From DURRAN@chem.surrey.ac.uk Thu Apr 6 06:27:13 1995 Received: from maila.surrey.ac.uk for DURRAN@chem.surrey.ac.uk by www.ccl.net (8.6.10/930601.1506) id GAA25644; Thu, 6 Apr 1995 06:21:04 -0400 Received: from chemcharon.chem.surrey.ac.uk by maila.surrey.ac.uk with SMTP (PP); Thu, 6 Apr 1995 11:20:02 +0100 Received: From CHEMISTRY-1/WORKQUEUE by chemcharon.chem.surrey.ac.uk via Charon-4.0-VROOM with IPX id 100.950406112020.352; 06 Apr 95 11:22:07 +500 Message-ID: To: chemistry@ccl.net From: Michael Organization: Chemistry Department, Uni of Surrey Date: Thu, 6 Apr 1995 11:20:09 GMT Subject: Basis sets Priority: normal X-mailer: WinPMail v1.0 (R1) I would be grateful if anybody could provide information / references concerning the availability of the following basis sets : 4-31+G 4-31G* Thanks Mike chp1dd@central.surrey.ac.uk From martin@link.sunet.se Thu Apr 6 08:12:12 1995 Received: from decnet.sunet.se for martin@link.sunet.se by www.ccl.net (8.6.10/930601.1506) id HAA26674; Thu, 6 Apr 1995 07:57:25 -0400 Received: from LINK.DECnet MAIL11D_V3 by decnet.sunet.se (5.57/2.01) id AA19680; Thu, 6 Apr 95 13:49:39 +0200 Date: Thu, 6 Apr 95 13:49:39 +0200 Message-Id: <9504061149.AA19680@decnet.sunet.se> From: martin@link.sunet.se (Martin Norin, Dept. Biochem., Royal Inst. Technol., Stockholm, tel. +46-8-7907512, e-mail; martin@physchem.kth.se) To: "chemistry@ccl.net"@kth.sunet.se Subject: GRID program as scoring function Dear colleauges, I've heard that the GRID program (Goodford et al.) may be used in scoring ligands bound at receptor sites (any protein cavities). Any comments or pointers to references are welcome. I'll summarize replies to the CCL. Best Regards Martin Norin\ Pharmacia Biopharmaceuticals e-mail:martin.norin@sto.pharmacia.se Dept. Struct. Biochem. S-11247 Stockholm Sweden From darryl@om3.ch.umist.ac.uk Thu Apr 6 09:12:13 1995 Received: from nessie.mcc.ac.uk for darryl@om3.ch.umist.ac.uk by www.ccl.net (8.6.10/930601.1506) id JAA27384; Thu, 6 Apr 1995 09:11:52 -0400 Received: from om3.ch.umist.ac.uk (actually trigger.ch.umist.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Thu, 6 Apr 1995 14:11:23 +0100 Received: by om3.ch.umist.ac.uk (940406.SGI/) for chemistry%ccl.net@nessie.mcc.ac.uk id AA02705; Thu, 6 Apr 95 14:24:46 +0100 Date: Thu, 6 Apr 1995 14:24:46 +0100 (BST) From: Darryl Ellson Subject: Program for coupling constants. To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am enquiring whether anyone has knowledge of the MELDF program, and whether it may be used for the calculation of isotropic and anisotropic coupling constants. I would also be grateful if anyone could inform me of any other program they have experience of for the calculation of coupling constants. Many Thanks. Darryl A. Ellson ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Darryl A. Ellson - Dept. Chemistry, UMIST, Manchester. M60 1QD Molecular Simulation & Design Laboratory Tel: 061-236-3311 x4476 Fax: 061-236-7677 E-mail: darryl@trigger.ch.umist.ac.uk ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From kamal@univ-orleans.fr Thu Apr 6 09:14:51 1995 Received: from centre.univ-orleans.fr for kamal@univ-orleans.fr by www.ccl.net (8.6.10/930601.1506) id JAA27342; Thu, 6 Apr 1995 09:07:04 -0400 Received: from mailhost.univ-orleans.fr ([193.49.81.2]) by centre.univ-orleans.fr (8.6.9/8.6.9) with SMTP id PAA27616 for ; Thu, 6 Apr 1995 15:12:25 +0200 LD?Resent-Date: Thu, 6 Apr 1995 15:12:25 +0200 Message-Id: <199504061312.PAA27616@centre.univ-orleans.fr> X-Sender: kamal@mailhost.univ-orleans.fr X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Thu, 06 Apr 1995 13:55:59 +0100 To: chemistry@ccl.net From: kamal@univ-orleans.fr (Kamal Azzaoui) Subject: Log P (o/w) of octanol ! Dear netters We are working in the field of quantitative structure-chromatographic retention relationships (QSSR) and , among various physico-chemical descriptors, we used the calculated Log P (o/w)( With Ghose and Crippen=92s parameters). One of our products is Octanol. It is very easy to calculate the Log P of Octanol ( we found 2.54), this value is a by evidence a descriptor of the structure , but we have a =91philosophic=92 problem: What is the physical meaning of Log P(o/w) of Octanol? Subsidiary question: What is the Log P of water? All suggestions are welcome !!