you the Fortran conversion programs! Regards, -leif ------=_NextPart_000_001B_01C0CD08.9B6342E0 Content-Type: text/x-vcard; name="Leif Laaksonen.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Leif Laaksonen.vcf" BEGIN:VCARD VERSION:2.1 N:Laaksonen;Leif FN:Leif Laaksonen ORG:Center for Scientific Computing;CSC New Technology Group TITLE:New Technology Group Manager NOTE:My personal Web page: http://www.csc.fi/~laaksone/ TEL;WORK;VOICE:+358 9 457 2378 TEL;CELL;VOICE:+358 +358400425203 TEL;WORK;FAX:+358 9 457 2302 ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;Tekniikantie 15 a D=0D=0AP.O.Box 405;Espoo;;FIN-02101;Finland LABEL;WORK;ENCODING=QUOTED-PRINTABLE:Tekniikantie 15 a D=0D=0AP.O.Box 405=0D=0AEspoo FIN-02101=0D=0AFinland URL:http://laaksonen.csc.fi/ URL:http://www.csc.fi/ EMAIL;PREF;INTERNET:Leif.Laaksonen@csc.fi EMAIL;INTERNET:Leif.Laaksone@csc.fi REV:20000906T051522Z END:VCARD ------=_NextPart_000_001B_01C0CD08.9B6342E0-- From chemistry-request@server.ccl.net Tue Apr 24 17:21:38 2001 Received: from ns2.carb.nist.gov ([129.6.112.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3OLLbI14013 for ; Tue, 24 Apr 2001 17:21:37 -0400 Received: from umbi.umd.edu (hatter.carb.nist.gov [129.6.113.76]) by ns2.carb.nist.gov (8.9.3/8.9.3) with ESMTP id RAA03158 for ; Tue, 24 Apr 2001 17:21:38 -0400 Message-ID: <3AE5EE66.ACCB0CC3@umbi.umd.edu> Date: Tue, 24 Apr 2001 17:21:42 -0400 From: "Michael K. Gilson" X-Mailer: Mozilla 4.77 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Binding Affinity Databases Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, I would greatly appreciate leads on academic or commercial databases of measured binding affinities, other than ProNIT, DIP, BIND, the Ligand-Protein Database, and our own BindingDB). Thanks in advance, Mike From chemistry-request@server.ccl.net Tue Apr 24 22:00:12 2001 Received: from phobos.email.Arizona.EDU (IDENT:root@[128.196.133.165]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3P20BI15373 for ; Tue, 24 Apr 2001 22:00:11 -0400 Received: from demetrio.ifi.unicamp.br (128.196.86.129) by phobos.email.Arizona.EDU (5.1.056) id 3ADF1C4F0006C6A2 for CHEMISTRY@ccl.net; Tue, 24 Apr 2001 19:00:10 -0700 Message-Id: <5.0.2.1.0.20010425063848.02a10b80@deimos.email.arizona.edu> X-Sender: dasf@deimos.email.arizona.edu X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Wed, 25 Apr 2001 06:58:32 -0700 To: CHEMISTRY@ccl.net From: Demetrio Antonio da Silva Filho Subject: Kohn Sham orbitals and Orbital Energies In-Reply-To: <3AE5EE66.ACCB0CC3@umbi.umd.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed >Dear Colleagues, When we run a default DFT (for exemple, B3LYP/6-31G single point) calculation using Gaussian 98, the occupied and virtual eigenvalues printed in the default output file are the Kohn-Sham orbital energies? and the orbitals plotted using MOLDEN (for example) are the Kohn-Sham orbitals? If not, there is a way to get those informations? Thanks in advance. Demetrio Filho From chemistry-request@server.ccl.net Tue Apr 24 19:15:16 2001 Received: from chmls20.mediaone.net ([24.147.1.156]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3ONFFI14481 for ; Tue, 24 Apr 2001 19:15:16 -0400 Received: from mediaone.net (h0080ad300762.ne.mediaone.net [66.31.123.121]) by chmls20.mediaone.net (8.11.1/8.11.1) with ESMTP id f3ONEL609779; Tue, 24 Apr 2001 19:14:21 -0400 (EDT) Message-ID: <3AE608C0.CAB4B9E6@mediaone.net> Date: Tue, 24 Apr 2001 19:14:08 -0400 From: "Larry A. DuLong" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Geoff Barton CC: Kevin Karplus , govind@bic.nus.edu.sg, manoj@chem.iitkgp.ernet.in, chemistry@ccl.net, pdb-l@rcsb.org Subject: Re: reg.molscript manual References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I could not agree more forcefully with your comments. That respond was totally inappropriate for this list. Kevin, you could of answered the question quicker than typing your rude response. Thinking is not your high point, I guess!. Larry Geoff Barton wrote: > Kevin, > > Some possible answers to your questions. > > 1. Not everyone in the world is as priviliged as you and me in the speed > and ease with which they can connect to the internet. > > 2. Not everyone in the world has English as their first language and so > the internet can be hard to navigate and learn. > > Oh yes, and since few countries in the world use the US education system > why should you expect people to know what a 'High School' is or how old > you have to be to go to one? > > Please, lets keep this list helpful to all levels of questions related to > structure. > > The URL you forgot to add to your email is: > > http://www.avatar.se/molscript/doc/molscript.html and yes, it can be > found with www.google.co.uk > > Geoff. > > On Tue, 24 Apr 