From chemistry-request@ccl.net Mon Aug 10 14:10:35 1992 Date: Mon, 10 Aug 92 15:50:07 +1000 From: mgw@stan.xx.swin.OZ.AU (Margaret Wong) To: chemistry@ccl.net Subject: nmr programs Status: R Dear Netters The following are the responses obtained on NMR processing software >From sauer@organik.uni-erlangen.de Thu Jul 30 23:27:06 1992 Subject: Re: NMR processing packages > Dear Netters > > We are currently looking for NMR programs to process our > data off-line. We would be very interested to hear > your opinions on any programable to work on a unix- > workstation, PC or MAC. > > ... > > Margaret Wong (mgw@stan.xx.swin.oz.au) > Hi, I'd be very interested to hear about the outcome of your survey, too. So, if you don't send a summary to the mailing list, maybe you could do so to my address below. I do think, however, that your results will be of interest to a larger audience, so a summary to the net should be a good idea. Best regards, Wolfgang Sauer. -- +======================================+=====================================+ | Wolfgang Sauer | | | Institut fuer Organische Chemie I | "You have to be three standard | | Henkestr. 42, D-8520 Erlangen, FRG | deviations away from a normal | | | personality to like UNIX." | | sauer@organik.uni-erlangen.de | | | Tel.: 49/0 - 9131 - 85 - 2952 | Morris Jones (C&T) | | Fax: - 9132 | | +======================================+=====================================+ ******************************************************************************* >From ssidner@unmc.edu Fri Jul 31 00:02:48 1992 Subject: Re: NMR processing packages Hare Research offers several products, formost among them FELIX. This is an excellent package (my researchers tell me) that supports the data formats of most current insturments and is very graphically oriented. They have a (new) port to Windows or (better yet) versions for Silicon Graphics, Sparc, and RS 6000. Their academic pricing is nearly free. Hare Research, Inc. 18943 - 120th Avenue NE, Suite #104 Bothell, WA 98011-9509 USA Phone (206) 487-9301 FAX (206) 487-9304 Steve Sidner Eppley Institute, University of Nebraska Medical Center 600 S. 42nd St., Omaha, NE, 68198-6805 (402) 559-4921, FAX: (402) 559-4651 ******************************************************************************* >From bauer@organik.uni-erlangen.de Fri Jul 31 04:24:34 1992 Dr. Walter Bauer Institute of Organic Chemistry NMR Laboratory University Erlangen-Nuernberg Henkestr. 42 D-W-8520 Erlangen Phone +49-9131-852987 FAX +49-9131-859132 E-mail bauer@organik.uni-erlangen.de Re.: NMR processing software Dear Margaret, responding to your broadcasted mail we recommend the FELIX NMR processing software, distributed by Hare Research. We use FELIX in our NMR lab since 1990 and have made very good experiences. FELIX is capable of handling data matrices up to 6D (!). It may be run on the Silicon Graphics IRIS, the INDIGO (which we use currently), on SUN SPARC Workstations, and on IBM compatible PCs. FELIX is extremely flexible and, in its new WINDOWS release, very easy to use. Data conversion routines are available for all kinds of spectrometers. The only drawback with respect to your needs is that FELIX does not allow processing of relaxation time data. Actually, I am not aware of ANY commercially available software package which meets this purpose. If you are interested in FELIX, contact Hare Research Inc. 18943 - 120th Avenue NE Suite #104 Bothell, WA 98011, USA FAX (206) 487-9304 (US internal #). I would be pleased to give you more information about FELIX from my own experiences; in case of interest, don't hesitate to contact me. Best regards, Walter ******************************************************************************* From: J_BROWN@uvmvax.uvm.edu Subject: NMR software There are many NMR simulation programs that are availible through QCPE (Quantum Chemistry Program Exchange) at Indiana University (Contact Richard Counts at bitnet countsr@iubacs or phone (812) 855-4784). Our group uses a modified version of DNMR (QCPE # 466) and UEANMR (QCPE #188). These programs simulate 1D spectra. ****************************************************************************** From: radomski@mond1.ccrc.uga.edu X-Mts: smtp Sender: chemistry-request@ccl.net Errors-To: owner-chemistry@ccl.net Precedence: bulk J_BROWN@uvmvax.uvm.edu wrote: >There are many NMR simulation programs that are >availible through QCPE (Quantum Chemistry Program Exchange) >at Indiana University (Contact Richard Counts at bitnet >countsr@iubacs or phone (812) 855-4784). Our group uses a >modified version of DNMR (QCPE # 466) and UEANMR (QCPE #188). >These programs simulate 1D spectra. Besides these, there is quite good (and unexpensive, singe license costs about $200) package sold by Hare Research Inc. 14810 216th Avenue NE, Woodinville, WA 98072, USA. They call it "Felix", and it is currently into ver 2.5. Both 1D and 2D modes are supported. It runs under Unix on SUNs and SGIs (promissed version for RISC DECstations under X failed to emerge so far), and which might be of some iterest - the same interface is implemented in the version running on PC under DOS (it is quick enough for uncomplicated 1D stuff; I know also about availability of the Windows version, but can't say how good it might be). Regards, Jan P. Radomski Complex Carbohydrate Research Center, University of Georgia, 220 Riverbend Rd., Athens, 30602 GA. Ph. (706) 542-4452 Fax (706) 542-4412 e-mail: radomski@mond1.ccrc.uga.edu ******************************************************************************* From: CBAS68@VAXE.STRATHCLYDE.AC.UK Subject: nmr processing packages Bruker have 2 unix processing packages, derived from the uxnmr software used on their amx spectrometers. The current remote version, uxnmrp, is available for Sun and Silicon Graphics machines, but is completely useless for 2D plotting as there is no plot editor. They have a new version of the standard uxnmr programme coming out soon, compatible with X-windows, which sounds much more promising. Other sources of programmes are SMIS in the UK, which is not very good, NMRI in the US or Varian, which is expensive. I haven't found any commercial packages that have any useful exponential deconvolutions for solid state relaxation data. Phil Dennison. ******************************************************************************* From: J_BROWN@uvmvax.uvm.edu Subject: least squates fitting 1D nmr spectra software To: Jim Macmillan (macmillian@iscsvax.uni.edu): There is a program from QCPC for least squares optimization of 1D NMR simulations (DNMR5: QCPE # 365). It will "optimize" up to 16 parameters including chemical shifts, coupling constants, populations, T2 values, and rate constants. It is only fair to warn you that it is a very "complex" program to use due to the nature of the calculations involved. ******************************************************************************* Thanks VERY MUCH to all who replied offering advice. Margaret Wong --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Mon Aug 10 19:16:03 1992 Date: Mon, 10 Aug 92 11:20:02 -0400 From: Scott Gregory Flicker To: chemistry@ccl.net, doug@star2.cm.utexas.edu Subject: Re: AVS chemistry viewer Status: R I've done chemistry viewing with the standard avs package and it is very good. I've seen the avs chemistry demenstrated on a SG machine and it is very good also. It also can do many molecular mechanics type calculations (extra bucks). I general I would say the drawbacks are that avs is quite pricey and you need very good hardware. Hope this helps Scott --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Mon Aug 10 22:26:15 1992 Date: Mon, 10 Aug 92 12:08:38 -0400 From: mckelvey@Kodak.COM To: osc@Kodak.COM Subject: Parallel diagonalisation routines for MOPAC Status: R Does anyone have parallel versions of HQRII and DIAG for MOPAC running on TITAN (CRAY?) available ? Machine has 4 processors. Would be glad to pass the word along if you like. Many thanks John McKelvey Research Labs Eastmak Kodak Co. Rochester NY MCKELVEY@KODAK.COM 716-477-3335 --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Mon Aug 10 23:08:26 1992 Date: Mon, 10 Aug 92 08:57:59 PDT From: d3f012@gator.pnl.gov Subject: PostScript problems? To: chemistry@ccl.net Status: R ---------- X-Sun-Data-Type: text X-Sun-Data-Description: text X-Sun-Data-Name: text X-Sun-Content-Lines: 24 I have been distributing the Argus User Manual as a Rich Text Format (.rft) file. I would like to make a PostScript file so that individuals without the ability to read .rtf files could print the manual. My problem is that Microsoft Word makes HUGE .ps files. The manual is > 1Mbyte as a single .ps file. Since many laserwriters will not accept files > 1Mbyte, this is not a good solution. Having Word just print out 1 page to a .ps file makes a file that is almost 400K; most of that is Word provided PostScript procedures, etc. Therefore printing out the manual as a series of smaller .ps files would require ~ 30-50 .ps files. I won't distribute the manual as a text (ASCII) file, since it would not survive the translation well (manual is "highly formatted" to make it more presentable, and may in the near future, include graphics). Any suggestions on a reasonable PostScript solution? Mark Thompson ---------- X-Sun-Data-Type: default X-Sun-Data-Description: default X-Sun-Data-Name: .signature X-Sun-Content-Lines: 9 ---------------------------------------------------------------- Mark A. Thompson email: d3f012@pnlg.pnl.gov Sr. Research Scientist voice: 509-375-6734 Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory PO Box 999, Mail Stop K1-90 Richland, WA. 99352 ---------------------------------------------------------------- --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Aug 11 00:50:03 1992 Date: Mon, 10 Aug 92 09:06:10 PDT From: d3f012@gator.pnl.gov Subject: Argus 1.0 To: chemistry@ccl.net Status: RO ---------- X-Sun-Data-Type: text X-Sun-Data-Description: text X-Sun-Data-Name: text X-Sun-Content-Lines: 21 I've recently announced the availability of Argus version 1.0 via anonymous ftp. I would appreciate it if, after you download the program, you could send me a one-line email message telling me you have the program and what is your email address. I am planning to make all general announcements to the OSC mail exploder. However, it would be very helpful to me to know roughly how many individuals are using the code, and who to send email to regarding bug fixes, etc. I am open to constructive criticisms from users regarding the program. Due to the number of requests for general information, I will repost the original Argus announcement (with minor modifications). Mark Thompson ---------- X-Sun-Data-Type: default X-Sun-Data-Description: default X-Sun-Data-Name: .signature X-Sun-Content-Lines: 9 ---------------------------------------------------------------- Mark A. Thompson email: d3f012@pnlg.pnl.gov Sr. Research Scientist voice: 509-375-6734 Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory PO Box 999, Mail Stop K1-90 Richland, WA. 99352 ---------------------------------------------------------------- --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Aug 11 01:20:53 1992 Date: Mon, 10 Aug 92 09:15:19 PDT From: d3f012@gator.pnl.gov Subject: Argus 1.0 To: chemistry@ccl.net Status: RO Here is a copy of my original posting regarding Argus. You can obtain Argus via anonymous ftp from pnlg.pnl.gov The file argus.tar is in the argus directory. Note, the geometry optimization and MD options are not included in version 1.0. I am distributing compiled executables at this time. Mark Thompson ************************************************************************** * * * Argus * * * ************************************************************************** An electronic structure code; mainly for semi-empirical model Hamiltonians. Its been used almost exclusively for spectroscopic calculations. Capabilities: ------------- SCF: RHF, UHF, Complex RHF, Complex UHF (latter two work, but are still experimental, and not exhaustively tested) 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: STO-NG basis sets) 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), INDO1/S and EHT only. 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, 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 Age : 1989 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. 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 ****************************************************************************** --- Administrivia: This message is automatically appended by the mail exploder. 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