=20 thanks Kamal=20 ------------------------------------------------------------------ Kamal AZZAOUI =20 LCBA. Universit=E9 d'Orl=E9ans. BP 6759. 45067 Orl=E9ans cedex 2 France Tel: 38-41-70-42 email: kamal@centre.univ-orleans.fr ------------------------------------------------------------------ From virtual@quantum.larc.nasa.gov Thu Apr 6 09:17:15 1995 Received: from quantum.larc.nasa.gov for virtual@quantum.larc.nasa.gov by www.ccl.net (8.6.10/930601.1506) id JAA27330; Thu, 6 Apr 1995 09:06:45 -0400 Message-Id: <199504061306.JAA27330@www.ccl.net> Received: by quantum.larc.nasa.gov (1.37.109.4/16.2) id AA04690; Thu, 6 Apr 95 09:08:46 -0400 Date: Thu, 6 Apr 95 09:08:46 -0400 From: "Don H. Phillips" To: CHEMISTRY@ccl.net Subject: Instability In reply to <9504051643.AA09878@vangogh.chem.uab.edu> Gavin: >...... We found that there is a > triplet state that is lower in energy than the singlet at HF levels of > theory, but singlet is lower for MP2 and DFT levels of theory. I suspect that your "HF level theory" singlet is closed shell and that the true ground state is an open shell singlet. My guess is that the orbitals involved are (essentially) p orbitals on the terminal oxygen and the nitrogen, but I haven't done any work on this compound so that's only a guess. Possible approaches to exploring this are: (1) Carry out an open shell singlet HF calculation. Use singles and doubles CI from the open shell reference to improve the description (or open shell MP4 if available). Note that, depending upon the relative importance of the single reference function, this may not yield an accurate result but it will be improved over what you have now. An MCSCF treatment to get orbitals and a multiple reference CI or equivalent coupled cluster calculation would be required for accuracy if the state isn't described well by a single reference function. (2) An alternative approach would be to obtain natural orbitals for the true ground state and base a CI treatment on these orbitals. The same caveats as above apply with regard to the suitability of a single function reference. The natural orbitals from a UHF treatment of the lowest triplet state might be a good starting point. INDO may not provide a qualitatively correct description of the lowest states. I would recommend sticking with ab-initio treatments throughout. I don't have any experience with Gaussian, which I assume you are using, or with DFT treatments of open shell singlets, so I am of no help to you there. The GAMESS and COLUMBUS packages offer alternatives. The latter has a lot of flexibility, but was difficult to use when I last looked. A recent posting to CCL indicated that there is a more user-friendly version available somewhere on the net. It sounds like you have discovered an "interesting" system. Have fun. Good luck, Don From d3e102@ames.pnl.gov Thu Apr 6 11:27:16 1995 Received: from pnl.gov for d3e102@ames.pnl.gov by www.ccl.net (8.6.10/930601.1506) id LAA00438; Thu, 6 Apr 1995 11:18:11 -0400 Received: from ames.