From laaksone@csc.fi Tue Nov 19 03:38:40 1996 Received: from voxopm.minedu.fi for laaksone@csc.fi by www.ccl.net (8.8.2/950822.1) id DAA16984; Tue, 19 Nov 1996 03:03:01 -0500 (EST) Received: (from laaksone@localhost) by voxopm.minedu.fi (8.7.5/8.6.11+CSC-2.0) id KAA14892; Tue, 19 Nov 1996 10:03:01 +0200 (EET) Content-Transfer-Encoding: 8bit Date: Tue, 19 Nov 1996 10:03:00 +0200 (EET) From: Leif Laaksonen X-Sender: laaksone@voxopm.minedu.fi To: Chemistry@www.ccl.net Subject: Gaussian Cube and gOpenMol Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I haven't received any messages for some time from the CC List so this message deals with an old subject but I still want to contribute. I wrote a long time ago a filter program to convert the Gaussian Cube files into a form readable by SCARECROW or gOpenMol. Please have a look at http://laaksonen.csc.fi/gopenmol/gopenmol.htmls Regards, -leif laaksonen Ps: It is interesting to see the increasing number of entries dealing with PC/Windows NT. I finally managed to port the full functionality of gOpenMol using the OpenGL and Tcl/Tk libraries and toolkits to the WINTEL NT platform and I'm still impressed by the speed of my computer and the graphics in particular. ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi ---------URL: http://laaksonen.csc.fi/leif.laaksonen.html---------- From dmit@nmr1.ioc.ac.ru Tue Nov 19 04:38:41 1996 Received: from nmr-dmit.ioc.ac.ru for dmit@nmr1.ioc.ac.ru by www.ccl.net (8.8.2/950822.1) id EAA17407; Tue, 19 Nov 1996 04:33:42 -0500 (EST) Received: from nmr-dmit (dmit@localhost [127.0.0.1]) by nmr-dmit.ioc.ac.ru (8.6.12/8.6.9) with SMTP id MAA00609 for ; Tue, 19 Nov 1996 12:33:23 +0300 Sender: dmit@nmr-dmit.ioc.ac.ru Message-ID: <32917EE3.123A71B6@nmr1.ioc.ac.ru> Date: Tue, 19 Nov 1996 12:33:23 +0300 From: "Dmitry E. Dmitriev" Organization: IOCh RAS X-Mailer: Mozilla 2.0 (X11; I; Linux 1.2.13 i486) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Re: CCL:Molecule Builder : Linux version bug References: <199611181433.PAA20284@odysseus.informatik.uni-stuttgart.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear netters, Is anybody there who try to run Linux version of CACTVS? I need help. When i try to run any application from package, i got a error: /usr/local/lib/cactvs/tkserver: can't resolve symbol '_h_errno' Segmentation fault Installation process produced no errors or warnings. I wrote to authors, but got no answers... System - Linux 1.2.13. Dmitry -- ************************************************************************ * Dmitry E. Dmitriev * Moscow , Russia * * Local Network Administrator * Phone : (095) 135-9094 * * NMR Centre * Fax : (095) 135-5328 * * Russian Academy of Sciences * Email : dmit@nmr1.ioc.ac.ru * ************************************************************************ From giovanni@sg2.csrsrc.mi.cnr.it Tue Nov 19 09:38:48 1996 Received: from sg2.csrsrc.mi.cnr.it for giovanni@sg2.csrsrc.mi.cnr.it by www.ccl.net (8.8.2/950822.1) id IAA18616; Tue, 19 Nov 1996 08:47:12 -0500 (EST) Received: by sg2.csrsrc.mi.cnr.it (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for chemistry@www.ccl.net id FAA27804; Tue, 19 Nov 1996 05:48:12 -0800 Date: Tue, 19 Nov 1996 05:48:12 -0800 From: giovanni@sg2.csrsrc.mi.cnr.it (Giovanni Scalmani) Message-Id: <199611191348.FAA27804@sg2.csrsrc.mi.cnr.it> To: chemistry@www.ccl.net Subject: XMol on AIX4.1 Dear friends, I am looking for someone who has already succeded in porting XMol on IBM RS6000 systems running AIX4.1. The XMol file (xmol.rs6000) I got at ftp.imb-jena.de does not work (I think it was build for AIX3.x). Thanks, Giovanni. ---------------------------------------------------------------------- ^^^ | SCALMANI Giovanni giovanni@sg2.csrsrc.mi.cnr.it o o | Universita' degli Studi di Milano | | Dipartimento di Chimica Fisica ed Elettrochimica \_/ | via C.Golgi, 19 Phone: ++39-2-26603254 | 20133 Milano (Italy) Fax : ++39-2-70638129 ---------------------------------------------------------------------- From