From chemistry-request@ccl.net Thu Jan 9 10:08:16 1992 Date: Thu, 9 Jan 92 09:39 EST From: Subject: Re: IUPAC naming program? To: paul.savage@carbon.chem.csiro.au Status: R The Beilstein Instittue has developed a program named AUTONOM which generates IUPAC names from connection table. From chemistry-request@ccl.net Thu Jan 9 10:59:33 1992 Date: 09 Jan 92 15:43:38 GMT From: Siegfried.Schneider@rrze2.rrze.uni-erlangen.de To: CHEMISTRY@ccl.net Subject: Molecular modelling software ? Status: R Hi, I'm looking for molecular modelling software,like PCmodel, for our IBM risc 6000 / 32h workstations, commercial or noncommercial. would like to get informations andd addresses. Thanks in advance, Peter Peter Gedeck Inst.f.Phys.Chem. 1 Universitat Erlangen-Nurnberg Egerlandstr. 3 8520 Erlangen Germany FAX 09131 - 858307 E-mail : PC1@cnve.rrze.uni-erlangen.dbp.de From chemistry-request@ccl.net Thu Jan 9 14:24:29 1992 Date: 9 Jan 92 14:09:00 EDT From: "STEPHEN R. HELLER" Subject: Software for Review To: "chemistry" Status: R 9 January, 1992 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I now have two packages in hand (see below) and I am looking for people who are willing to review the software. In return for the review you get to keep the software. The review should be completed in 1-2 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. I have tried this approach with some software for review in the past few months and it is working reasonably well. As a result, I am continuing this new method to find reviewers using this e-mail system. I hope it continues to work. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. I can be reached on INTERNET, or if necessary, by phone at 301-504-6055. PLEASE BE SURE TO INCLUDE AN STREET ADDRESS AND PHONE NUMBER!!! (I send the software by Federal Express.) Steve Heller The packages I now have are: 1. Ami-Pro for Windows, Release 2, from Lotus. A word processor. 2. Edifice for the IBM PC. It is a database management program for environmental lab analytical reports. It allows you to generate tables and reports from lab data and has graphics capabilities. Requires a hard disk, 640K RAM, EGA/VAG graphics card, 2 MB of disk space. The list price of the software is $850. From chemistry-request@ccl.net Thu Jan 9 14:47:19 1992 Date: Thu, 09 Jan 92 17:33:57 BRA From: "Joao O.M.A. Lins" Subject: Address To: "Comp.Chem.List" Status: R Hi, could you please send me the Dr. Dieter Cramer address? I need to contact him to request a reference. Thanks in advance. Joao O.M.A. Lins Depto. Fisico-Quimica Instituto de Quimica - UFRJ BRASIL From chemistry-request@ccl.net Thu Jan 9 14:49:07 1992 Date: Thu, 09 Jan 92 13:27:58 CST From: "Dr. Piotr Paneth" Subject: imaginary frequencies To: Computational Chemistry Group Status: R Hi Folks, jumping into recent discussion on imaginary frequencies I have long lasting problem, which someone might already know the answer to. I do a lot of isotope effect calculations and have no problem with the concept of imaginary vibration in unimolecular reactions although its sad to see that what appears to be a transition state in eq. Mopac 5.0 (one imaginary vibration) has two such frequencies in Mopac 6.0. But this is understandable (at least to the extend). What bothers me is concept of medelling a two-molecules reactions, or for that matter inclusion of a discreet model of solvent. If two molecules have n1 and n2 number of atoms, respectively one would expect to have (3n1-6) + (3n2-6) normal vibrations and therefore positive (real) frequencies. If one tries to model such a system using Ampac or Mopac package the default model has (n1+n2) atoms, and therefore 3(n1+n2)-6 normal modes of vibrations. How do we treat this discrepancy? Usually I end up with extra negative frequencies which are not possible to get rid of. Also separa- tion of two molecules by a large distance does not help, although it improves the results a little. Any comments will be appreciated and I'll summerize for the list. Thanks, Piotr From chemistry-request@ccl.net Thu Jan 9 17:39:43 1992 Date: Thu, 9 Jan 92 14:02:20 PST From: d3f012@gator.pnl.gov Subject: Argus Free Software Announcement To: chemistry@ccl.net Status: R Dear Chemists, Due to the increasing number of well known academic codes turning commercial, I have become inclined to distribute my electronic structure program for free. The program's name is Argus. An informal description is included below. I am posting this message to see if there is a sufficient level of interest. If there is, I'll repost distribution instructions. While the program is free, it copyrighted and will be