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01HP0FTL6OY80008BX@pnl.gov>; Thu, 06 Apr 1995 08:17:57 -0700 (PDT) Received: by ames.pnl.gov (931110.SGI/930416.SGI.AUTO) for @gate.pnl.gov:chemistry@ccl.net id AA11451; Thu, 6 Apr 95 08:17:57 -0700 Date: Thu, 06 Apr 1995 08:17:57 -0700 From: d3e102@ames.pnl.gov (Dave Feller) Subject: Ab Initio Benchmark Report To: chemistry@ccl.net Message-id: <9504061517.AA11451@ames.pnl.gov> Content-transfer-encoding: 7BIT All: The 1995 version of the EMSL Ab Initio Benchmark Report has finally been clearer and is now available. It can be found at URL http://www.emsl.pnl.gov:2080/ under the "Technical Reports" section. PostScript and Microsoft Word (Mac) versions are also available via anonymous FTP from pnlg.pnl.gov under directory qcbenchmarks. Hardcopies are being printed, but in order to keep down the printing costs we are only printing abridged versions of the report. These abridged copies will not include the detailed tables of performance data. People who have expresses an interest in the report should receive an abridged copy in the mail in 2 - 3 months. Dave David Feller Environmental Molecular Sciences Laboratory Battelle Pacific Northwest Labs Mail Stop K1-96 Battelle Blvd Richland, WA 99352 From noy@tci002.uibk.ac.at Thu Apr 6 12:27:16 1995 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.10/930601.1506) id MAA01818; Thu, 6 Apr 1995 12:15:41 -0400 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA19267 (5.65c/IDA-1.4.4 for ); Thu, 6 Apr 1995 18:15:33 +0200 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA29665; Thu, 6 Apr 1995 18:15:31 +0200 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9504061615.AA29665@tci002.uibk.ac.at> Subject: ab initio benchmark available ! To: chemistry@ccl.net Date: Thu, 6 Apr 1995 18:15:31 +0200 (DFT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 881 Dear Netters, Forgive me if I double this news. I just came across the ab initio benchmark report worked by Dr. David Feller at EMSL WWW http://www.emsl.pnl.gov:2080/homes/tms/tmshome.html As I remembered, he used to post once that this report will be available on-line and a lot of people are looking forward to this benchmark. Now, it is available. best wishes, Teerakiat ---------------------------------------------------------------------------- E-mail: noy@tci2.uibk.ac.at (University of Innsbruck) noy@atc.atccu.chula.ac.th (Bangkok) (Permanent E-mail address) Homepage http://www-c724.uibk.ac.at/noy/ http://atc.atccu.chula.ac.th/noyhome/ ----------------------------------------------------------------------------- Early to bed and early to rise. Makes a man healthy, wealthy and wise. -- Benjamin Franklin From BGoodin@UNEX.ucla.edu Thu Apr 6 15:57:19 1995 Received: from grizzly.ucla.edu for BGoodin@UNEX.ucla.edu by www.ccl.net (8.6.10/930601.1506) id PAA05994; Thu, 6 Apr 1995 15:44:00 -0400 Received: from UNEXGW.UCLA.EDU ([128.97.218.2]) by grizzly.ucla.edu (8.6.9/8.6.9) with SMTP id LAA29703; Thu, 6 Apr 1995 11:29:26 -0800 Received: by UNEXGW.UCLA.EDU with Microsoft Mail id <2F84407D@UNEXGW.UCLA.EDU>; Thu, 06 Apr 95 12:26:53 PDT From: "Goodin, Bill" To: "'List-Biomaterials'" , List-Biotechnology , List-Biotechnology business , "'List-Computational chem2'" , List-Chemistry modeling , "'List-Chemical engineering'" , List-Computational chemistry To: List-Materials , List-Materials synthesis , List-Macromolecular engineerin , List-Polymers , List-Polymer chemistry , List-SAMPE Cc: "Goodin, Bill" Subject: UCLA short course on "Computational Chemistry for Materials and Drug Design" Date: Thu, 06 Apr 95 12:19:00 PDT Message-ID: <2F84407D@UNEXGW.UCLA.EDU> Encoding: 48 TEXT X-Mailer: Microsoft Mail V3.0 On August 14-17, 1995, UCLA Extension will present the short course, "Computational Chemistry for Materials and Drug Design", on the UCLA campus in Los Angeles. The instructors are Richard Judson, PhD, Senior Member of the Technical Staff, Sandia National Laboratories; Tony Hopfinger, PhD, Professor, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago; and Michael Colvin, PhD, Senior Member of the Technical Staff, Sandia National Laboratories. This course provides a broad introduction to computational molecular modeling. A variety of methods are discussed which range from statistical methods based on experimental data to high-level ab initio quantum chemical calculations. The course stresses how different methods can be appropriately applied in a variety of situations. These methods include molecular dynamics, quantum chemistry, and