kochw@argon.chem.tu-berlin.de Tue Nov 19 09:48:32 1996 Received: from mail.zrz.TU-Berlin.DE for kochw@argon.chem.tu-berlin.de by www.ccl.net (8.8.2/950822.1) id JAA18922; Tue, 19 Nov 1996 09:18:05 -0500 (EST) Received: from argon.chem.tu-berlin.de by mail.zrz.TU-Berlin.DE with SMTP (PP); Tue, 19 Nov 1996 15:15:04 +0100 Received: by argon.chem.tu-berlin.de (AIX 3.2/UCB 5.64/ZRZ-AIX) id AA50554; Tue, 19 Nov 1996 15:20:45 +0100 From: Wolfram Koch Message-Id: <9611191420.AA50554@argon.chem.tu-berlin.de> Subject: 2 electron problem: full CI To: CHEMISTRY@www.ccl.net Date: Tue, 19 Nov 1996 15:20:44 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Hi everyone, I am facing a problem that is difficult because it is too easy ;-) We are considering to enter a project for which we require as accurate as possible information about the potential curves of a large variety of excited states of the He2(++) dimer. This is a 2 electron system and one is tempted to employ methods such as Hylleras CI or some variant thereof (i.e. wave functions that explicitly contain the e-e distance). Can anyone give us a hint who might have such a piece of software and would be willing to share it with us? Also, more general comments on how to deal with two electron problems are welcome. Doing a full CI with a general purpose program is probably not the smartest thing to do. I know that there are of course a lot of calc's on the He2(++) ground state (after all, it is a metastable, experimentally well established molecule!) but I am not aware of too many studies considering excited states. But this could well be due to the fact that I am not following the physics literature as closely as I should. Should you know of any recent and good investigation on that subject that might have escaped my attention, pls. let me know as well. Many thanks in advance. Wolfram -- _________________________________________________________________________ Prof. Dr. Wolfram Koch Institut fuer Organische Chemie, Sekr.C3 Technische Universitaet Berlin Strasse des 17.Juni 135, D-10623 Berlin Fon: +49 30 314 27870, Fax: +49 30 314 21102 e-mail: kochw@argon.chem.TU-Berlin.DE _________________________________________________________________________ From gdp@charon.ppco.com Tue Nov 19 09:51:43 1996 Received: from relay.ppco.com for gdp@charon.ppco.com by www.ccl.net (8.8.2/950822.1) id JAA18768; Tue, 19 Nov 1996 09:03:08 -0500 (EST) Received: by relay.ppco.com id AA00030 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Tue, 19 Nov 1996 08:03:08 -0600 Received: by relay.ppco.com (Internal Mail Agent-1); Tue, 19 Nov 1996 08:03:08 -0600 Message-Id: <1.5.4.32.19961119140307.013235d4@pop3-host.ppco.com> X-Sender: gdp@pop3-host.ppco.com X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 19 Nov 1996 08:03:07 -0600 To: CHEMISTRY@www.ccl.net From: "George D. Parks" Subject: G2MP2 to G2 Summary I recently posed the following question to the list: >I've carried out G2MP2 calculations using Gaussian 94 and would >like to take some of the calculations to the G2 level. Is there >an easy way to do this, utilizing the results of the G2MP2 >calculations and only doing the additional calculations necessary >for the G2 method. I don't want to have to repeat calculations >I've already done. The two replies I received are summarized below. Thanks Brian & Anwar! George Parks ============== To go from G2(MP2) to G2 still you need to complete the rest of the jobs you need to calculate G2 energies. As far as I can tell you must have done QCISD(T)/6-311G(d,p), MP2/6-311+G(3df,2p). Still you need MP4/6-311+G(d,p) job, and MP4/6-311G(2df,p). I hope you included in you QCISD(T) the option E4T. IF so, you can read the MP4/6-311(d,p) from the same job. If you did not use the option E4T in you QCISD(T), still you need to run it. Keep in mind the time consuming part is the MP4/6-311(2df,p) job. I hope that should be of a good help for you. If there is an alternative solution, I will be glad to learn it. Anwar G. Baboul ============== Assuming you have not got a chk file from the G2MP2, you should:- 1. Extract the geometry from the MP2(FULL)/6-31G(d) run. 2. Run single point at 6-311+G(d,p) 3. Run single point at 6-311G(2df,p) If you have the chk file you should be able to miss out step 1 and get the geometry from the chk file using "geom=checkpoint guess=read" on the control line. You now have everything needed to get the G2 energy. Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Mathematical and Physical Sciences, Northern Territory University, Darwin, NT 0909, Australia. Phone 089-466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@quoll.ntu.edu.au *********************************************************** * George D. Parks (918) 661-7780 (work) * * 356 PL PRC (918) 662-1097 (FAX) * * Phillips Petroleum (918) 336-3041 (home) * * Bartlesville, OK 74004 gdp@ppco.com (work) * * gdparks@galstar.com (home) * *********************************************************** From Pietro.Perseo@fpms.ac.be Tue Nov 19 10:38:42 1996 Received: from fpms.fpms.ac.be for Pietro.Perseo@fpms.ac.be by www.ccl.net (8.8.2/950822.1) id KAA19380; Tue, 19 Nov 1996 10:17:55 -0500 (EST) Received: from carnot.fpms.ac.be by fpms.fpms.ac.be; (5.65v3.2/1.1.8.2/06Mar96-0204PM) id AA18771; Tue, 19 Nov 1996 16:17:37 +0100 Date: Tue, 19 Nov 1996 16:17:37 +0100 Message-Id: <9611191517.AA18771@fpms.fpms.ac.be> X-Sender: Perseo@fpms.fpms.ac.be X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Pietro Perseo Subject: Vapor-liquid equilibria calculations Dear netters I develop a software which is able to calculate physico-chemical properties of pure compounds and/or mixtures and vapor-liquid equilibria (VLE). I am looking for subroutines or algorithms for VLE calculations for "all the cases". i.e. If you know the Temperature ( T) and the liquid phase composition (X) you need the Pressure (P) and the vapor phase composition (Y). T,X --> P,Y T,Y --> P,X P,X --> T,Y P,Y --> T,X and "flash calculations" the alimentation composition Z, T, P --> X,Y I realy appreciate all contributions. I will summarize the answers. Tanks ********************************************************* * Ir. Pietro Perseo * * EUROLOCIEL s.a./Service de Thermodynamique * * FACULTE POLYTECHNIQUE DE MONS * * Boulevard Dolez 31 * * B-7000 MONS (BELGIUM) * * * * E-mail: Pietro.Perseo@fpms.ac.be * * Tel: +32 65 37 42 08 * * Fax: +32 65 37 43 00 * ********************************************************* From WSMITH@msnet.mathstat.uoguelph.ca Tue Nov 19 10:45:19 1996 Received: from ccshst09.cs.uoguelph.ca for WSMITH@msnet.mathstat.uoguelph.ca by www.ccl.net (8.8.2/950822.1) id KAA19565; Tue, 19 Nov 1996 10:37:27 -0500 (EST) Received: from msnet.nw.uoguelph.ca (msnet.mathstat.uoguelph.ca) by ccshst09.cs.uoguelph.ca with ESMTP (1.40.112.3/16.2) id AA066197897; Tue, 19 Nov 1996 10:38:17 -0500 Received: from MSNET/MAILQ by msnet.nw.uoguelph.ca (Mercury 1.21); 19 Nov 96 10:48:36 GMT-5 Received: from MAILQ by MSNET (Mercury 1.21); 19 Nov 96 10:48:16 GMT-5 From: "William R. Smith" Organization: Dept. of Math & Stats. To: chemistry@www.ccl.net Date: Tue, 19 Nov 1996 10:48:14 EDT Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL:Molecule Builder X-Confirm-Reading-To: "William R. Smith" X-Pmrqc: 1 Priority: normal X-Mailer: Pegasus Mail v3.2 (pr2) Message-Id: <210A71D1AB6@msnet.nw.uoguelph.ca> Hi again, I received several helpful replies to my previous posting: -------------------------------------------------------------------------- Does anyone know of a simple Windows 3.1/NT/95 product that can be used to build molecules? -------------------------------------------------------------------------- I'm sorry I didn't make my question more explict. What I want is a .DLL (or .VBX(preferably) or .OCX) that I can incorporate within other software. i.e. I don't want a stand-alone product. I don't think any of the replies refer to products that can be used this way (but the individual posters should please contact me if I'm wrong) Preferably, the price