2001, Kevin Karplus wrote: > > > The molscript manual is found in less than a second by using the google.com > > search engine with > > molscript manual > > > > Why do people continue to ask for websites that are so easily found? > > Please, folks, use this list for questions where expert advice and > > discussion is needed, not for questions that any high school student > > should be able to answer. > > > > ------------------ > Geoff Barton, EMBL-European Bioinformatics Institute, Genome Campus, > Hinxton, Cambs CB10 1SD, U.K., mailto:geoff@ebi.ac.uk > http://barton.ebi.ac.uk, Tel: +44 1223 494414, Fax: +44 1223 494496 > > *** Details on how to be removed from this list as well as an *** > *** archive of recent postings are available at *** > *** http://www.rcsb.org/pdb/forum.html *** From chemistry-request@server.ccl.net Tue Apr 24 19:35:40 2001 Received: from ifcsun1.ifisiol.unam.mx ([132.248.16.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3ONZdI14530 for ; Tue, 24 Apr 2001 19:35:40 -0400 Received: from tuxx ([132.248.16.49]) by ifcsun1.ifisiol.unam.mx (8.10.1/8.10.1) with SMTP id f3ONjjh31340; Tue, 24 Apr 2001 18:45:45 -0500 Message-ID: <000901c0cd10$5ec69fa0$3110f884@tuxx> From: "Lenin Dominguez" To: "Larry A. DuLong" , "Geoff Barton" Cc: "Kevin Karplus" , , , , References: <3AE608C0.CAB4B9E6@mediaone.net> Subject: Re: reg.molscript manual Date: Tue, 24 Apr 2001 17:46:15 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 Disposition-Notification-To: "Lenin Dominguez" X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Please, Don't be agressive. Everything will be okay if all of us just answers politely. ----- Original Message ----- From: "Larry A. DuLong" To: "Geoff Barton" Cc: "Kevin Karplus" ; ; ; ; Sent: Tuesday, April 24, 2001 6:14 PM Subject: Re: reg.molscript manual > I could not agree more forcefully with your comments. That respond was totally > inappropriate for this list. Kevin, you could of answered the question quicker > than typing your rude response. Thinking is not your high point, I guess!. > > Larry > > Geoff Barton wrote: > > > Kevin, > > > > Some possible answers to your questions. > > > > 1. Not everyone in the world is as priviliged as you and me in the speed > > and ease with which they can connect to the internet. > > > > 2. Not everyone in the world has English as their first language and so > > the internet can be hard to navigate and learn. > > > > Oh yes, and since few countries in the world use the US education system > > why should you expect people to know what a 'High School' is or how old > > you have to be to go to one? > > > > Please, lets keep this list helpful to all levels of questions related to > > structure. > > > > The URL you forgot to add to your email is: > > > > http://www.avatar.se/molscript/doc/molscript.html and yes, it can be > > found with www.google.co.uk > > > > Geoff. > > > > On Tue, 24 Apr 2001, Kevin Karplus wrote: > > > > > The molscript manual is found in less than a second by using the google.com > > > search engine with > > > molscript manual > > > > > > Why do people continue to ask for websites that are so easily found? > > > Please, folks, use this list for questions where expert advice and > > > discussion is needed, not for questions that any high school student > > > should be able to answer. > > > > > > > ------------------ > > Geoff Barton, EMBL-European Bioinformatics Institute, Genome Campus, > > Hinxton, Cambs CB10 1SD, U.K., mailto:geoff@ebi.ac.uk > > http://barton.ebi.ac.uk, Tel: +44 1223 494414, Fax: +44 1223 494496 > > > > *** Details on how to be removed from this list as well as an *** > > *** archive of recent postings are available at *** > > *** http://www.rcsb.org/pdb/forum.html *** > > > > *** Details on how to be removed from this list as well as an *** > *** archive of recent postings are available at *** > *** http://www.rcsb.org/pdb/forum.html *** > From chemistry-request@server.ccl.net Tue Apr 24 19:51:33 2001 Received: from alpha.cse.ucsc.edu ([128.114.48.14]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f3ONpXI14571 for ; Tue, 24 Apr 2001 19:51:33 -0400 Received: (from karplus@localhost) by alpha.cse.ucsc.edu (8.6.10/8.6.12) id QAA303847; Tue, 24 Apr 2001 16:51:29 -0700 Date: Tue, 24 Apr 2001 16:51:29 -0700 Message-Id: <200104242351.QAA303847@alpha.cse.ucsc.edu> From: Kevin Karplus To: govind@bic.nus.edu.sg CC: manoj@chem.iitkgp.ernet.in, chemistry@ccl.net, pdb-l@rcsb.org In-reply-to: <200104241023.f3OANhI15092@leonis.nus.edu.sg> (govind@bic.nus.edu.sg) Subject: Re: reg.molscript manual I publically apologize to Govind for the tone of my previous message about finding the molscript manual on the web. Several people pointed out that I did not actually provide him or her with website for the manual. This