statistical methods such as QSAR (Quantitative Structure Activity Relationships). Lectures also introduce homology-based protein modeling and general-purpose optimization methods used across a range of computational chemistry methods. The course combines descriptions of methods with applications to specific areas, including predictions of physical properties of molecules (solubilities, conformations, pKa, diffusion coefficients, etc.), predictions of binding properties of drugs (binding geometries and energetics), and statistical prediction of various properties from experimental data. Methods are illustrated with case studies, and the course also addresses the use of available commercial modeling software both in lectures and hands-on sessions. Specific topics include: Molecular Modeling, Computer Lab Session, Quantum Chemistry, Case Study, Continuum Solvent Models, Case Study, Polarizable Treatment of Metals, Computer Lab Session, Quantitative Structure Activity Relationship (QSAR), Molecular Diversity and Computer -Assisted Molecular Design, Case Study, Computer Lab Session, Applications of Computational Methods to Polymeric Materials Design, Commonly Used Optimization Methods in Chemical Calculations, Protein Homology Modeling, and Commercially Available Modeling Software. For additional information and a complete course description, please contact Marcus Hennessy at: (310) 825-1047 (310) 206-2815 fax mhenness@unex.ucla.edu From moret@far.ruu.nl Thu Apr 6 16:27:21 1995 Received: from nic.cc.ruu.nl for moret@far.ruu.nl by www.ccl.net (8.6.10/930601.1506) id QAA06573; Thu, 6 Apr 1995 16:22:41 -0400 Received: from far.ruu.nl (ruucmc.far.ruu.nl) by nic.cc.ruu.nl with SMTP id AA03316 (5.67b/IDA-1.5 for ); Thu, 6 Apr 1995 22:22:40 +0200 Message-Id: <199504062022.AA03316@nic.cc.ruu.nl> Received: by ruucmc.far.ruu.nl (16.6/16.2) id AA17003; Thu, 6 Apr 95 22:18:18 +0200 From: "E.E.Moret" Subject: Why is trimethoprim selective for bacterial DHFR?? To: chemistry@ruucmc.far.ruu.nl Date: Thu, 6 Apr 95 22:18:17 METDST Name: Ed Moret Organisation: Utrecht University Phone: 030 - 536979 Mailer: Elm [revision: 66.25] Dear colleagues, The following question is of a rather detailed nature. Still, in view of the omnipresence of DHFR research in the modelling literature of the last decade, I think many of you can help us out. Trimethoprim (TMP) is a valuable antibacterial compound used in pharmacotherapy. Its value is based on its 10000 times higher affinity for bacterial over human Dihydrofolate Reductase (DHFR). It is a classical example in medicinal chemistry and drug design. In ligand modelling, the DHFR and methotrexate (MTX) complex (for example 4dfr.pdb) has been the de facto standard example for testing new programs like Ludi, Leapfrog, Apex-3D, MCSS, Grow and others. The X-ray structure of TMP with vertebrate or bacterial DHFR has never been deposited at the PDB. The selectivity of TMP for bacterial DHFR is believed to be based on a somewhat different binding mode, caused by decreased accessibility of the hydrophobic pocket, as compared to vertebrate DHFR. Although it is possible to generate a complex with energy minimisation and docking algorithms, the giant effect of these subtle changes remains mysterious to me. Although our docking method seems to work fine, given the precise prediction of the crystal structure positions of MTX and DHF, the interaction energies for TMP in human and bacterial DHFR are roughly the same. Some workers have pointed to changes in a histidines protonation state and its effect on the co-factor NADPH. Other workers have pointed out the importance of buried water molecules. Some workers have pointed at the protonation state of an aspartate or glutamate residue. A mutative loss of a valine in human DHFR compared to E.Coli DHFR seems to explain the loss of one hydrogen bond. The crystallographers describe the hydrophobic pocket in vertebrate DHFR as being too wide. A