would also be right :- ) Best Regards, W. R. Smith Professor Dept. of Mathematics and Statistics and School of Engineering University of Guelph FAX: 519-837-0221 Guelph, Ontario Tel: 519-824-4120, ext. 3038 CANADA N1G 2W1 From elazhary@theochem.uni-stuttgart.de Tue Nov 19 11:38:45 1996 Received: from artemis.rus.uni-stuttgart.de for elazhary@theochem.uni-stuttgart.de by www.ccl.net (8.8.2/950822.1) id KAA19789; Tue, 19 Nov 1996 10:55:06 -0500 (EST) Received: from tc8.theochem.uni-stuttgart.de (tc8.theochem.uni-stuttgart.de [129.69.55.128]) by artemis.rus.uni-stuttgart.de with SMTP id QAA20035 (8.6.13/IDA-1.6); Tue, 19 Nov 1996 16:54:38 +0100 Message-ID: <199611191554.QAA20035@artemis.rus.uni-stuttgart.de> Received: by tc8.theochem.uni-stuttgart.de (1.38.193.4/16.2/BelWue-2.1) id AA14294; Tue, 19 Nov 1996 16:54:37 +0100 From: "Dr. Adel El-Azhary" Subject: summary: DFT vibrational frequencies of anions. To: chemistry@www.ccl.net Date: Tue, 19 Nov 96 16:54:37 MET Cc: suter@physik.unizh.ch Mailer: Elm [revision: 70.85] Dear ccl: I submitted the following question yesterday: ----------------------------------------------------------------------------- Does anyone know of vibrational study of anions by the DFT method other than that reported in: S. R. Langhoff, J. Phys. Chem., 100 (1996) 15073. Please send all replies to me and I will summarize to the list. Thank you in advance for your cooperation. ----------------------------------------------------------------------------- I thank everyone who responded to my query. The following are the answers. Adel El-Azhary Institute for Theortical Chemistry Stuttgart University Stuttgart, Germany 1) From: Jan Hrusak ========================================================== I do probably not understand your question properly but anyhow, we did recently some comparative DFT calculations on the anions. Mainly we are working on cations where the DFT frequencies are generally better than MP(n) and very close to the CCSD(T) one. You may have a look to J. Phys. Chem 100 (1996) 100 Jan Hrusak ========================================================== 2) From: Rollin King ========================================================== The following are papers the CCQC has published containing DFT harmonic vibrational frequencies of anions: "The Electron Affinities of the Silicon Fluorides SiFn, (n=1-5)" Rollin A. King, Vladimir S. Mastryukov, and H.F. Schaefer, J. Chem. Phys., 105, 6880 (1996). "Negative Ion Thermochemistry: The Sulfur Fluorides (SFn, n=1-7)" Rollin A. King, John Morrison Galbraith, and H. F. Schaefer, J. Phys. Chem., 100, 6061 (1995). "The Monochlorine Fluorides (ClFn) and Their Anions (ClFn-) n=1-7: Structures and Energetics" T. J. Van Huis, J. M. Galbraith and H. F. Schaefer III. Mol. Phys., 89, 607 (1996). "Structures, thermochemistry, and electron affinities of the PFn and PFn-series, n=1-6" G. S. Tschumper, J. T. Fermann and H. F. Schaefer J. Chem. Phys. 104, 3676 (1996). If you have any questions, please let me know. Sincerely, Rollin King *********************************************** * Rollin A. King * * Center for Computational Quantum Chemistry * * Chemistry Building, Rm 605 * * University of Georgia * * Athens, GA 30602 * * (706)-542-7738 * * rking@tigranes.ccqc.uga.edu * *********************************************** ========================================================== 3) From: Jeffrey C. Stephens ========================================================== These might be of some help... ``The Monochloride Fluorides (ClFn) and their Anions (ClFn-), n=1-7: Structures and Energetics,'' T. J. Van Huis, J. M. Galbraith, and H. F. Schaefer, Mol. Phys. 89,607 (1996). ``Concerning the Applicability of Density Functional Methods to Atomic and Molecular Negative Ions,'' J. M. Galbraith and H. F. Schaefer, J. Chem. Phys. 105,862 (1996). ``Negative Ion Thermochemistry: the Sulfur Fluorides SFn/SFn- (n=1-7) ,'' R. A. King, J. M. Galbraith, and H. F. Schaefer, J. Phys. Chem. 100, 6061 (1996). "The Electron