was a deliberate, pedagogic omission. Instead of providing one URL, which might become obsolete, I provided a general mechanism for finding the URL quickly, a method that might prove useful for other similar questions. Indeed it is my fervent hope that many people on the mailing list will have read the message and seen that they could answer their similar questions (where can I find X on the web?) with the same mechanism, and so avoid wasting the time of the 100s of researchers who read these mailing lists to share their knowledge. I spend some time trying to answer every question that comes in on the pdb-l list and succeed on a fair fraction of them. None of this service is paid for, but I regard it as a fair exchange for the value I get from the other participants on the PDB list. Had the particular desired web site been difficult to find, I would have spent a fair amount of my time looking for it and been glad to be of assistance, but I was irritated that someone would ask hundreds of other people to look for something without first trying the obvious, standard methods. My response was unnecessarily rude, but perhaps may be more memorable for that. If my rudeness has caused half a dozen people to decide to learn to use google rather than risking an embarassing rude reply, then it was worth the social cost to me. Some people have pointed out that it is quite likely that Govind has less web access than me. Agreed, but Govind was asking for a website for a substantial document, so must have web access sufficient for getting to google.com. From chemistry-request@server.ccl.net Tue Apr 24 21:44:12 2001 Received: from cpimssmtpu11.email.msn.com ([207.46.181.86]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3P1iCI15229 for ; Tue, 24 Apr 2001 21:44:12 -0400 Received: from vaio ([63.17.31.92]) by cpimssmtpu11.email.msn.com with Microsoft SMTPSVC(5.0.2195.3225); Tue, 24 Apr 2001 18:44:05 -0700 From: "cbooth100" To: "Geoff Barton" Cc: "Kevin Karplus" , , , , Subject: RE: reg.molscript manual Date: Tue, 24 Apr 2001 18:43:55 -0700 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 In-reply-to: <3AE608C0.CAB4B9E6@mediaone.net> Importance: Normal X-OriginalArrivalTime: 25 Apr 2001 01:44:06.0978 (UTC) FILETIME=[37327220:01C0CD29] Please I am cbooth100@msn.com remove me from your communications. I have asked to be removed from list on numerous occasions only to return there must be some lonely dude out there all interested in molscript but I'm not him thank you Claude -----Original Message----- From: owner-pdb-l@rcsb.org [mailto:owner-pdb-l@rcsb.org]On Behalf Of Larry A. DuLong Sent: Tuesday, April 24, 2001 4:14 PM To: Geoff Barton Cc: Kevin Karplus; govind@bic.nus.edu.sg; manoj@chem.iitkgp.ernet.in; chemistry@ccl.net; pdb-l@rcsb.org Subject: Re: reg.molscript manual I could not agree more forcefully with your comments. That respond was totally inappropriate for this list. Kevin, you could of answered the question quicker than typing your rude response. Thinking is not your high point, I guess!. Larry Geoff Barton wrote: > Kevin, > > Some possible answers to your questions. > > 1. Not everyone in the world is as priviliged as you and me in the speed > and ease with which they can connect to the internet. > > 2. Not everyone in the world has English as their first language and so > the internet can be hard to navigate and learn. > > Oh yes, and since few countries in the world use the US education system > why should you expect people to know what a 'High School' is or how old > you have to be to go to one? > > Please, lets keep this list helpful to all levels of questions related to > structure. > > The URL you forgot to add to your email is: > > http://www.avatar.se/molscript/doc/molscript.html and yes, it can be > found with www.google.co.uk > > Geoff. > > On Tue, 24 Apr 2001, Kevin Karplus wrote: > > > The molscript manual is found in less than a second by using the google.com > > search engine with > > molscript manual > > > > Why do people continue to ask for websites that are so easily found? > > Please, folks, use this list for questions where expert advice and > > discussion is needed, not for questions that any high school student > > should be able to answer. > > > > ------------------ > Geoff Barton, EMBL-European Bioinformatics Institute, Genome Campus, > Hinxton, Cambs CB10 1SD, U.K., mailto:geoff@ebi.ac.uk > http://barton.ebi.ac.uk, Tel: +44 1223 494414, Fax: +44 1223 494496 > > *** Details on how to be removed from this list as well as an *** > *** archive of recent postings are available at *** > *** http://www.rcsb.org/pdb/forum.html *** *** Details on how to be removed from this list as well as an *** *** archive of recent postings are available at *** *** http://www.rcsb.org/pdb/forum.html ***