cooperative binding effect of NADPH has been experimentally determined. I still do not grasp what interactions are missing in vertebrate DHFR. What prevents TMP from adopting the conformation found in bacterial DHFR? What are the extra interactions in bacterial DHFR which account for the 10000-fold difference, roughly equal to 23 kJ/mole or 2 to 3 salt bridges? (No flames on my estimates please; the difference is HUGE and complete therapy is based on this) Among you, there should be numerous workers who have studied this complex. What do you think is the main determinant for this selectivity? With best regards, Ed Moret -- ------------------------------------------------------------------------- E.E. Moret (@more@) E.E.Moret@far.ruu.nl Computational Medicinal Chemistry/Department of Pharmaceutical Chemistry Faculty of Pharmacy/Utrecht University/the Netherlands Telephone (31-30)536979/536958 Facsimile (31-30)516674 ------------------------------------------------------------------------- From paul@simulate.chem.vt.edu Thu Apr 6 17:27:19 1995 Received: from simulate.chem.vt.edu for paul@simulate.chem.vt.edu by www.ccl.net (8.6.10/930601.1506) id RAA07802; Thu, 6 Apr 1995 17:26:11 -0400 Received: by simulate.chem.vt.edu (AIX 3.2/UCB 5.64/4.03) id AA14973; Thu, 6 Apr 1995 17:23:49 -0400 From: paul@simulate.chem.vt.edu (Paul Gregory) Message-Id: <9504062123.AA14973@simulate.chem.vt.edu> Subject: Re: CCL:heterogeneous nucleation To: rmiller@hplato.hpl.hp.com (Robert Miller) Date: Thu, 6 Apr 1995 17:23:49 +22300129 (EDT) Cc: chemistry@ccl.net (complist) In-Reply-To: <9504060155.AA21824@hplato.hpl.hp.com> from "Robert Miller" at Apr 5, 95 06:55:09 pm X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 2177 > > Colleagues; > Have any of you attempted to simulate vapor nucleation? > Do any of you have thoughts on the topic? > I will post a summary of any and all replies. > -- > Sincerely, > Robert Miller, PhD > Hewlett-Packard Laboratories > e-mail: rmiller@hplato.hpl.hp.com I published a paper on homogeneous nucleation. The reference is: V.P. Gregory and J.C. Schug, "Clustering of Lennard-Jones Particles Below the Critical Temperature", 1993, Molecular Physics, 78, 407. The abstract follows: The clustering properties of sub-critical 3D Lennard-Jones particles have been determined by Monte Carlo computer simulation. The goal was to study liquid formation, which results in the definition of a cluster that is based on the radial distribution function of the LJ liquid. The cluster distribution was compared with that predicted by classical nucleation theory and analyzed with the cluster distribution scaling law. It was found that the surface tension must vary with cluster size in order for classical theory to fit the simulation data. Also, the scaling law was determined to have limited usefullness over the range of system densities and was most applicable to lower densities and higher temperatures. The density profile revealed that the clusters did not have well defined surfaces and were liquid-like in the interior. The fractal dimension was calculated from the radius of gyration and found to agree with the accepted value. The presence of a phase transition was determined from the cluster energy plots. ------------ V. Paul Gregory, PhD Department of Chemistry Internet: paul@simulate.chem.vt.edu Virginia Tech ,/\ IBM RISC System/6000 Model 350 Blacksburg, Virginia ,/ `\/`'\ 24061-0212 ,/\/ / ,/ <_ ._. / `\ / / ,/\_ _/' `-`-\ |/ ,/' `_'_' * Blacksburg \_> ' ,/' \__>_/\ +----------------------------------------------+ From butch@sunlc2.chem.uga.edu Thu Apr 6 19:27:24 1995 Received: from dns1.uga.edu for butch@sunlc2.chem.uga.edu by www.ccl.net (8.6.10/930601.1506) id TAA09717; Thu, 6 Apr 1995 19:26:34 -0400 Received: from sunlc2.chem.uga.edu (sunlc2.chem.uga.edu [128.192.5.175]) by dns1.uga.edu (8.6.10/8.6.10) with ESMTP id SAA09055 for ; Thu, 6 Apr 1995 18:26:34 -0500 Received: (from butch@localhost) by