Affinities of the Silicon Fluorides SiFn, (n=1-5)" Rollin A. King, Vladimir S. Mastryukov, and H. F. Schaefer, J. Chem. Phys., in press. ``Structures, thermochemistry, and electron affinities of the PFn and PFn-series, n=1-6,'' G. S. Tschumper, J. T. Fermann and H. F. Schaefer J. Chem. Phys. 104, 3676 (1996). Jeffrey C. Stephens Center for Computational Quantum Chemistry University of Georgia Athens, GA 30602 ========================================================== From rienstra@xerxes.ccqc.uga.edu Tue Nov 19 12:38:44 1996 Received: from xerxes.ccqc.uga.edu for rienstra@xerxes.ccqc.uga.edu by www.ccl.net (8.8.2/950822.1) id MAA20493; Tue, 19 Nov 1996 12:28:23 -0500 (EST) Received: from badres.ccqc.uga.edu by xerxes.ccqc.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA22215; Tue, 19 Nov 1996 12:22:36 -0500 Date: Tue, 19 Nov 1996 12:22:33 -0500 (EST) From: Jon Rienstra X-Sender: rienstra@badres.ccqc.uga.edu Reply-To: Jon Rienstra To: Giovanni Scalmani Cc: chemistry@www.ccl.net Subject: Re: CCL:XMol on AIX4.1 In-Reply-To: <199611191348.FAA27804@sg2.csrsrc.mi.cnr.it> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 19 Nov 1996, Giovanni Scalmani wrote: > I am looking for someone who has already succeded in porting XMol on > IBM RS6000 systems running AIX4.1. The XMol file (xmol.rs6000) I got > at ftp.imb-jena.de does not work (I think it was build for AIX3.x). Change your language to C: setenv LANG C XMol should run fine then. Incidently, this also appears to be the problem in getting Netscape 3.0 to run under AIX4.1 -- Jon ||||| | | (0 0) ----------------------------oOOo---oOOo---------------------------------------- | JON RIENSTRA | | e-mail: rienstra@xerxes.ccqc.uga.edu | | WWW: http://zopyros.ccqc.uga.edu/~rienstra/index.html | |-----------------------------------------------------------------------------| | work: CCQC at the University of Georgia | "Reality has taken a leaf | | office: Room 506 | from my book and set itself | | Athens, GA 30602-2556 | to supersede me." | | | -- H.G. Wells | ------------------------------------------------------------------------------- From tp@elptrs7.rug.ac.be Tue Nov 19 12:43:54 1996 Received: from elptrs7.rug.ac.be for tp@elptrs7.rug.ac.be by www.ccl.net (8.8.2/950822.1) id MAA20433; Tue, 19 Nov 1996 12:19:54 -0500 (EST) Received: by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA16516; Tue, 19 Nov 1996 18:20:46 +0100 Newsgroups: comp.sys.mac.apps,comp.sys.mac.comm,comp.sys.mac.graphics,comp.sys.mac.hardware.misc,comp.sys.mac.misc,comp.sys.mac.system,comp.sys.mac.printing Date: Tue, 19 Nov 1996 18:20:42 +0100 (NFT) From: "Park, Tae-Yun" To: Computational Chemistry List , Chemical Engineering List Subject: Help on making high quality color slide Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Sorry if this message is out of topic for this newsgroup/mailing list. I need some advice concerning making good quality of slides for presentation. My situation is the following: 1. Computer Available: IBM RS/6000(43P) Powerstation Apple Mac. IIvx 2. Software Available: Various graphics softwares, such as Photoshop3.0, Chem3D Pro, Excell 3.0, Mac Draw Pro, Igor Pro... 3. Printing Device: Personal Laserwriter 320 My question is the following: What additional device should I purchase for making a high quality color slides for presentation? All I can do now is drawing the objects(graphics, charts..) on the screen of my computer, but I need to put them on slide films for presentation. I have thought this problem for relatively long time and probably the easiest ways that I can consider now are (i) buying a color laser printer and print my figures on a paper, and then take a photograph with a camera installed with slide film; but I do not like this way because I do not need to have the color image on the paper but only on the slide film. I mean the high price for the color laser printer to print on a paper does not have to be paid for me, I think. (ii) Taking a photograph directly from the screen by