distributed under license only. Argus is an experimental program and is not warrantied in any way. The interested chemist would be someone who wants to do semi-empirical electronic structure calculations as well as code development. If you're interested, send me email. ************************************************************************** * * * Argus * * * ************************************************************************** An electronic structure code; mainly for semi-empirical model Hamiltonians. Its been used mostly for spectroscopic calculations. Capabilities: ------------- SCF: RHF, UHF, Complex RHF, Complex UHF (latter two work, but are still experimental) CI: Single-excitation used for INDO1/S spectroscopic option. Geometry optimization: BFGS update. (analytic gradients) MD: Classical MD using forces from Hartree Fock (still very much experimental, we're adding features now to make this useful to do more than just run trajectories). Hamiltonians/parameterizations ------------------------------ EHT INDO1, INDO1/S : non-spectroscopic and spectroscopic, respectively NDDO1 ab initio : SCF only (limited capability) Misc (not exhaustive and in no particular order) ------------------------------------------------ 1. UV/vis spectra using either single excited CI (TDA) or RPA. 2. State and transition dipole moments. 3. Magnetic moments, rotational strengths. 4. Dipole length, and dipole velocity integrals. 5. Some fragment properties. 6. Self Consistent Reaction Field (SCRF) solvent effects. 7. Some transition metals, (no F-orbitals yet). 8. User's manual (~50 pages) 9. Name-list input. 10. no hardwired array sizes, all memory dynamically allocated; size of problem limited only by machine resources, budget, and the ability of the various algorithms employed. 11. Integrals: 1. various recipe type integrals for semi-empirical. 2. one and two-ele integrals over contracted gaussians using the Rys-King-Dupuis formalism. Also some limited Obara & Saika integral routines. Systems ------- Portability has not been an issue yet. Compiles and runs on all Unix systems I've tried to date including Sun, HP, IBM/6000, Cray YMP (Unicos), Cray 2 (Unicos), also on IBM compatible PC's. On Unix systems I call FORTRAN Eispack routines for matrix diagonalization. On PCs, I have C diagonalization routines since many (including myself) do not have FORTRAN compilers on their PC. I've added some preprocessor directives to use the Scientific libraries on the Crays (including their Eispack routines). General ------- Language: C Size : ~40,000 - 50,000 lines of code if that matters to anyone (note, lots of comments in the above line count). Age : ~4 years. Well thought out modular structured program. If you want spagetti code, go elsewhere. Caveats ------- Some features of Argus are still experimental and not fully tested. Not all options work with all model Hamiltonians. You will find bugs. Argus is an experimental code developed for designing new model Hamiltonians and doing UV/vis spectra of large systems. While it is well designed and structured, it does not deliver an exhaustive set of options like MOPAC or Gaussian. I've "typed" in parameters for only those elements that I want to study. If needs be, I'll type in the remainder of the parameters. Development thus far has been almost totally driven by my personal research interests. Some key features are missing. However, we will be developing Argus at PNL and this should fill out the code quite nicely. In progress ----------- 1. Argus is partially ported to the Intel iPSC/860 Gamma & Delta parallel computers. Argus will be further developed in conjunction with projects we have at the Molecular Science Research Center. 2. Restricted Open Shell Hartree Fock (ROHF). 3. Adding features to the HF MD so we can do real science with it. Some recent publications using Argus ------------------------------------ 1. "A Theoretical Examination of the Electronic Structure and Spectroscopy of the Photosynthetic Reaction Center from Rhodopseudomonas viridis" JACS 113, (1991) p. 8210 2. "Effect of a Polarizable Medium on the Charge-Transfer States of the Photosynthetic Reaction Center from Rhodopseudomonas viridis" JACS 112 (1990) p. 7828 3. "A Theoretical Examination of the Electronic Structure and Excited States of the Bacteriochlorophyll-b Dimer from Rhodopseudomonas viridis" J. Phys. Chem. 95, (1991) p. 5693 ****************************************************************************** Mark A. Thompson Molecular Science Research Center Pacific Northwest Laboratory PO Box 999, Mail Stop K1-87 Richland, Wa. 99352 email: d3f012@pnlg.pnl.gov