sunlc2.chem.uga.edu (8.6.10/8.6.10) id TAA04981 for chemistry@ccl.net; Thu, 6 Apr 1995 19:26:32 -0400 Date: Thu, 6 Apr 1995 19:26:32 -0400 From: Butch Carreira Message-Id: <199504062326.TAA04981@sunlc2.chem.uga.edu> To: chemistry@ccl.net Subject: Log P (o/w) of octanol X-Sun-Charset: US-ASCII Dear Kamal, > Date: Thu, 06 Apr 1995 13:55:59 +0100 > To: chemistry@ccl.net > From: kamal@univ-orleans.fr (Kamal Azzaoui) > Subject: CCL:Log P (o/w) of octanol ! > Sender: Computational Chemistry List > Errors-To: ccl@ccl.net > Precedence: bulk > > Dear netters > > We are working in the field of quantitative structure-chromatographic > retention relationships (QSSR) and , > among various physico-chemical descriptors, we used the calculated Log P > (o/w)( With Ghose and Crippen=92s parameters). > > One of our products is Octanol. > > It is very easy to calculate the Log P of Octanol ( we found 2.54), this > value is a by evidence a descriptor of the structure , but we have a >philosophic problem: > > What is the physical meaning of Log P(o/w) of Octanol? > Subsidiary question: What is the Log P of water? The answer is this: Log P(o/w) for a solute is the difference in the log activities of that solute in water and octanol solvents. The log activity of octanol in octanol is 0.0 (~0.04 or so if you take into account that it is really wetted octanol). However, the log activity for octanol in water is about 4.0. If you express the log P using a moles/l reference rather than a mole fraction reference (the usual) then the difference in the log of the molecularites of the solvents must be taken into account, for o/w this is ~0.82. So the log P would be 4.0-0.8 or around 3.1-3.2. The same scheme will hold for the log P(o/w) of water. Hope that helps. Butch Carreira ==================================================================== Butch Carreira butch@sunlc2.chem.uga.edu Department of Chemistry (706) 542-2050 or 2051 The University of Georgia (706) 542-9454 FAX Athens, GA 30602 From tony@schroeder.newcastle.edu.au Thu Apr 6 20:12:22 1995 Received: from schroeder.newcastle.edu.au for tony@schroeder.newcastle.edu.au by www.ccl.net (8.6.10/930601.1506) id UAA10247; Thu, 6 Apr 1995 20:03:35 -0400 Received: by schroeder.newcastle.edu.au (AIX 3.2/UCB 5.64/4.03) id AA18609; Fri, 7 Apr 1995 11:02:29 +1100 Date: Fri, 7 Apr 1995 11:02:27 +1100 (E ) From: Tony Dyson To: Computational Chemistry List Subject: Gaussian & VAX/VMS Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I don't see VAX/VMS amongst the list of current or proposed platforms for Gaussian94. Why is this so? We ourselves use the unix version, but the fact that a VMS version is not promised has meant that our associates in the Chemistry department are refusing to share the cost of the license upgrade this time. Does anyone know why Gaussian seems to be moving off VMS platforms? Tony ================================================================ Mr. Anthony J. Dyson tony@schroeder.newcastle.edu.au Dept. of Physics phone: +49 21 5425 University of Newcastle fax: +49 21 6907 Callaghan, Australia, 2308 ================================================================ From JWANG@ac.dal.ca Thu Apr 6 21:12:22 1995 Received: from SYSWRK.UCIS.Dal.Ca for JWANG@ac.dal.ca by www.ccl.net (8.6.10/930601.1506) id UAA10748; Thu, 6 Apr 1995 20:59:08 -0400 From: Received: from AC.Dal.Ca by SYSWRK.UCIS.DAL.CA (PMDF V4.3-13 #6307) id <01HP18IDZGS0003YCO@SYSWRK.UCIS.DAL.CA>; Thu, 06 Apr 1995 21:58:56 -0300 Received: from AC.DAL.CA by AC.DAL.CA (PMDF V4.3-13 #6307) id <01HP18H3AYM800515W@AC.DAL.CA>; Thu, 06 Apr 1995 21:58:45 -0300 Date: Thu, 06 Apr 1995 21:58:44 -0300 Subject: Summary of internal coordinates --> normal coordinates To: CHEMISTRY@ccl.net Message-id: <01HP18H3LERM00515W@AC.DAL.CA> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, Many thanks to people who replied to my query about converting internal coordinates to the normal coordinates. Here is a summary of