using a camera; this would be the cheapest way to produce the color slide since I don't need any additional device except a camera. However, the quality of the slide is not good enough in this case, since, for example, the PICT image on a Mac. screen has much less resolution than the printed postscript file. (iii) Buying a special device only for preparing slide; I've considered this possibility since I heared that there is a special device for Mac. which prints the image of the graphics files directly onto the slide film, and this kind of device has very high resolution; but I do not know anything else about this equippment(name, price, company, etc.) Is there any other possibility to make a high resolution color slide film for presentation? How do you make your color slide if you need to give some presentation? Any suggestion/information/advice will be greatly appreciated. Thanks a lot in advance. Sincerely, Park, TAE-YUN =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= State University of Ghent Laboratorium voor Petrochemische Techniek Krijgslaan 281, Blok S5 9000 Gent, Belgium TEL:+(32)-0(9)-264-4527 FAX:+(32)-0(9)-264-4999 e-mail: tp@elptrs7.rug.ac.be =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From tim@mdli.com Tue Nov 19 12:47:29 1996 Received: from one.mind.net for tim@mdli.com by www.ccl.net (8.8.2/950822.1) id MAA20420; Tue, 19 Nov 1996 12:18:21 -0500 (EST) Received: from nec.mentat.org ([206.99.67.99]) by one.mind.net (8.6.12/8.6.10) with SMTP id JAA20393; Tue, 19 Nov 1996 09:16:03 -0800 Message-Id: <3.0b26.32.19961119091131.00bb5f2c@mind.net> X-Sender: tim@mind.net X-Mailer: Windows Eudora Pro Version 3.0b26 (32) Date: Tue, 19 Nov 1996 09:11:36 -0800 To: "William R. Smith" , Frank Herrmann , Computational Chemistry List , chemistry@www.ccl.net From: Tim Maffett Subject: Re: CCL:Molecule Builder Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 02:15 PM 11/18/96 -0800, William R. Smith wrote: >Hi, > > Does anyone know of a simple Windows 3.1/NT/95 product that can be used >to build molecules? > MDL's ISIS/Draw 2.0 is available *FREE* for academic or personal use at home. The ISIS/Draw 2.0 user interface was completely redesigned with input from many users, and I think that you will find it very intuitive and easy to use. You can download ISIS/Draw 2.0 for Windows or Mac at: http://www.mdli.com/prod/download.html (there are links to download sites in Australia and England here as well) You can also find extensive online help files available for download here as well. For 3D model generation you can use ISIS/Draw to create MDL 2D Molfiles which you can send to CORINA for automatic generation of 3D Molfile models. You can find our more about CORINA at: http://schiele.organik.uni-erlangen.de/services/3d.html The CORINA system is very nice and easy to use. You can simply email a 2D Molfile to CORINA, and get a 3D Molfile emailed back to you. (You can also send 'SDFiles' to convert many structures at once. SDFiles are basically just a bunch of Molfiles appended together in one file.) - I encourage you to also check out our Chemscape Chime Netscape Plug-in as well. Chime has a FREE use license for academic, personal AND commercial use (for presentation purposes). The URL to the Chime main page is: http://www.mdli.com/chemscape/chime Chime allows you to view a variety of molecule format files, in 2D or 3D, from within a web browser such as Netscape Navigator. These structures are 'live' molecular data, and can be manipulated in place, or saved to disk. If you have ISIS/Draw and Chime you can try out our Chemscape server example interface to NCI 3D database at: http://www.mdli.com/chemscape/clientserver/proto.html This example allows you to you to do text AND structure/substructure based queries over the NCI database of ~125,000 compounds. You can retrieve 2D or 3D structures from your queries. Again, Chime allows you to view these structures 'live' within your webpage, and they can be saved to disk as Molfiles. I hope you find these tools useful. -tim Tim Maffett tim@mdli.com Principal Architect, Internet Technologies MDL Information Systems, Inc. > >Best Regards, > > >W. R. Smith Professor > Dept. of Mathematics and Statistics > and School of Engineering > University of Guelph >FAX: 519-837-0221 Guelph, Ontario >Tel: 519-824-4120, ext. 3038 CANADA N1G 2W1 > From jaimeco@pecos.rc.arizona.edu Tue Nov 19 13:39:27 1996 Received: from pecos.rc.arizona.edu for jaimeco@pecos.rc.arizona.edu by www.ccl.net (8.8.2/950822.1) id NAA21080; Tue, 19 Nov 1996 13:12:45 -0500 (EST) Received: (from jaimeco@localhost) by pecos.rc.arizona.edu (8.7.5/8.7) id LAA19432; Tue, 19 Nov 1996 11:05:47 -0700 Date: Tue, 19 Nov 1996 11:05:47 -0700 From: "Jaime E. Combariza" Message-Id: <199611191805.LAA19432@pecos.rc.arizona.edu> To: giovanni@sg2.csrsrc.mi.cnr.it, rienstra@xerxes.ccqc.uga.edu Subject: Re: CCL:XMol on AIX4.1 Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: multipart/mixed;boundary=59e2_1cfb-3f54_ff6-abd_31df --59e2_1cfb-3f54_ff6-abd_31df Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-MD5: V3uL9R3JPUNSPZjn85I84w== You may want to consider renaming the executable to xmol.exe and then run it by using a script file similar to this one: (you can call it xmol). As stated before same applies to netscape 3.0 #!/bin/sh LANG=C LC_ALL=C exec /usr/local/bin/xmol.exe "$@" jaime Combariza jaimeco@arizona.edu --59e2_1cfb-3f54_ff6-abd_31df-- From berriz@chasma.harvard.edu Tue Nov 19 16:38:48 1996 Received: from chasma.harvard.edu for berriz@chasma.harvard.edu by www.ccl.net (8.8.2/950822.1) id QAA22211; Tue, 19 Nov 1996 16:01:58 -0500 (EST) Received: by chasma.harvard.edu (AIX 3.2/UCB 5.64/4.03) id AA16654; Tue, 19 Nov 1996 16:00:41 -0500 Date: Tue, 19 Nov 1996 16:00:41 -0500 From: berriz@chasma.harvard.edu (Gabriel Berriz) Message-Id: <9611192100.AA16654@chasma.harvard.edu> To: chemistry@www.ccl.net Subject: Parallelized SHAKE? Dear netters: I am trying to find a *published* parallelization of the SHAKE algorithm. All I've been able to find is the analytic algorithm SETTLE of Miyamoto and Kollman, but as far as I can tell, it is only good for water molecules. I have also found on the Web various mentions of parallelized SHAKE routines that are part of recent versions of CHARMM, AMBER, or GROMOS, but (a) I don't have access to the source codes, and (b) I find somewhat daunting the idea of poring through what is surely voluminous code to extract the desired fragment. (But maybe it'll come to this... :-/ ) I appreciate any pointers to the literature. Gabriel Berriz berriz@chasma.harvard.edu Dept. of Chemistry and Chemical Biology Harvard University From bruno@antas.agraria.uniss.it Tue Nov 19 18:38:47 1996 Received: from ICINECA.CINECA.IT for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.2/950822.1) id SAA23016; Tue, 19 Nov 1996 18:05:40 -0500 (EST) Received: from cinymp.cineca.it by ICINECA.CINECA.IT (IBM VM SMTP V2R2) with TCP; Wed, 20 Nov 96 00:04:27 SOL Received: from antas.agraria.uniss.it by cinymp.cineca.it with SMTP (5.61/CRI-80.1) id AA28024; Wed, 20 Nov 96 00:05:13 +0100 Date: Wed, 20 Nov 1996 00:06:27 +0100 (NFT) From: "Dr. Bruno Manunza" To: Gabriel Berriz Cc: chemistry@www.ccl.net Subject: Re: CCL:Parallelized SHAKE? In-Reply-To: <9611192100.AA16654@chasma.harvard.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 19 Nov 1996, Gabriel Berriz wrote: > > > > > Dear netters: > > I am trying to find a *published* parallelization of the SHAKE > algorithm. All I've been able to find is the analytic algorithm > SETTLE of Miyamoto and Kollman, but as far as I can tell, it is only > good for water molecules. I have also found on the Web various > mentions of parallelized SHAKE routines that are part of recent > versions of CHARMM, AMBER, or GROMOS, but (a) I don't have access to > the source codes, and (b) I find somewhat daunting the idea of poring > through what is surely voluminous code to extract the desired > fragment. (But maybe it'll come to this... :-/ ) > > I appreciate