replies I have received. Jian Wang Department of Chemistry Dalhousie University Halifax, Nova Scotia Canada B3H 4J3 Tel: (902)-494-7921 Fax: (902)-494-1310 ---------- Original Question ---------- Dear Netters, I am looking for a code to calculate the matrix which converts the internal coordinates to the normal mode coordinates. I can get the force constant matrix with respect to the internal coordinates, but I need a code to calculate the G matrix, which is necessary for the diagonization of the FG matrix. From there I will be able to obtain the transformation matrix. Thanks in advance. Jian Wang ------------ Replies ------- From: IN%"cas@softshell.com" "Craig Shelley" ============================== I will be gone the week of March 20th. I will be back on the 27th. If you need support or other information before then, e-mail development@softshell.com, call our office at 303-242-7502, or fax at 303-242-6469. Thanks, Craig A Shelley From: IN%"youkha@biosym.com" ============================== If you already have code that calculates normal modes in cartesian X = Lx Q and to determine the "B matrix" R = B X ... (a program that does the former does the latter if the force constants are expresse d in internal space) then the Lr matrix you are looking for is Lr = B * Lx where R = int coords X cartesian coords Q normal coords this is much simpler. programs at QCPE exist for these things. see the book of Wilson on that topic ************************************************************************** Dr. Philippe Youkharibache e-mail: youkha@biosym.com Biosym Technologies Inc. 9685 Scranton Road tel: (619) 546 5562 San Diego, CA 92121 fax: (619) 458 0136 ************************************************************************** From: IN%"GOVENDEM@che.und.ac.za" "Magan Govender - PG" ============================== Dear Sir, I have some codes available, and shall be happy to forward them to you, on request. Greatings from South Africa M.G. Govender Centre for Theoretical and Computational Chemistry Dept of Chemistry University of Natal King George V Avenue Durban South Africa M.G. Govender's second reply: ============================== Dear Sir, The program we are using does a complete vibrational calc. of the secular equation, it is called Vibra by Dr. STeele. We also have ASYM20, by Ian Mills , obtained from QCPE. A also have a code from SPectro, author Handy, and Willets, I can send you this code, and lastly there is a program obtainable via ftp iqm.unicamp.br, in the chem or pub dir, which is called BGF and NCA, similar to ASyM20. Anyway I shall forward you the code soon which is in fortran. The address of Dr STeele is aslc801@vmsfe.ulcc.ac.uk. regards Magan From: IN%"nowak@ibm320.chemie.th-merseburg.de" ============================== Dear Jian Wang If you have the B matrix which transform the cartesian force constant matrix to the internal force constant matrix you can build the G matrix by G=B M**-1 B#. Where B# is the transpose of the B matrix and M**-1 is the inverse of the M matrix. M is a diagonal matrix of tripels of the mass. The product FG is a nonsymmetric matrix. The simplest way to get the eigenvalue and eigenvectors is to bring the matrix to a hessenberg matrix then you can get the eigenvalue and eigenvectors by the qr methode. I wrote a FORTRAN program which can build the internal force constants matrix from the cartesian force constant matrix. Futhermore it will calculate the G matrix and frequences. There is also a procedure which bild the B matrix. If you are interested in my program please send me a e-mail. If you are loocking for some literature for this topic: Califano Vibrational States JOHN WILLEY & SONS 1976 T.Miyazawa J. Chem. Phys. 1958 29 P.246 R.J.Malriot J. Chem. Phys. 1955 23 P.30 Futhermore I am intrested in your way to get the internal force constant matrix. Thanks in advance. Thomas Nowak e-mail nowak@ibm320.chemie.th-merseburg.de -------------- End of Replies ---------