any pointers to the literature. > > Gabriel Berriz > berriz@chasma.harvard.edu > Dept. of Chemistry and Chemical Biology > Harvard University Gabriel, you may found interesting to take a look to the DLPOLY parralel MD package at the URL http://gserv1.dl.ac.uk/TCSC/Software/DL_POLY/main.html The source is freely available (Licence agreement needed) The shake algorithm should work with molecules different from water. bye Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it From berriz@chasma.harvard.edu Tue Nov 19 21:38:48 1996 Received: from chasma.harvard.edu for berriz@chasma.harvard.edu by www.ccl.net (8.8.2/950822.1) id VAA23535; Tue, 19 Nov 1996 21:03:07 -0500 (EST) Received: by chasma.harvard.edu (AIX 3.2/UCB 5.64/4.03) id AA17162; Tue, 19 Nov 1996 21:01:56 -0500 Date: Tue, 19 Nov 1996 21:01:56 -0500 From: berriz@chasma.harvard.edu (Gabriel Berriz) Message-Id: <9611200201.AA17162@chasma.harvard.edu> To: rvenable@deimos.cber.nih.gov Cc: chemistry@www.ccl.net In-Reply-To: (message from Rick Venable on Tue, 19 Nov 1996 20:37:26 -0500 (EST)) Subject: Re: CCL:Parallelized SHAKE? Date: Tue, 19 Nov 1996 20:37:26 -0500 (EST) From: Rick Venable A caveat on parallelized SHAKE in CHARMM... Thank you for the information. Gabriel Berriz From rvenable@deimos.cber.nih.gov Tue Nov 19 21:57:59 1996 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.2/950822.1) id UAA23483; Tue, 19 Nov 1996 20:43:31 -0500 (EST) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA159673846; Tue, 19 Nov 1996 20:37:26 -0500 Date: Tue, 19 Nov 1996 20:37:26 -0500 (EST) From: Rick Venable To: Gabriel Berriz Cc: chemistry@www.ccl.net Subject: Re: CCL:Parallelized SHAKE? In-Reply-To: <9611192100.AA16654@chasma.harvard.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 19 Nov 1996, Gabriel Berriz wrote: > I am trying to find a *published* parallelization of the SHAKE > algorithm. All I've been able to find is the analytic algorithm > SETTLE of Miyamoto and Kollman, but as far as I can tell, it is only > good for water molecules. I have also found on the Web various > mentions of parallelized SHAKE routines that are part of recent > versions of CHARMM, AMBER, or GROMOS, but (a) I don't have access to > the source codes, and (b) I find somewhat daunting the idea of poring > through what is surely voluminous code to extract the desired > fragment. (But maybe it'll come to this... :-/ ) A caveat on parallelized SHAKE in CHARMM-- a SHAKE constraint may not be imposed across a parallel partition. For situations when only bonds to H atoms are constrained, this isn't a problem, since the GROUP structure defined in the RTF is respected when the parallel partitioning is done. However, attempting to constrain all bond lengths will lead to problems for heavy atom to heavy atom bonds that reside in different parallel partitions (and that will almost always be the case for a macromolecule). -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov \/ |=| position of the FDA; for that, http://nmr1.cber.nih.gov/venable.html |=| see http://www.fda.gov ) From wong@chem.chemistry.uq.oz.au Tue Nov 19 23:38:49 1996 Received: from chem.chemistry.uq.oz.au for wong@chem.chemistry.uq.oz.au by www.ccl.net (8.8.2/950822.1) id WAA23845; Tue, 19 Nov 1996 22:48:54 -0500 (EST) Received: (from wong@localhost) by chem.chemistry.uq.oz.au (8.8.3/8.7.3) id NAA16966 for chemistry@www.ccl.net; Wed, 20 Nov 1996 13:48:26 +1000 Date: Wed, 20 Nov 1996 13:48:26 +1000 From: Richard Wong Message-Id: <199611200348.NAA16966@chem.chemistry.uq.oz.au> To: chemistry@www.ccl.net Subject: electron donating ability Dear Netter, I am looking for papers which discuss the electron donating ability of simple molecules such as NH3, OH2, FH, PH3, SH2, Cl, CO and N2, etc. In particular, I would like to know the comparison between the first and second-row systems, e.g. HCl versus H2O. I greatly appreciate any pointers to the literature. Cheers! Richard wong@chem.chemistry.uq.oz.au Department of Chemistry University of Queensland, Australia